). Default None.
+ qualifier: Qualifier or str
+ The qualifier for the relationship. Default `Qualifier.Biological_is`.
+ annotations: list or None, optional
+ List of StandardizedAnnotation objects that represent additional (nested)
+ annotations of this object.
+ """
+
+ def __init__(
+ self,
+ resources: Optional[
+ Union["Resource", str, Iterable[Union["Resource", str]]]
+ ] = None,
+ qualifier: Union[Qualifier, str] = Qualifier.Biological_is,
+ annotations: Optional[Iterable["StandardizedAnnotation"]] = None,
+ ):
+ """Initialize a standardized annotation."""
+ self._resources = []
+ self.resources = resources
+ self._qualifier: Qualifier = self.check_qualifier_type(qualifier)
+ self._annotations: Optional[StandardizedAnnotationStore] = (
+ StandardizedAnnotationStore.from_data(annotations)
+ if annotations is not None
+ else None
+ )
+ self._parent: Optional[StandardizedAnnotationStore] = None
+
+ def _set_parent(self, parent):
+ if self._parent is None or parent is None:
+ self._parent = parent
+ else:
+ raise ValueError(
+ "StandardizedAnnotation already has a parent. Create a new "
+ "annotation if you would like to add an annotation to a second object."
+ )
+
+ def remove_from_parent(self) -> None:
+ """Remove annotation from parent (`StandardizedAnnotationStore`).
+
+ Raises
+ ------
+ ValueError
+ If there is no known parent object.
+
+ See Also
+ --------
+ StandardizedAnnotationStore.remove
+ """
+ if self._parent is None:
+ raise ValueError(
+ "Cannot remove annotation, since no object is associated with it."
+ )
+ self._parent.remove(self)
+
+ def _remove_resource(self, resource):
+ self.resources.remove(resource)
+
+ @property
+ def qualifier(self) -> Qualifier:
+ """Get the qualifier.
+
+ Returns
+ -------
+ Qualifier
+ """
+ return self._qualifier
+
+ @qualifier.setter
+ def qualifier(self, qualifier: Union[str, Qualifier]) -> None:
+ """Set the qualifier.
+
+ Parameters
+ ----------
+ qualifier: str or Qualifier
+
+ See Also
+ --------
+ StandardizedAnnotation.check_qualifier_type()
+ """
+ self._qualifier = self.check_qualifier_type(qualifier)
+
+ @property
+ def resources(self) -> List["Resource"]:
+ """Get the list of resources.
+
+ Returns
+ -------
+ list of Resource objects
+ """
+ return self._resources
+
+ @resources.setter
+ def resources(self, resources: Iterable[Union[str, "Resource"]]) -> None:
+ """Set the resources.
+
+ Parameters
+ ----------
+ resources: list of str or Resource
+
+ See Also
+ --------
+ StandardizedAnnotation.check_resource_type()
+ """
+ for idf in self._resources:
+ idf._set_parent(None)
+ self._resources = self.check_resource_type(resources)
+ for idf in self._resources:
+ idf._set_parent(self)
+
+ def add_resources(self, resources: Iterable[Union[str, "Resource"]]) -> None:
+ """Add resources to the standardized annotation.
+
+ Parameters
+ ----------
+ resources: list of str or Resource objects
+ List of resources to append to the existing ones.
+ """
+ resources = self.check_resource_type(resources)
+ for resource in resources:
+ resource._set_parent(self)
+ self.resources.extend(resources)
+
+ @property
+ def uris(self) -> FrozenSet[str]:
+ """Get the set of URIs represented by the resources of this annotation.
+
+ Returns
+ -------
+ Set of URIs
+
+ See Also
+ --------
+ all_uris
+ Resource.uri
+ """
+ return frozenset({entry.uri for entry in self.resources})
+
+ @property
+ def all_uris(self) -> FrozenSet[str]:
+ """Get all the URIs in this annotation, including nested annotations.
+
+ Returns
+ -------
+ Set of URIs
+
+ See Also
+ --------
+ uris
+ Resource.uri
+ """
+ resources = {entry.uri for entry in self.resources}
+ for entry in self.annotations:
+ resources.update(entry.uris)
+ return frozenset(resources)
+
+ @property
+ def annotations(self) -> "StandardizedAnnotationStore":
+ """Get the nested annotations.
+
+ Returns
+ -------
+ List of annotations
+ """
+ if self._annotations is None:
+ self._annotations = StandardizedAnnotationStore()
+ return self._annotations
+
+ @annotations.setter
+ def annotations(self, annotations: Iterable["StandardizedAnnotation"]) -> None:
+ """Set the nested annotations.
+
+ Parameters
+ ----------
+ annotations - list of StandardizedAnnotation objects.
+ """
+ self._annotations = StandardizedAnnotationStore.from_data(annotations)
+
+ @staticmethod
+ def check_resource_type(
+ resources: Optional[
+ Union[
+ "Resource",
+ str,
+ Dict[str, str],
+ Tuple[str, str],
+ Iterable[Union["Resource", str, Dict[str, str], Tuple[str, str]]],
+ ]
+ ],
+ ) -> List["Resource"]:
+ """Check and parse resources.
+
+ Parameters
+ ----------
+ resources: Resource, str, dict, tuple, or list thereof, optional
+ Input data to check if it is or can be transformed to Resource objects.
+ String must start with http:// or https:// to be acceptable.
+ Dictionary must match the format required by from_data.
+ If None is given, an empty StandardizedAnnotation object is returned.
+ No parsing of identifiers/URIs is done, perhaps in future versions.
+
+ Returns
+ -------
+ list of Resource objects
+
+ See Also
+ --------
+ Resource.from_dict
+ """
+ if resources is None:
+ return []
+ elif isinstance(resources, (Resource, str, dict)):
+ return [Resource.from_data(resources, strict=False)]
+ elif isinstance(resources, ABCIterable):
+ return [
+ Resource.from_data(resource, strict=False) for resource in resources
+ ]
+ else:
+ raise TypeError(
+ f"Allowed types for resources are Resource, str, or a list thereof,"
+ f"not {type(resources)}: {resources}"
+ )
+
+ @staticmethod
+ def check_qualifier_type(qual: Union[str, Qualifier]) -> Qualifier:
+ """Check and parse input to Qualifier class.
+
+ Parameters
+ ----------
+ qual: str or Qualifier, optional
+ Input data to check if it is or can be transformed to Qualifier class.
+ Strings must be a member of the Qualifier values.
+ If None is given, an empty Qualifier is returned.
+
+ Returns
+ -------
+ Qualifier
+
+ Raises
+ ------
+ TypeError
+ If given anything other than None, str, or Qualifier.
+ Will raise this error if given a string that does not match the defined
+ Qualifier members.
+ """
+ if isinstance(qual, str) and qual not in Qualifier._value2member_map_:
+ raise TypeError(f"{qual} is not a supported enum Qualifier")
+ elif isinstance(qual, Qualifier):
+ return qual
+ elif isinstance(qual, str):
+ return Qualifier._value2member_map_[qual]
+ else:
+ raise TypeError(
+ f"Allowed types for StandardAnnotation qualifiers are Qualifier or"
+ f"str member of the Qualifier enum {type(qual)}, {qual}"
+ )
+
+ def to_dict(self) -> Dict:
+ """Convert annotation to a python dict.
+
+ Returns
+ -------
+ dict:
+ A dict that has up to three keys
+ "qualifier" - the qualifier as a string
+ "resources" - the resources as list
+ "annotations" (optionally) - the nested annotations as a list
+ """
+ d = {
+ "qualifier": self.qualifier.value,
+ "resources": [resource.uri for resource in self.resources],
+ }
+ if self.annotations:
+ d["annotations"] = self.annotations.to_list_of_dicts()
+ return d
+
+ def to_tuples(self) -> List[Tuple[str, str]]:
+ """Convert the annotation to a list of tuples of namespace-identifier pairs.
+
+ This does not contain the qualifier or nested annotations.
+
+ Returns
+ -------
+ List of namespace-identifier pairs as tuples
+ """
+ return [
+ (resource.namespace, resource.identifier)
+ for resource in self.resources
+ if resource.namespace is not None and resource.identifier is not None
+ ]
+
+ def to_records(self) -> List[Dict[str, Any]]:
+ """Convert the annotation to a list of dictionaries that represent resources.
+
+ Each entry in the list represents a resource associated with this object,
+ either directly or as nested annotation. The resulting list is thus a flattened
+ representation of all resources. The hierarchical information is included
+ using the "annotation_group" and "parent_group" entries in the dictionaries.
+ Each annotation group represents a single StandardizedAnnotation object (without
+ its nested annotations). If a resource is found in a nested annotation, the
+ "parent_group" value will be set to the "annotation_group" value of its parent
+ StandardizedAnnotation object.
+
+ Returns
+ -------
+ list of dict objects
+ Each dict represents a Resource records.
+
+ See Also
+ --------
+ StandardizedAnnotationStore.to_records
+ """
+ records, _ = self._to_records()
+ return records
+
+ def _to_records(
+ self, group_counter: int = 1, parent_group: int = 0
+ ) -> Tuple[List[Dict[str, Any]], int]:
+ records = []
+ for resource in self.resources:
+ entry = {
+ "qualifier": self.qualifier.value,
+ "uri": resource.uri,
+ "namespace": resource.namespace,
+ "identifier": resource.identifier,
+ "annotation_group": group_counter,
+ "parent_group": parent_group,
+ }
+ records.append(entry)
+ if self.annotations:
+ new_records, group_counter = self.annotations._to_records(
+ group_counter=(group_counter + 1), parent_group=group_counter
+ )
+ records.extend(new_records)
+ else:
+ group_counter = group_counter + 1
+ return records, group_counter
+
+ @classmethod
+ def from_dict(cls, data_dict: Dict) -> "StandardizedAnnotation":
+ """Generate a StandardizedAnnotation object from a python dict.
+
+ Parameters
+ ----------
+ data_dict: dict
+ A dict that has up to three keys
+ "qualifier" - the qualifier as a string, optional. If not present, the
+ qualifier is set to `Qualifier.Biological_is`.
+ "resources" - the resources as a list of strings, optional.
+ "annotations" - the nested annotations as a list of dicts, optional.
+
+ Returns
+ -------
+ StandardizedAnnotation
+
+ See Also
+ --------
+ to_dict
+
+ """
+ return cls(
+ resources=data_dict.get("resources", None),
+ qualifier=data_dict.get("qualifier", Qualifier.Biological_is),
+ annotations=data_dict.get("annotations", None),
+ )
+
+ def __eq__(self, other: Any) -> bool:
+ """Compare StandardizedAnnotation to another object and determine equality.
+
+ If a dict is given, it is transformed to `StandardizedAnnotation` before
+ comparison. Will return False for any other type. The order of the resources
+ is ignored.
+
+ Parameters
+ ----------
+ other
+
+ Returns
+ -------
+ bool
+ False if other is not StandardizedAnnotation or dict.
+ False if qualifiers, resources or nested annotations are different.
+ True otherwise.
+
+ See Also
+ --------
+ StandardizedAnnotation.from_dict()
+ """
+
+ if isinstance(other, dict):
+ return self == StandardizedAnnotation.from_dict(other)
+ if isinstance(other, StandardizedAnnotation):
+ if self.qualifier != other.qualifier:
+ return False
+ if len(self.resources) != len(other.resources):
+ return False
+ for idf in self.resources:
+ if idf not in other.resources:
+ return False
+ if self.annotations != other.annotations:
+ return False
+ return True
+ return False
+
+ def __repr__(self) -> str:
+ """Return the StandardizedAnnotation as str with module and class.
+
+ Returns
+ -------
+ str
+ """
+ return (
+ f"{self.__class__.__module__}.{self.__class__.__qualname__}"
+ f"({self.to_dict()})"
+ )
+
+ def _repr_html_(self) -> str:
+ """Return the StandardizedAnnotation as HTML string.
+
+ Returns
+ -------
+ str
+ HTML formatted string
+ """
+ # TODO: Fix this HTML
+ cols = {
+ "uri": "| URI | ",
+ "namespace": "Namespace | ",
+ "identifier": "Identifier | ",
+ "address": "Memory address | ",
+ }
+ n = len(self.resources)
+ s = f"""
+
+ | Qualifier |
+
+ {self.qualifier}
+ |
+
"""
+ for resource in self.resources:
+ cols["uri"] += f"{resource.uri} | "
+ cols["namespace"] += f"{resource.namespace} | "
+ cols["identifier"] += f"{resource.identifier} | "
+ cols["address"] += f"{id(resource):#x} | "
+ for v in cols.values():
+ s += f"{v}
"
+ if self.annotations:
+ s += f"""
+ Nested
annotations |
+ """
+ for annotation in self.annotations:
+ s += annotation._repr_html_()
+ s += " |
"
+
+ s += "
"
+ return s
+
+ def __deepcopy__(self, memo: Optional[dict] = None):
+ """Copy the StandardizedAnnotation efficiently with memo.
+
+ Parameters
+ ----------
+ memo: dict
+ Automatically passed parameter, dict of already copied items.
+
+ Returns
+ -------
+ StandardizedAnnotation
+ A new annotation that is a deep copy of the original.
+ """
+
+ new = StandardizedAnnotation(
+ qualifier=self.qualifier,
+ )
+ # memo[id(self)] = new
+ new.resources = [r.__deepcopy__() for r in self._resources]
+ if self._annotations is not None:
+ new._annotations = self._annotations.__deepcopy__()
+ return new
+
+ def copy(self) -> "StandardizedAnnotation":
+ """Copy the annotation and all its nested annotations.
+
+ Returns
+ -------
+ StandardizedAnnotation
+ A new annotation that is a deep copy of the original.
+ """
+
+ return self.__deepcopy__()
+
+
+class StandardizedAnnotationStore(UserList):
+ """A list-like object that stores a collection of `StandardizedAnnotation` objects.
+
+ Stores a collection of standardized annotations that define the relation of
+ MIRIAM-compliant resources to a cobra modelling object. In practice, this class is
+ automatically instantiated as the `standardized` attribute of the `Metadata` class,
+ which can be accessed through `object.metadata.standardized`. In addition, nested
+ annotations in a `StandardizedAnnotation` object also make use of the
+ `StandardizedAnnotationStore` class.
+
+ Parameters
+ ----------
+ data: list of StandardizedAnnotation, dict, str or Resource objects
+ List of standardized annotations to initialize the store with. Dictionaries
+ are converted to standardized annotations using
+ `StandardizedAnnotation.from_dict`. Strings are interpreted as identifier
+ URIs and together with other Resource objects stored in a new
+ `StandardizedAnnotation` with `Qualifier.Biological_is` as qualifier.
+ """
+
+ def __init__(
+ self,
+ data: Optional[
+ Iterable[Union[StandardizedAnnotation, Dict, Resource, str]]
+ ] = None,
+ ):
+ """Initialize a standardized annotation store."""
+ self._take_ownership_of_resources: bool = getattr(
+ self, "_take_ownership_of_resources", True
+ )
+ if data is None:
+ data = []
+
+ checked_data = [
+ filtered_entry
+ for entry in data
+ if (not isinstance(entry, (str, Resource)))
+ and (filtered_entry := self._check_standardized_annotation(entry))
+ is not None
+ ]
+ # str and Resource instances are handled separately and added as one
+ # Standardized annotation instance with the default qualifier (Biological_is).
+ if no_qualifier_data := [
+ entry for entry in data if isinstance(entry, (str, Resource))
+ ]:
+ checked_data.insert(0, StandardizedAnnotation(resources=no_qualifier_data))
+ if self._take_ownership_of_resources:
+ for entry in checked_data:
+ entry._set_parent(self)
+ super().__init__(checked_data)
+
+ @staticmethod
+ def _check_standardized_annotation(
+ ann: Optional[Union[StandardizedAnnotation, Dict, str, Resource]],
+ ) -> Optional["StandardizedAnnotation"]:
+ if ann is None:
+ return None
+ if isinstance(ann, StandardizedAnnotation):
+ return ann
+ elif isinstance(ann, (str, Resource)):
+ return StandardizedAnnotation(ann)
+ elif isinstance(ann, dict):
+ return StandardizedAnnotation.from_dict(ann)
+ else:
+ raise TypeError(
+ f"Allowed types for StandardizedAnnotation are str and"
+ f"StandardizedAnnotation, not {type(ann)}: {ann}"
+ )
+
+ @staticmethod
+ def from_data(
+ data: Optional[
+ Union[
+ Iterable[Union[str, Dict, "StandardizedAnnotation"]],
+ str,
+ Dict,
+ "StandardizedAnnotation",
+ "StandardizedAnnotationStore",
+ ]
+ ],
+ ) -> "StandardizedAnnotationStore":
+ """Create a StandardizedAnnotationStore object from given data.
+
+ Parameters
+ ----------
+ data: StandardizedAnnotation, dict, str or Resource, or list thereof, or
+ StandardizedAnnotationStore or None
+ A standardized annotation or a list of standardized annotations to use to
+ create a store with. Dictionaries are converted to standardized annotations
+ using `StandardizedAnnotation.from_dict`. Strings are interpreted as
+ identifier URIs and together with other Resource objects stored in a new
+ `StandardizedAnnotation` with `Qualifier.Biological_is` as qualifier.
+ If data is already a StandardizedAnnotationStore, this object will simply be
+ returned.
+
+ Returns
+ -------
+ StandardizedAnnotationStore
+
+ Raises
+ ------
+ TypeError
+ """
+ if data is None:
+ return StandardizedAnnotationStore()
+ elif isinstance(data, StandardizedAnnotationStore):
+ return data
+ elif isinstance(data, (StandardizedAnnotation, dict, str)):
+ if not data:
+ return StandardizedAnnotationStore()
+ return StandardizedAnnotationStore([data])
+ elif isinstance(data, ABCIterable):
+ return StandardizedAnnotationStore(data)
+ else:
+ raise TypeError(f"Invalid format for StandardizedAnnotationStore: '{data}'")
+
+ def to_list_of_dicts(self) -> List[dict]:
+ """Convert the StandardizedAnnotationStore to a list of python dicts.
+
+ Returns:
+ -------
+ list:
+ a list where each item is a dict representing a standardized annotation
+ object, as created by StandardizedAnnotation.to_dict(). Mainly used for JSON
+ and YAML export.
+
+ See Also
+ --------
+ StandardizedAnnotation.to_dict
+ """
+ return [annotation.to_dict() for annotation in self]
+
+ def to_records(self):
+ """Convert the store to a list of dictionaries that represent resources.
+
+ Each entry in the list represents an resources associated with one of the
+ standardized annotation in this object, either directly or as nested annotation.
+ The resulting list is thus a flattened representation of all resources.
+ The hierarchical information is included using the "annotation_group" and
+ "parent_group" entries in the dictionaries. Each annotation group represents a
+ single StandardizedAnnotation object (without its nested annotations). If a
+ resource is found in a nested annotation, the "parent_group" value will be set
+ to the "annotation_group" value of its parent StandardizedAnnotation object.
+
+ Returns
+ -------
+ List of dictionaries representing Resource records
+
+ See Also
+ --------
+ StandardizedAnnotation.to_records
+ """
+ records, _ = self._to_records()
+ return records
+
+ def _to_records(
+ self, group_counter: int = 1, parent_group: int = 0
+ ) -> Tuple[List[Dict], int]:
+ records = []
+ for entry in self.data:
+ new_l, group_counter = entry._to_records(
+ group_counter=group_counter, parent_group=parent_group
+ )
+ records.extend(new_l)
+ return records, group_counter
+
+ def _find_first_by_qualifier(
+ self,
+ qualifier: Qualifier = Qualifier.Biological_is,
+ ) -> Optional[StandardizedAnnotation]:
+ for entry in self.data:
+ if entry.qualifier == qualifier:
+ return entry
+ return None
+
+ def _find_first_or_create_by_qualifier(
+ self, qualifier: Qualifier = Qualifier.Biological_is
+ ) -> StandardizedAnnotation:
+ entry = self._find_first_by_qualifier(qualifier)
+ if entry is None:
+ entry = StandardizedAnnotation(qualifier=qualifier, resources=[])
+ if self._take_ownership_of_resources:
+ entry._set_parent(self)
+ self.data.insert(0, entry)
+ return entry
+
+ def add(
+ self,
+ annotations: Union[
+ "StandardizedAnnotationStore",
+ StandardizedAnnotation,
+ Dict,
+ str,
+ Resource,
+ List[Union[StandardizedAnnotation, Dict, str, Resource]],
+ ],
+ ) -> None:
+ """Add one or multiple standardized annotations to the store.
+
+ Dictionaries are converted to standardized annotations using
+ `StandardizedAnnotation.from_dict`. Strings are interpreted as identifier
+ URIs and together with other Resource objects stored in a new
+ `StandardizedAnnotation` with `Qualifier.Biological_is` as qualifier.
+
+ If a list is passed, this method is equivalent to
+ `StandardizedAnnotationStore.extend` and if a single annotation is passed, this
+ method is equivalent to `StandardizedAnnotationStore.append`.
+
+ Parameters
+ ----------
+ annotations : StandardizedAnnotation, dict, str or Resource, or list thereof
+ Single or multiple annotations to add to the store.
+
+ See Also
+ --------
+ append
+ extend
+ """
+ if isinstance(annotations, (StandardizedAnnotation, dict, str, Resource)):
+ self.append(annotations)
+ else:
+ self.extend(annotations)
+
+ def append(self, item: Union[StandardizedAnnotation, Dict, str, Resource]) -> None:
+ """Append a single annotation to the end of the store.
+
+ Parameters
+ ----------
+ item: StandardizedAnnotation, dict, str or Resource
+ Annotation to append to the standardized annotation store.
+ """
+ self.extend([item])
+
+ def extend(
+ self,
+ other: Union[
+ "StandardizedAnnotationStore",
+ Iterable[Union[StandardizedAnnotation, Dict, str, Resource]],
+ ],
+ ) -> None:
+ """Extend store by appending elements from the iterable.
+
+ Parameters
+ ----------
+ iterable : Iterable
+ Annotations to add to the store.
+ """
+ if isinstance(other, StandardizedAnnotationStore):
+ self.extend(other.data)
+ elif isinstance(other, Iterable):
+ checked_data = [
+ checked_item
+ for item in other
+ if (checked_item := self._check_standardized_annotation(item))
+ is not None
+ ]
+ if self._take_ownership_of_resources:
+ for d in checked_data:
+ d._set_parent(self)
+ self.data.extend(checked_data)
+
+ def remove(self, item: "StandardizedAnnotation"):
+ """Remove a standardized annotation from the store.
+
+ Parameters
+ ----------
+ item: StandardizedAnnotation
+ Annotation to remove from the store.
+ """
+ self.data.remove(item)
+ item._set_parent(None)
+
+ @property
+ def resources(self) -> FrozenSet[Resource]:
+ """Get resources.
+
+ Returns
+ -------
+ FrozenSet
+ a set of resources in the standardized annotation store, not including
+ resources of nested annotations.
+ """
+ resources = set()
+ for entry in self.data:
+ resources.update(entry.resources)
+ return frozenset(resources)
+
+ @property
+ def all_resources(self) -> FrozenSet[Resource]:
+ """Get all resources, including resources in nested annotations.
+
+ Returns
+ -------
+ FrozenSet
+ a set of all resources in the standardized annotation store, including
+ resources of nested annotations.
+ """
+ resources = set()
+ for entry in self.data:
+ resources.update(entry.resources)
+ if entry.annotations:
+ resources.update(entry.annotations.all_resources)
+ return frozenset(resources)
+
+ def resources_for(
+ self,
+ namespace: Optional[Union[str, List[str]]] = None,
+ qualifier: Optional[
+ Union[
+ Qualifier,
+ QualifiersAlias,
+ List[Union[Qualifier, QualifiersAlias]],
+ ]
+ ] = None,
+ nested: bool = False,
+ ) -> List[Resource]:
+ """Get resources for a namespace or qualifier.
+
+ Filter annotations based on their qualifier and its resources on their
+ namespace. Optionally also return and filter nested resources on their
+ namespace.
+
+ Parameters
+ ----------
+ namespace: None, str or list of str, optional
+ One or multiple namespaces to filter resources with. Selects a resource when
+ its namespace matches any of the provided namespaces. If it is set to None,
+ no filtering based on the namespace will be performed. Default None.
+ qualifier: None, Qualifier, QualifiersAlias or list of Qualifier/QualifiersAlias
+ One or multiple qualifiers to filter annotations with. Selects an annotation
+ when its qualifier matches any of the provided qualifiers. If it is set to
+ None, no filtering based on qualifiers will be performed. Nested annotations
+ are never filtered based on their qualifier. Default None.
+ nested: bool
+ Whether to return resources from nested annotations. Nested annotations are
+ selected when `nested` is True and the top-level annotation is selected
+ based on its qualifier. I.e. nested annotations are not filtered on their
+ own qualifier. Conversely, resources in nested annotations are selected
+ based on their namespace. Default False.
+
+ Returns
+ -------
+ list of Resource objects
+ """
+ # TODO: Examples
+ namespace_sel, qualifier_sel = True, True
+ if namespace is None:
+ namespace_sel = False
+ namespace = []
+ if not isinstance(namespace, list):
+ namespace = [namespace]
+
+ if qualifier is None:
+ qualifier_sel = False
+ qualifier = []
+ if not isinstance(qualifier, list):
+ qualifier = [qualifier]
+ qualifiers_and_aliases = qualifier
+ qualifier = []
+ for q in qualifiers_and_aliases:
+ if isinstance(q, Qualifier):
+ qualifier.append(q)
+ elif isinstance(q, QualifiersAlias):
+ qualifier.extend(q)
+ else:
+ raise TypeError(
+ "Qualifiers should have type Qualifier or QualifiersAlias,"
+ f"not {type(q)}"
+ )
+
+ qualifier_set = set(qualifier)
+ namespace_set = set(namespace)
+ resources = []
+ for annotation in self:
+ if qualifier_sel and annotation.qualifier not in qualifier_set:
+ continue
+ if not namespace_sel:
+ resources.extend(annotation.resources)
+ else:
+ for resource in annotation.resources:
+ if resource.namespace is None:
+ continue
+ if resource.namespace in namespace_set:
+ resources.append(resource)
+ if nested and annotation.annotations:
+ # Do not select for qualifiers in nested annotations
+ resources.extend(
+ annotation.annotations.resources_for(
+ namespace=list(namespace_set) if namespace_sel else None,
+ nested=nested,
+ )
+ )
+ return resources
+
+ @property
+ def uris(self) -> FrozenSet[str]:
+ """Get URIs.
+
+ Returns
+ -------
+ FrozenSet
+ A set of URIs in the standardized annotation store, not including URIs of
+ nested annotations.
+ """
+ resources = set()
+ for entry in self.data:
+ resources.update(entry.uris)
+ return frozenset(resources)
+
+ @property
+ def all_uris(self) -> FrozenSet[str]:
+ """Get all URIs, including URIs of nested annotations.
+
+ Returns
+ -------
+ FrozenSet
+ A set of URIs in the standardized annotation store, including URIs of
+ nested annotations.
+ """
+ resources = set()
+ for entry in self.data:
+ resources.update(entry.uris)
+ if entry.annotations:
+ resources.update(entry.annotations.all_uris)
+ return frozenset(resources)
+
+ @property
+ def qualifiers(self) -> FrozenSet[Qualifier]:
+ """Get qualifiers of annotations in the store, not including nested annotations.
+
+ Returns
+ -------
+ FrozenSet
+ A set of qualifiers in the standardized annotation store, not including
+ qualifiers of nested annotations.
+ """
+ qualifier_set = set()
+ for entry in self.data:
+ qualifier_set.add(entry.qualifier)
+ return frozenset(qualifier_set)
+
+ @property
+ def all_qualifiers(self) -> FrozenSet[Qualifier]:
+ """Get all qualifiers of annotations in the store, including nested annotations.
+
+ Returns
+ -------
+ FrozenSet
+ A set of qualifiers in the standardized annotation store, including
+ qualifiers of nested annotations.
+ """
+ qualifier_set = set()
+ for entry in self.data:
+ qualifier_set.add(entry.qualifier)
+ if entry.annotations:
+ qualifier_set.update(entry.annotations.all_qualifiers)
+ return frozenset(qualifier_set)
+
+ def __iter__(self) -> Iterator[StandardizedAnnotation]:
+ """Get an iterator for the standardized annotations in the store.
+
+ Returns
+ -------
+ Iterator
+ """
+ return iter(self.data)
+
+ def __len__(self) -> int:
+ """Get the number of standardized annotations in the store.
+
+ Returns
+ -------
+ int
+ """
+ return len(self.data)
+
+ def query(
+ self,
+ search_function: Union[str, Pattern, Callable],
+ attribute: Union[str, None] = None,
+ ) -> "StandardizedAnnotationList":
+ """Query the annotation store for matching StandardizedAnnotation objects.
+
+ Parameters
+ ----------
+ search_function : a string, regular expression or function
+ Used to find the matching elements in the store.
+ - a regular expression (possibly compiled), in which case the
+ given attribute of the object should match the regular expression.
+ - a function which takes one argument and returns True for
+ desired values
+
+ attribute : string or None
+ the name attribute of the object to passed as argument to the
+ `search_function`. If this is None and a regular expression/string is given,
+ will match the regular expression to both qualifier and resources.
+
+ Returns
+ -------
+ StandardizedAnnotationList
+ A list-like collection of StandardizedAnnotation objects which match the
+ query.
+
+ Examples
+ --------
+ >>> from cobra.io import load_model
+ >>> model = load_model('iJO1366')
+ >>> model.metadata.standardized.query('Biological_', 'qualifier')
+ >>> import re
+ >>> regex = re.compile('^Modelling')
+ >>> model.annotation.standardized.query(regex, 'qualifier')
+ """
+
+ # TODO: Clean up this whole method.
+ def select_attribute(
+ x: StandardizedAnnotation,
+ ) -> Union[StandardizedAnnotation, Resource, Qualifier, set]:
+ if attribute is None:
+ return x
+ else:
+ return getattr(x, attribute)
+
+ try:
+ # if the search_function is a regular expression
+ regex_searcher = re.compile(search_function)
+ print(f"Search function: '{search_function}'")
+ if attribute is None:
+ attribute = ""
+
+ if attribute == "qualifier":
+ matches = [
+ annotation
+ for annotation in self
+ if (
+ regex_searcher.findall(select_attribute(annotation).name) != []
+ or regex_searcher.findall(select_attribute(annotation).value)
+ != []
+ )
+ ]
+ elif attribute == "resources":
+ matches = [
+ annotation
+ for annotation in self.data
+ if any(
+ regex_searcher.findall(res.uri)
+ for res in select_attribute(annotation)
+ )
+ ]
+ else:
+ matches = [
+ annotation
+ for annotation in self.data
+ if regex_searcher.findall(annotation.qualifier.name) != []
+ or regex_searcher.findall(annotation.qualifier.value) != []
+ or any(
+ regex_searcher.findall(res.uri) for res in annotation.resources
+ )
+ ]
+ except TypeError as err:
+ print(err)
+ matches = [
+ annotation
+ for annotation in self.data
+ if search_function(select_attribute(annotation))
+ ]
+
+ return StandardizedAnnotationList(matches)
+
+ def __setitem__(self, key: int, value: StandardizedAnnotationInput) -> None:
+ """Set item in the store at the provided index.
+
+ Removes the current annotation at the provided index and replaces it with the
+ provided annotation.
+
+ Parameters
+ ----------
+ key: int
+ value: StandardizedAnnotation, dict, str or Resource
+ """
+ checked_value = self._check_standardized_annotation(value)
+ if checked_value is None:
+ raise TypeError("Value cannot be None.")
+ # TODO: Elaborate (or automatically delete when None)
+ if self._take_ownership_of_resources:
+ self.data[key]._set_parent(None)
+ checked_value._set_parent(self)
+ UserList.__setitem__(self, key, checked_value)
+
+ def __getitem__(
+ self,
+ key: Union[
+ int,
+ Qualifier,
+ QualifiersAlias,
+ List[Union[int, Qualifier, QualifiersAlias]],
+ ],
+ ) -> Union[StandardizedAnnotation, "StandardizedAnnotationList"]:
+ """Access standardized annotations by integer index or qualifier.
+
+ Parameters
+ ----------
+ key: int, Qualifier, QualifiersAlias or list thereof
+ If `key` is an integer, the `StandardizedAnnotation` at that position in the
+ list will be returned. When a list of integers is provided, a
+ `StandardizedAnnotationList` with the corresponding annotations is returned.
+ When one or more Qualifier or `QualifiersAlias` enums are provided, a
+ `StandardizedAnnotationList` of all annotations (not nested) with any of
+ those qualifiers is returned.
+ """
+ if isinstance(key, int):
+ return self.data[key]
+ if isinstance(key, (Qualifier, QualifiersAlias)):
+ key = [key]
+ if not isinstance(key, list):
+ raise TypeError(f"Indexed using key of wrong type: {type(key)}")
+ selection = []
+ for k in key:
+ if isinstance(k, int):
+ selection.append(self.data[k])
+ elif isinstance(k, Qualifier):
+ selection.extend(
+ annotation for annotation in self if annotation.qualifier == k
+ )
+ elif isinstance(k, QualifiersAlias):
+ selection.extend(
+ annotation for annotation in self if annotation.qualifier in k
+ )
+ else:
+ raise TypeError(f"Indexed using a key of wrong type: {type(key)}")
+ return StandardizedAnnotationList(selection)
+
+ def __eq__(self, other: Any) -> bool:
+ """Compare two standardized annotation stores and determine equality.
+
+ Equality is defined as them having the same data, but not necessarily being the
+ same object. If the given item is not a StandardizedAnnotationStore, list or
+ dict, this function will return False.
+
+ Parameters
+ ----------
+ other
+
+ Returns
+ -------
+ bool: True if the data matches, False otherwise
+ """
+ if isinstance(other, (ABCIterable, dict)) and not isinstance(
+ other, StandardizedAnnotationStore
+ ):
+ return self.__eq__(StandardizedAnnotationStore.from_data(other))
+ if not isinstance(other, StandardizedAnnotationStore):
+ return False
+ if len(self.data) != len(other.data):
+ return False
+ for other_entry in other.data:
+ if other_entry not in self.data:
+ return False
+ return True
+
+ def _repr_html_(self) -> str:
+ """Convert StandardizedAnnotationStore to HTML.
+
+ Returns
+ -------
+ str
+ HTML representation of the annotation store.
+ """
+ entries = [annotation._repr_html_() for annotation in self]
+ return f"""StandardizedAnnotationStore{"".join(entries)}"""
+
+ def __deepcopy__(self, memo: Optional[dict] = None):
+ """Copy the StandardizedAnnotationStore efficiently with memo.
+
+ Parameters
+ ----------
+ memo: dict
+ Automatically passed parameter, dict of already copied items.
+
+ Returns
+ -------
+ StandardizedAnnotationStore
+ A new annotation store that is a deep copy of the original.
+ """
+
+ new = StandardizedAnnotationStore()
+ # memo[id(self)] = new
+ new.extend([ann.__deepcopy__() for ann in self])
+ return new
+
+ def copy(self) -> "StandardizedAnnotationStore":
+ """Copy the annotation store and all its annotations.
+
+ Returns
+ -------
+ StandardizedAnnotationStore
+ A new store that is a deep copy of the original store.
+ """
+
+ return self.__deepcopy__()
+
+
+class StandardizedAnnotationList(StandardizedAnnotationStore):
+ """Class to create lists of StandardizedAnnotation objects.
+
+ This class is very similar to the StandardizedAnnotationStore class, which stores
+ all standardized annotation objects of a cobrapy object. The difference is that this
+ class does not take ownership (becomes parent of) its resources. It can therefore be
+ used to create lists of StandardizedAnnotation objects of different cobrapy objects,
+ or create views of a subset of the annotations of a single object.
+
+ Parameters
+ ----------
+ data: list of StandardizedAnnotation, dict, str or Resource objects
+ List of standardized annotations to initialize the store with. Dictionaries
+ are converted to standardized annotations using
+ `StandardizedAnnotation.from_dict`. Strings are interpreted as identifier
+ URIs and together with other Resource objects stored in a new
+ `StandardizedAnnotation` with `Qualifier.Biological_is` as qualifier.
+
+ """
+
+ def __init__(
+ self,
+ data: Optional[
+ Iterable[Union[StandardizedAnnotation, Dict, Resource, str]]
+ ] = None,
+ ):
+ """Initialize a standardized annotation store."""
+
+ self._take_ownership_of_resources: bool = False
+ super(StandardizedAnnotationList, self).__init__(data)
+
+
+class SimplifiedAnnotationInterface(MutableMapping):
+ """Class to interface with metadata using a dict-like interface.
+
+ This class is used to maintain compatibility with older cobrapy versions. It is
+ typically accessed through an objects annotation attribute. It allows a user to get
+ and set standardized annotations through a dict-like interface. When reading
+ existing annotations, qualifiers are ignored and resources are pooled. When
+ setting new annotations, qualifiers are set based on defaults (typically
+ `Qualifiers.Biological_is`).
+ This class is automatically instantiated as the `annotation` attribute of cobrapy
+ objects.
+
+ Warnings
+ --------
+ * This is not the preferred method to access annotations, since information and
+ hierarchy is lost in this interface.
+ * This interface was added to not break existing code, for new code
+ `object.metadata.standardized` should be preferred.
+ * Editing existing annotations using this interface can cause the annotations to
+ become less organized.
+
+ Parameters
+ ----------
+ metadata: Metadata
+ Metadata object where annotations will be stored and retrieved from.
+ """
+
+ def __init__(self, metadata: Metadata) -> None:
+ """Initialize the simplified annotation interface using a `Metadata` object."""
+ self._metadata: Metadata = metadata
+
+ def add(
+ self,
+ data: Optional[
+ Union[
+ Dict,
+ str,
+ "SimplifiedAnnotationInterface",
+ Tuple[str, Union[str, List[str]]],
+ Resource,
+ List[Union[str, Resource, Tuple[str, Union[str, List[str]]]]],
+ ]
+ ] = None,
+ ) -> None:
+ """Add an annotation.
+
+ Parameters
+ ----------
+ data: str, tuple, Resource or list thereof, or dict or
+ SimplifiedAnnotationInterface
+ Add resources as annotations, using default qualifiers. Tuples are
+ interpreted as namespace-identifiers pairs, strings should be valid URIs and
+ if a dictionary is provided, its keys should represent namespaces and its
+ values identifiers.
+
+ Raises
+ ------
+ TypeError
+ If values could not be converted to Resource objects.
+ ValueError
+ If tuples of lengths other than 2 were provided.
+ """
+ if data is None:
+ data = []
+
+ if isinstance(data, SimplifiedAnnotationInterface):
+ data = data.to_dict()
+
+ if isinstance(data, dict):
+ data = list(data.items())
+
+ if isinstance(data, (str, tuple)):
+ data = [data]
+
+ if not isinstance(data, list):
+ raise TypeError(
+ "The supplied annotations were not of type List, or could "
+ "not be converted to a list."
+ )
+
+ annotations = {}
+ for entry in data:
+ if isinstance(entry, tuple):
+ if len(entry) != 2:
+ raise ValueError(
+ "Only tuples of length 2 can be converted to annotations."
+ )
+ expanded_entries = []
+ if isinstance(entry[1], list):
+ expanded_entries.extend([(entry[0], v) for v in entry[1]])
+ else:
+ expanded_entries.append(entry)
+ entry = expanded_entries
+ elif isinstance(entry, str):
+ entry = [entry]
+ else:
+ raise TypeError("Entry could could not be converted to an Resource.")
+ for x in entry:
+ if isinstance(x, tuple) and x[0].lower() == "sbo":
+ self._metadata.sbo = x[1]
+ continue
+ if not isinstance(x, Resource):
+ x = Resource.from_data(x, strict=False)
+ if x.namespace is None:
+ raise ValueError(f"Could not determine namespace of resource {x}.")
+
+ qualifier = get_default_qualifier(x.namespace)
+ if qualifier not in annotations:
+ annotations[qualifier] = []
+ annotations[qualifier].append(x)
+
+ for qualifier, resources in annotations.items():
+ ann = self._metadata.standardized._find_first_or_create_by_qualifier(
+ qualifier
+ )
+ ann.add_resources(resources)
+
+ @property
+ def sbo(self) -> str:
+ """Get the SBO term of the annotations.
+
+ Returns
+ -------
+ str
+
+ See Also
+ --------
+ Metadata.sbo
+ """
+ return self._metadata.sbo
+
+ @sbo.setter
+ def sbo(self, value: str) -> None:
+ """Set the SBO term of the annotations.
+
+ Parameters
+ ----------
+ value: str
+
+ See Also
+ --------
+ Metadata.sbo
+ """
+ self._metadata.sbo = value
+
+ def __getitem__(self, key: str) -> List[str]:
+ """Get resources for a given namespace.
+
+ Collects all standardized annotations for namespace `key` and returns a list of
+ all resources as strings, or raise IndexError if none were found.
+
+ Parameters
+ ----------
+ key: str
+ Namespace of the resources.
+
+ Returns
+ -------
+ list of str
+ List of resources as strings.
+
+ Raises
+ ------
+ IndexError
+ If no resources were found for the given namespace.
+ """
+ if not isinstance(key, str):
+ raise TypeError("Index should be of type str.")
+ key = key.lower()
+ if key == "sbo":
+ return [self._metadata.sbo]
+
+ results = []
+ for ann in self._metadata.standardized:
+ for resource in ann.resources:
+ if (v := resource.identifier) is not None and resource.namespace == key:
+ results.append(v)
+
+ if results:
+ # Deduplicate and sort results to have consistent results and make
+ # comparisons easier. E.g. __eq__(...) relies on this.
+ return list(sorted(set(results)))
+ else:
+ raise IndexError(f"No resources found for namespace '{key}'")
+
+ def get(self, key: str, default: Any = None):
+ """Get resources for a given namespace.
+
+ Performs indexing in the same manner as `__get__`, except it will not raise
+ IndexError when the index does not exist, but rather returns a default value.
+
+ Parameters
+ ----------
+ key: str
+ Namespace of the resources.
+ default: optional
+ Default value to return when index is not found. Default None.
+
+ Returns
+ -------
+ list of str or `default`
+ List of resources as strings or the `default` value.
+ """
+ # Example of usage:
+ # https://github.com/opencobra/memote/blob/develop/src/memote/support/thermodynamics.py
+ try:
+ return self[key]
+ except IndexError:
+ return default
+
+ def __delitem__(self, key: str) -> None:
+ """Delete all resources for a given namespace.
+
+ Deletes all resources for namespace `key` from their `StandardizedAnnotation`
+ objects or raise IndexError if none were found.
+
+ Parameters
+ ----------
+ key: str
+ Namespace of the resources.
+
+ Raises
+ ------
+ IndexError
+ If no resources were found for the given namespace.
+ """
+ if not isinstance(key, str):
+ raise TypeError("Index should be of type str.")
+
+ key = key.lower()
+
+ if key == "sbo":
+ self._metadata.sbo = ""
+ return
+
+ deleted_any = False
+ for ann in self._metadata.standardized:
+ for resource in list(ann.resources):
+ if resource.namespace is not None and resource.namespace == key:
+ resource.remove_from_parent()
+ deleted_any = True
+ if not deleted_any:
+ raise IndexError(f"Could not find annotations for f'{key}')")
+
+ def __setitem__(self, key: str, value: Union[str, List[str]]) -> None:
+ """Set resources for a given namespace.
+
+ Removes all existing resources with namespace `key` and inserts
+ the provided resources.
+
+ Parameters
+ ----------
+ key: str
+ Namespace of the resources.
+ value: str or list of str
+ Resources to set for the provided namespace.
+ """
+ if not isinstance(key, str):
+ raise TypeError("Index should be of type str.")
+ key = key.lower()
+
+ try:
+ del self[key]
+ except IndexError:
+ pass
+
+ self.add({key: value})
+
+ def __eq__(self, other: Any) -> bool:
+ """Determine equality between the simplified annotations and another object.
+
+ If the other object is of a type other than dict or
+ `StandardizedAnnotationInterface`, the objects are considered not equal.
+ Otherwise, objects are equal if there dictionary representation is equal.
+
+ Parameters
+ ----------
+ other
+
+ Returns
+ -------
+ bool
+ """
+ self_dict = self.to_dict()
+ if isinstance(other, dict):
+ other_dict = other
+ elif isinstance(other, SimplifiedAnnotationInterface):
+ other_dict = other.to_dict()
+ else:
+ return False
+ return self_dict == other_dict
+
+ def objects(self) -> Generator[Tuple[str, List[Resource]], None, None]:
+ """Get a generator for all pairs of namespace and Resource objects.
+
+ Creates a generator that can be used to iterate over the data as pairs (tuples)
+ of a namespace and a list of its corresponding Resource objects. This method
+ is very similar to the `items` method, except that it yields Resource objects
+ instead of strings.
+
+ Returns
+ -------
+ generator
+ Yields pairs of namespace and a list of Resource objects.
+
+ See Also
+ --------
+ items
+ """
+ visited_namespaces = set("sbo")
+ while True:
+ current_namespace = None
+ resources = []
+ for entry in self._metadata.standardized:
+ for resource in entry.resources:
+ if resource.namespace is None:
+ continue
+ if resource.namespace in visited_namespaces:
+ continue
+ if current_namespace is None:
+ current_namespace = resource.namespace
+ resources.append(resource)
+ else:
+ if resource.namespace == current_namespace:
+ resources.append(resource)
+ if current_namespace is not None:
+ visited_namespaces.add(current_namespace)
+ resources = list(sorted(set(resources), key=lambda x: x.identifier))
+ if resources:
+ yield (current_namespace, resources)
+ else:
+ break
+ if sbo_term := self._metadata.sbo:
+ yield ("sbo", [Resource.from_data(("sbo", sbo_term))])
+
+ def items(self) -> Iterator[Tuple[str, List[str]]]:
+ """Get a generator for all pairs of namespace and identifiers.
+
+ Creates a generator that can be used to iterate over the data as pairs (tuples)
+ of a namespace and a list of its corresponding identifiers. This method is very
+ similar to the `objects` method, except that it yields strings instead of
+ Resource objects.
+
+ Returns
+ -------
+ generator
+ Yields pairs of namespace and a list of identifiers.
+
+ See Also
+ --------
+ objects
+ """
+ for k, v in self.objects():
+ yield (k, [x.identifier for x in v])
+
+ def __iter__(self):
+ """Get an iterator for the namespaces (keys) of the annotations.
+
+ Returns
+ -------
+ Iterator
+ """
+
+ for k, _ in self.objects():
+ yield k
+
+ def keys(self):
+ """Get a view of the namespaces (keys) of the annotations.
+
+ Returns
+ -------
+ Iterator
+ """
+
+ return KeysView(self)
+
+ def values(self):
+ """Get a generator for the values of the annotations.
+
+ The values are lists of identifiers with the same namespace.
+
+ Returns
+ -------
+ Generator
+
+ See Also
+ --------
+ identifiers
+ tuples
+ """
+ for _, v in self.items():
+ yield v
+
+ def identifiers(self):
+ """Get a generator for the individual identifiers of the annotations.
+
+ Returns
+ -------
+ Generator
+
+ See Also
+ --------
+ values
+ tuples
+ """
+ for _, v in self.items():
+ for identifier in v:
+ yield identifier
+
+ def tuples(self):
+ """Get a generator for the individual identifiers as namespace-identifier pairs.
+
+ Returns
+ -------
+ Generator
+
+ See Also
+ --------
+ values
+ identifiers
+ """
+ for k, v in self.items():
+ for identifier in v:
+ yield (k, identifier)
+
+ @property
+ def number_of_resources(self) -> int:
+ """The number of individual resources.
+
+ Is different from the length of the object, since a single namespace can have
+ multiple resources associated with it.
+
+ Returns
+ -------
+ int
+
+ See Also
+ --------
+ __len__
+ """
+ return sum(1 for _ in self.identifiers())
+
+ def __len__(self) -> int:
+ """Get the length of the object, which corresponds to the number of namespaces.
+
+ Returns
+ -------
+ int
+
+ See Also
+ --------
+ number_of_resources
+ """
+ return sum(1 for _ in self)
+
+ def delete_annotation(self, value: str) -> None:
+ """Delete a resource based on its identifier value.
+
+ Parameters
+ ----------
+ value: str
+ Identifier value of the resource to delete.
+
+ Raises
+ ------
+ ValueError
+ If no resource was found for the provided value.
+ """
+ for _, entries in self.objects():
+ for entry in entries:
+ if entry.identifier == value:
+ entry.remove_from_parent()
+ return
+ raise ValueError(f"No annotation found for '{value}'")
+
+ def to_dict(self) -> Dict[str, List[str]]:
+ """Convert the simplified annotations to a dictionary.
+
+ The keys of the dictionary represent namespaces and the values are lists of
+ corresponding identifiers.
+
+ Returns
+ -------
+ dict
+ """
+ return dict(self)
+
+ def copy(self) -> Dict[str, List[str]]:
+ """Convert the simplified annotations to a dictionary.
+
+ This method returns a dictionary and not a new `SimplifiedAnnotationInterface`,
+ since the interface is in place for compatibility purposes. Existing code will
+ expect a copy of an object's `annotation` attribute to be a dictionary. This
+ method is thus equivalent to `to_dict`.
+
+ Returns
+ -------
+ dict
+
+ See Also
+ --------
+ to_dict
+ """
+ # Example of usage of this method:
+ # https://github.com/draeger-lab/MassChargeCuration/blob/main/MCC/ModelInterface/CobraPyInterface.py
+ return self.to_dict()
+
+ def clear(self) -> None:
+ """Remove all annotations."""
+ # Could probably handle this better by directly removing all standardized
+ # annotations. Currently, empty StandardizedAnnotation objects will remain.
+ for k in self:
+ del self[k]
+
+ def __deepcopy__(self, memo: dict):
+ """Create a deepcopy of the SimplifiedAnnotationStore.
+
+ Parameters
+ ----------
+ memo: dict
+ Automatically passed parameter, dict of already copied items.
+
+ Returns
+ -------
+ SimplifiedAnnotationInterface
+ A new interface that is a deep copy of the original.
+ """
+ new = SimplifiedAnnotationInterface(self._metadata.__deepcopy__(memo))
+ # memo[id(self)] = new
+ return new
diff --git a/src/cobra/core/model.py b/src/cobra/core/model.py
index 2d1215a12..3b56bf08f 100644
--- a/src/cobra/core/model.py
+++ b/src/cobra/core/model.py
@@ -382,28 +382,43 @@ def copy(self) -> "Model":
cobra.Model: new model copy
"""
new = self.__class__()
+ memo = {id(self): new}
do_not_copy_by_ref = {
"metabolites",
"reactions",
"genes",
"notes",
- "annotation",
+ "_annotation",
+ "_metadata",
"groups",
}
+
+ def copy_metadata(old_obj, new_obj):
+ if old_obj._metadata is not None:
+ new_obj.metadata = old_obj._metadata.__deepcopy__(memo)
+ # new_obj.metadata.history = old_obj.metadata.history.to_dict()
+ # new_obj.metadata.standardized.add(
+ # old_obj.metadata.standardized.to_list_of_dicts()
+ # )
+ # new_obj.metadata.custom = old_obj.metadata.custom.to_dict()
+ # new_obj.metadata.sbo = old_obj.metadata.sbo
+
+ # raise ValueError()
for attr in self.__dict__:
if attr not in do_not_copy_by_ref:
new.__dict__[attr] = self.__dict__[attr]
new.notes = deepcopy(self.notes)
- new.annotation = deepcopy(self.annotation)
+ copy_metadata(self, new)
new.metabolites = DictList()
- do_not_copy_by_ref = {"_reaction", "_model"}
+ do_not_copy_by_ref = {"_reaction", "_model", "_annotation", "_metadata"}
for metabolite in self.metabolites:
new_met = metabolite.__class__()
for attr, value in metabolite.__dict__.items():
if attr not in do_not_copy_by_ref:
new_met.__dict__[attr] = copy(value) if attr == "formula" else value
new_met._model = new
+ copy_metadata(metabolite, new_met)
new.metabolites.append(new_met)
new.genes = DictList()
@@ -415,16 +430,24 @@ def copy(self) -> "Model":
copy(value) if attr == "formula" else value
)
new_gene._model = new
+ copy_metadata(gene, new_gene)
new.genes.append(new_gene)
new.reactions = DictList()
- do_not_copy_by_ref = {"_model", "_metabolites", "_genes"}
+ do_not_copy_by_ref = {
+ "_model",
+ "_metabolites",
+ "_genes",
+ "_annotation",
+ "_metadata",
+ }
for reaction in self.reactions:
new_reaction = reaction.__class__()
for attr, value in reaction.__dict__.items():
if attr not in do_not_copy_by_ref:
new_reaction.__dict__[attr] = copy(value)
new_reaction._model = new
+ copy_metadata(reaction, new_reaction)
new.reactions.append(new_reaction)
# update awareness
for metabolite, stoic in reaction._metabolites.items():
@@ -434,7 +457,7 @@ def copy(self) -> "Model":
new_reaction.update_genes_from_gpr()
new.groups = DictList()
- do_not_copy_by_ref = {"_model", "_members"}
+ do_not_copy_by_ref = {"_model", "_members", "_annotation", "_metadata"}
# Groups can be members of other groups. We initialize them first and
# then update their members.
for group in self.groups:
@@ -443,6 +466,7 @@ def copy(self) -> "Model":
if attr not in do_not_copy_by_ref:
new_group.__dict__[attr] = copy(value)
new_group._model = new
+ copy_metadata(group, new_group)
new.groups.append(new_group)
for group in self.groups:
new_group = new.groups.get_by_id(group.id)
@@ -683,7 +707,7 @@ def add_boundary(
rxn = Reaction(id=reaction_id, name=name, lower_bound=lb, upper_bound=ub)
rxn.add_metabolites({metabolite: -1})
if sbo_term:
- rxn.annotation["sbo"] = sbo_term
+ rxn.metadata.sbo = sbo_term
self.add_reactions([rxn])
return rxn
diff --git a/src/cobra/core/object.py b/src/cobra/core/object.py
index 78d092d05..4b2bb6f45 100644
--- a/src/cobra/core/object.py
+++ b/src/cobra/core/object.py
@@ -1,6 +1,16 @@
"""Define base Object class in Cobra."""
-from typing import Optional
+from typing import TYPE_CHECKING, Dict, Iterable, List, Optional, Tuple, Union
+
+
+if TYPE_CHECKING:
+ from cobra.core.metadata import (
+ CustomAnnotation,
+ Metadata,
+ Resource,
+ StandardizedAnnotation,
+ )
+ from cobra.core.metadata.standardized import SimplifiedAnnotationInterface
class Object:
@@ -16,17 +26,16 @@ def __init__(self, id: Optional[str] = None, name: str = "") -> None:
name: string, optional
The name to associate with the object. Default "".
- Objects will have notes and _annotation as dicitionaries, initialized as empty
- dictionaries.
+ Objects will have notes and metadata as empty attributes.
"""
self._id = id
self.name = name
self.notes = {}
- self._annotation = {}
+ self.metadata = None
@property
- def id(self) -> str:
+ def id(self) -> Optional[str]:
"""Get the Object id.
Returns
@@ -70,33 +79,216 @@ def _set_id_with_model(self, value) -> None:
self._id = value
@property
- def annotation(self) -> dict:
- """Get annotation dictionary.
+ def metadata(self) -> "Metadata":
+ """Get objects metadata.
Returns
-------
- _annotation: dict
- Returns _annotation as a dictionary.
+ Metadata
+ Metadata object containing annotations and object creator and history.
"""
+ from cobra.core.metadata import Metadata
+ from cobra.core.metadata.standardized import SimplifiedAnnotationInterface
+
+ if self._metadata is None:
+ self._metadata = Metadata()
+ self._annotation = SimplifiedAnnotationInterface(self._metadata)
+ return self._metadata
+
+ @metadata.setter
+ def metadata(self, metadata: Optional["Metadata"]):
+ """Set the metadata of the object.
+
+ Parameters
+ ----------
+ metadata: Metadata
+ Metadata object containing annotations and object history.
+ """
+ from cobra.core.metadata import Metadata
+ from cobra.core.metadata.standardized import SimplifiedAnnotationInterface
+
+ if metadata is None:
+ self._metadata = None
+ self._annotation = None
+ elif isinstance(metadata, Metadata):
+ self._metadata = metadata
+ self._annotation = SimplifiedAnnotationInterface(self._metadata)
+ else:
+ raise TypeError(
+ f"The data passed for annotation must be inside "
+ f"a dictionary or Metadata: {metadata}"
+ )
+
+ @property
+ def annotation(self) -> "SimplifiedAnnotationInterface":
+ """Access standardized annotations through a dict-like interface.
+
+ Warnings
+ --------
+ This attribute is in place to retain compatibility with older cobrapy versions.
+ For new code, it is recommended to directly use the methods of
+ StandardizedAnnotationStore, which can be accessed through
+ `object.metadata.standardized`.
+
+ Returns
+ -------
+ SimplifiedAnnotationInterface
+
+ See Also
+ --------
+ StandardizedAnnotationStore
+ SimplifiedAnnotationInterface
+ """
+ from cobra.core.metadata.standardized import SimplifiedAnnotationInterface
+
+ if self._annotation is None:
+ self._annotation = SimplifiedAnnotationInterface(self.metadata)
return self._annotation
@annotation.setter
- def annotation(self, annotation):
- """Set annotation.
+ def annotation(
+ self,
+ value: Optional[
+ Union[
+ Dict,
+ "SimplifiedAnnotationInterface",
+ List[Union[str, "Resource", Tuple[str, Union[str, List[str]]]]],
+ ]
+ ],
+ ):
+ """Set the standardized annotations using a dict-like object.
+
+ This method removes all standardized annotations and adds the ones provided as
+ argument.
+
+ Warnings
+ --------
+ This attribute is in place to retain compatibility with older cobrapy versions.
+ For new code, it is recommended to directly use the methods of
+ StandardizedAnnotationStore, which can be accessed through
+ `object.metadata.standardized`.
Parameters
----------
- annotation: dict
- Annotation dictionary to set _annotation to. Will raise error if not dict.
+ value: dict, SimplifiedAnnotationInterface, list of str, Resource or tuples.
+ Sets resources as annotations, using default qualifiers. Tuples are
+ interpreted as namespace-identifiers pairs, strings should be valid URIs and
+ if a dictionary is provided, its keys should represent namespaces and its
+ values identifiers.
- Raises
- ------
- TypeError if annotation not a dict.
+ See Also
+ --------
+ SimplifiedAnnotationInterface.clear
+ SimplifiedAnnotationInterface.add
"""
- if not isinstance(annotation, dict):
- raise TypeError("Annotation must be a dict")
- else:
- self._annotation = annotation
+ self.annotation.clear()
+ if value is not None:
+ self.annotation.add(value)
+
+ def add_annotations(
+ self,
+ annotations: Union[
+ str,
+ "Resource",
+ Tuple[str, str],
+ "StandardizedAnnotation",
+ "CustomAnnotation",
+ Iterable[
+ Union[
+ str,
+ "Resource",
+ Tuple[str, str],
+ "StandardizedAnnotation",
+ "CustomAnnotation",
+ ]
+ ],
+ ],
+ ):
+ """Add annotations to the metadata object by inferring the annotation type.
+
+ If a StandardizedAnnotation or CustomAnnotation object is present, it is added
+ to the `standardized` or `custom` attribute, respectively. Strings, tuples, and
+ Resource objects are added using the `SimplifiedAnnotationInterface`, which
+ means that they are added to the `standardized` attribute using a default
+ qualifier (typically Qualifier.Biological_is).
+
+ Parameters
+ ----------
+ annotations: (list of) StandardizedAnnotation, CustomAnnotation, str, tuple
+ Annotations to add to the metadata.
+
+ See Also
+ --------
+ StandardizedAnnotationStore.add
+ CustomAnnotationStore.add
+ SimplifiedAnnotationInterface.add
+ """
+ from cobra.core.metadata import (
+ CustomAnnotation,
+ Resource,
+ StandardizedAnnotation,
+ )
+
+ if isinstance(
+ annotations,
+ (str, tuple, Resource, StandardizedAnnotation, CustomAnnotation),
+ ):
+ annotations = [annotations]
+
+ for annotation in annotations:
+ if isinstance(annotation, (str, tuple, Resource)):
+ self.annotation.add(annotation)
+ elif isinstance(annotation, StandardizedAnnotation):
+ self.metadata.standardized.add([annotation])
+ elif isinstance(annotation, CustomAnnotation):
+ self.metadata.custom.add(annotation)
+ else:
+ raise TypeError(
+ "Could not convert object to annotation: "
+ f"{annotation} ({type(annotation)})"
+ )
+
+ def remove_annotations(
+ self,
+ annotations: Union[
+ "StandardizedAnnotation",
+ "CustomAnnotation",
+ Iterable[Union["StandardizedAnnotation", "CustomAnnotation"]],
+ ],
+ ):
+ """Remove an annotation from the Metadata object.
+
+ This method only accepts StandardizedAnnotation and CustomAnnotation objects,
+ or a list thereof, and removes them from the corresponding annotation stores at
+ Metadata.standardized and Metadata.custom.
+
+ Parameters
+ ----------
+ annotations: (list of) StandardizedAnnotation or CustomAnnotation objects
+ Annotations to remove from metadata.
+
+ See Also
+ --------
+ StandardizedAnnotationStore.remove
+ CustomAnnotationStore.remove
+ """
+ from cobra.core.metadata import CustomAnnotation, StandardizedAnnotation
+
+ if isinstance(annotations, StandardizedAnnotation) or isinstance(
+ annotations, CustomAnnotation
+ ):
+ annotations = [annotations]
+
+ for annotation in annotations:
+ if isinstance(annotation, StandardizedAnnotation):
+ self.metadata.standardized.remove(annotation)
+ elif isinstance(annotation, CustomAnnotation):
+ self.metadata.custom.remove(annotation)
+ else:
+ raise TypeError(
+ "All annotations should be of type StandardizedAnnotation "
+ f"or CustomAnnotation, not: {type(annotation)}."
+ )
def __getstate__(self) -> dict:
"""Get state of annotation.
diff --git a/src/cobra/core/reaction.py b/src/cobra/core/reaction.py
index 9b1755dfe..9b711463e 100644
--- a/src/cobra/core/reaction.py
+++ b/src/cobra/core/reaction.py
@@ -1679,25 +1679,26 @@ def _repr_html_(self) -> str:
return f"""
- | Reaction identifier | {format_long_string(
- self.id, 100)} |
+ Reaction identifier | {
+ format_long_string(self.id, 100)} |
- | Name | {format_long_string(
- self.name, 100)} |
+ Name | {
+ format_long_string(self.name, 100)} |
| Memory address |
{f"{id(self):#x}"} |
| Stoichiometry |
- {format_long_string(
- self.build_reaction_string(), 200)}
- {format_long_string(
- self.build_reaction_string(True), 200)}
+ {
+ format_long_string(self.build_reaction_string(), 200)
+ }
+ {
+ format_long_string(self.build_reaction_string(True), 200)}
|
- | GPR | {format_long_string(
- self.gene_reaction_rule, 100)} |
+ GPR | {
+ format_long_string(self.gene_reaction_rule, 100)} |
| Lower bound | {self.lower_bound} |
diff --git a/src/cobra/data/mini.json b/src/cobra/data/mini.json
index df70c0a4f..8414ac8ab 100644
--- a/src/cobra/data/mini.json
+++ b/src/cobra/data/mini.json
@@ -5,1120 +5,1166 @@
},
"genes": [
{
- "id": "b0755",
+ "id": "G_b0755",
"name": "gpmA"
},
{
- "id": "b0875",
+ "id": "G_b0875",
"name": "aqpZ"
},
{
- "id": "b1101",
+ "id": "G_b1101",
"name": "ptsG"
},
{
- "id": "b1380",
+ "id": "G_b1380",
"name": "ldhA"
},
{
- "id": "b1621",
+ "id": "G_b1621",
"name": "malX"
},
{
- "annotation": {
- "ncbiprotein": [
- "1208453",
- "1652654"
+ "id": "G_b1676",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "https://identifiers.org/ncbiprotein:1208453",
+ "https://identifiers.org/ncbiprotein:1652654"
+ ]
+ }
]
},
- "id": "b1676",
"name": "pykF"
},
{
- "id": "b1723",
+ "id": "G_b1723",
"name": "pfkB"
},
{
- "id": "b1773",
+ "id": "G_b1773",
"name": "ydjI"
},
{
- "id": "b1779",
+ "id": "G_b1779",
"name": "gapA"
},
{
- "id": "b1817",
+ "id": "G_b1817",
"name": "manX"
},
{
- "id": "b1818",
+ "id": "G_b1818",
"name": "manY"
},
{
- "id": "b1819",
+ "id": "G_b1819",
"name": "manZ"
},
{
- "id": "b1854",
+ "id": "G_b1854",
"name": "pykA"
},
{
- "id": "b2097",
+ "id": "G_b2097",
"name": "fbaB"
},
{
- "id": "b2133",
+ "id": "G_b2133",
"name": "dld"
},
{
- "id": "b2415",
+ "id": "G_b2415",
"name": "ptsH"
},
{
- "id": "b2416",
+ "id": "G_b2416",
"name": "ptsI"
},
{
- "id": "b2417",
+ "id": "G_b2417",
"name": "crr"
},
{
- "annotation": {
- "ncbiprotein": "1653839"
+ "id": "G_b2779",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "https://identifiers.org/ncbiprotein:1653839"
+ ]
+ }
+ ]
},
- "id": "b2779",
"name": "eno"
},
{
- "id": "b2925",
+ "id": "G_b2925",
"name": "fbaA"
},
{
- "annotation": {
- "ncbiprotein": "1653609"
+ "id": "G_b2926",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "https://identifiers.org/ncbiprotein:1653609"
+ ]
+ }
+ ]
},
- "id": "b2926",
"name": "pgk"
},
{
- "id": "b2987",
+ "id": "G_b2987",
"name": "pitB"
},
{
- "id": "b3493",
+ "id": "G_b3493",
"name": "pitA"
},
{
- "id": "b3612",
+ "id": "G_b3612",
"name": "gpmM"
},
{
- "annotation": {
- "ncbiprotein": [
- "1006614",
- "1651919"
+ "id": "G_b3916",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "https://identifiers.org/ncbiprotein:1006614",
+ "https://identifiers.org/ncbiprotein:1651919"
+ ]
+ }
]
},
- "id": "b3916",
"name": "pfkA"
},
{
- "id": "b3919",
+ "id": "G_b3919",
"name": "tpiA"
},
{
- "annotation": {
- "ncbiprotein": "1653253"
+ "id": "G_b4025",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "https://identifiers.org/ncbiprotein:1653253"
+ ]
+ }
+ ]
},
- "id": "b4025",
"name": "pgi"
},
{
- "id": "b4395",
+ "id": "G_b4395",
"name": "ytjC"
},
{
- "id": "s0001",
+ "id": "G_s0001",
"name": "G_s0001"
}
],
+ "groups": [],
"id": "mini_textbook",
"metabolites": [
{
- "annotation": {
- "bigg.metabolite": "13dpg",
- "biocyc": "DPG",
- "chebi": [
- "CHEBI:16001",
- "CHEBI:1658",
- "CHEBI:20189",
- "CHEBI:57604",
- "CHEBI:11881"
- ],
- "hmdb": "HMDB01270",
- "kegg.compound": "C00236",
- "pubchem.substance": "3535",
- "reactome": "REACT_29800",
- "seed.compound": "cpd00203",
- "unipathway.compound": "UPC00236"
- },
"charge": -4,
"compartment": "c",
"formula": "C3H4O10P2",
- "id": "13dpg_c",
+ "id": "M_13dpg_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/13dpg",
+ "http://identifiers.org/biocyc/DPG",
+ "http://identifiers.org/chebi/CHEBI:16001",
+ "http://identifiers.org/chebi/CHEBI:1658",
+ "http://identifiers.org/chebi/CHEBI:20189",
+ "http://identifiers.org/chebi/CHEBI:57604",
+ "http://identifiers.org/chebi/CHEBI:11881",
+ "http://identifiers.org/hmdb/HMDB01270",
+ "http://identifiers.org/kegg.compound/C00236",
+ "http://identifiers.org/pubchem.substance/3535",
+ "http://identifiers.org/reactome/REACT_29800",
+ "http://identifiers.org/seed.compound/cpd00203",
+ "http://identifiers.org/unipathway.compound/UPC00236"
+ ]
+ }
+ ]
+ },
"name": "3-Phospho-D-glyceroyl phosphate"
},
{
- "annotation": {
- "bigg.metabolite": "2pg",
- "biocyc": "2-PG",
- "chebi": [
- "CHEBI:1267",
- "CHEBI:58289",
- "CHEBI:17835",
- "CHEBI:21028",
- "CHEBI:11651",
- "CHEBI:12986",
- "CHEBI:24344",
- "CHEBI:39868"
- ],
- "hmdb": [
- "HMDB03391",
- "HMDB00362"
- ],
- "kegg.compound": "C00631",
- "pubchem.substance": "3904",
- "reactome": "REACT_30485",
- "seed.compound": "cpd00482",
- "unipathway.compound": "UPC00631"
- },
"charge": -3,
"compartment": "c",
"formula": "C3H4O7P",
- "id": "2pg_c",
+ "id": "M_2pg_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/2pg",
+ "http://identifiers.org/biocyc/2-PG",
+ "http://identifiers.org/chebi/CHEBI:1267",
+ "http://identifiers.org/chebi/CHEBI:58289",
+ "http://identifiers.org/chebi/CHEBI:17835",
+ "http://identifiers.org/chebi/CHEBI:21028",
+ "http://identifiers.org/chebi/CHEBI:11651",
+ "http://identifiers.org/chebi/CHEBI:12986",
+ "http://identifiers.org/chebi/CHEBI:24344",
+ "http://identifiers.org/chebi/CHEBI:39868",
+ "http://identifiers.org/hmdb/HMDB03391",
+ "http://identifiers.org/hmdb/HMDB00362",
+ "http://identifiers.org/kegg.compound/C00631",
+ "http://identifiers.org/pubchem.substance/3904",
+ "http://identifiers.org/reactome/REACT_30485",
+ "http://identifiers.org/seed.compound/cpd00482",
+ "http://identifiers.org/unipathway.compound/UPC00631"
+ ]
+ }
+ ]
+ },
"name": "D-Glycerate 2-phosphate"
},
{
- "annotation": {
- "bigg.metabolite": "3pg",
- "biocyc": "G3P",
- "chebi": [
- "CHEBI:40016",
- "CHEBI:58272",
- "CHEBI:57998",
- "CHEBI:11879",
- "CHEBI:1657",
- "CHEBI:1659",
- "CHEBI:17050",
- "CHEBI:21029",
- "CHEBI:11882",
- "CHEBI:11880",
- "CHEBI:12987",
- "CHEBI:17794",
- "CHEBI:24345"
- ],
- "hmdb": "HMDB00807",
- "kegg.compound": [
- "C00197",
- "C00597"
- ],
- "pubchem.substance": "3497",
- "reactome": "REACT_29728",
- "seed.compound": "cpd00169",
- "unipathway.compound": [
- "UPC00597",
- "UPC00197"
- ]
- },
"charge": -3,
"compartment": "c",
"formula": "C3H4O7P",
- "id": "3pg_c",
+ "id": "M_3pg_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/3pg",
+ "http://identifiers.org/biocyc/G3P",
+ "http://identifiers.org/chebi/CHEBI:40016",
+ "http://identifiers.org/chebi/CHEBI:58272",
+ "http://identifiers.org/chebi/CHEBI:57998",
+ "http://identifiers.org/chebi/CHEBI:11879",
+ "http://identifiers.org/chebi/CHEBI:1657",
+ "http://identifiers.org/chebi/CHEBI:1659",
+ "http://identifiers.org/chebi/CHEBI:17050",
+ "http://identifiers.org/chebi/CHEBI:21029",
+ "http://identifiers.org/chebi/CHEBI:11882",
+ "http://identifiers.org/chebi/CHEBI:11880",
+ "http://identifiers.org/chebi/CHEBI:12987",
+ "http://identifiers.org/chebi/CHEBI:17794",
+ "http://identifiers.org/chebi/CHEBI:24345",
+ "http://identifiers.org/hmdb/HMDB00807",
+ "http://identifiers.org/kegg.compound/C00197",
+ "http://identifiers.org/kegg.compound/C00597",
+ "http://identifiers.org/pubchem.substance/3497",
+ "http://identifiers.org/reactome/REACT_29728",
+ "http://identifiers.org/seed.compound/cpd00169",
+ "http://identifiers.org/unipathway.compound/UPC00597",
+ "http://identifiers.org/unipathway.compound/UPC00197"
+ ]
+ }
+ ]
+ },
"name": "3-Phospho-D-glycerate"
},
{
- "annotation": {
- "bigg.metabolite": "adp",
- "biocyc": [
- "ADP",
- "ADP-GROUP"
- ],
- "cas": [
- "58-64-0"
- ],
- "chebi": [
- "CHEBI:13222",
- "CHEBI:16761",
- "CHEBI:2342",
- "CHEBI:22244",
- "CHEBI:40553",
- "CHEBI:456216"
- ],
- "hmdb": "HMDB01341",
- "kegg.compound": "C00008",
- "kegg.glycan": "G11113",
- "pubchem.substance": "3310",
- "reactome": [
- "REACT_190072",
- "REACT_481002",
- "REACT_211606",
- "REACT_429160",
- "REACT_29370",
- "REACT_196180",
- "REACT_113581",
- "REACT_113582",
- "REACT_114564",
- "REACT_114565",
- "REACT_429153"
- ],
- "seed.compound": "cpd00008",
- "unipathway.compound": "UPC00008"
- },
"charge": -3,
"compartment": "c",
"formula": "C10H12N5O10P2",
- "id": "adp_c",
+ "id": "M_adp_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/adp",
+ "http://identifiers.org/biocyc/ADP",
+ "http://identifiers.org/biocyc/ADP-GROUP",
+ "http://identifiers.org/cas/58-64-0",
+ "http://identifiers.org/cas/58-64-0",
+ "http://identifiers.org/chebi/CHEBI:13222",
+ "http://identifiers.org/chebi/CHEBI:16761",
+ "http://identifiers.org/chebi/CHEBI:2342",
+ "http://identifiers.org/chebi/CHEBI:22244",
+ "http://identifiers.org/chebi/CHEBI:40553",
+ "http://identifiers.org/chebi/CHEBI:456216",
+ "http://identifiers.org/hmdb/HMDB01341",
+ "http://identifiers.org/kegg.compound/C00008",
+ "http://identifiers.org/kegg.glycan/G11113",
+ "http://identifiers.org/pubchem.substance/3310",
+ "http://identifiers.org/reactome/REACT_190072",
+ "http://identifiers.org/reactome/REACT_481002",
+ "http://identifiers.org/reactome/REACT_211606",
+ "http://identifiers.org/reactome/REACT_429160",
+ "http://identifiers.org/reactome/REACT_29370",
+ "http://identifiers.org/reactome/REACT_196180",
+ "http://identifiers.org/reactome/REACT_113581",
+ "http://identifiers.org/reactome/REACT_113582",
+ "http://identifiers.org/reactome/REACT_114564",
+ "http://identifiers.org/reactome/REACT_114565",
+ "http://identifiers.org/reactome/REACT_429153",
+ "http://identifiers.org/seed.compound/cpd00008",
+ "http://identifiers.org/unipathway.compound/UPC00008"
+ ]
+ }
+ ]
+ },
"name": "ADP"
},
{
- "annotation": {
- "bigg.metabolite": "atp",
- "biocyc": "ATP",
- "cas": [
- "56-65-5"
- ],
- "chebi": [
- "CHEBI:40938",
- "CHEBI:15422",
- "CHEBI:57299",
- "CHEBI:13236",
- "CHEBI:10789",
- "CHEBI:30616",
- "CHEBI:22249",
- "CHEBI:10841",
- "CHEBI:2359"
- ],
- "hmdb": "HMDB00538",
- "kegg.compound": "C00002",
- "kegg.drug": "D08646",
- "pubchem.substance": "3304",
- "reactome": [
- "REACT_190078",
- "REACT_113592",
- "REACT_113593",
- "REACT_114570",
- "REACT_29358",
- "REACT_389573",
- "REACT_139836",
- "REACT_211579"
- ],
- "seed.compound": "cpd00002",
- "unipathway.compound": "UPC00002"
- },
"charge": -4,
"compartment": "c",
"formula": "C10H12N5O13P3",
- "id": "atp_c",
+ "id": "M_atp_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/atp",
+ "http://identifiers.org/biocyc/ATP",
+ "http://identifiers.org/cas/56-65-5",
+ "http://identifiers.org/cas/56-65-5",
+ "http://identifiers.org/chebi/CHEBI:40938",
+ "http://identifiers.org/chebi/CHEBI:15422",
+ "http://identifiers.org/chebi/CHEBI:57299",
+ "http://identifiers.org/chebi/CHEBI:13236",
+ "http://identifiers.org/chebi/CHEBI:10789",
+ "http://identifiers.org/chebi/CHEBI:30616",
+ "http://identifiers.org/chebi/CHEBI:22249",
+ "http://identifiers.org/chebi/CHEBI:10841",
+ "http://identifiers.org/chebi/CHEBI:2359",
+ "http://identifiers.org/hmdb/HMDB00538",
+ "http://identifiers.org/kegg.compound/C00002",
+ "http://identifiers.org/kegg.drug/D08646",
+ "http://identifiers.org/pubchem.substance/3304",
+ "http://identifiers.org/reactome/REACT_190078",
+ "http://identifiers.org/reactome/REACT_113592",
+ "http://identifiers.org/reactome/REACT_113593",
+ "http://identifiers.org/reactome/REACT_114570",
+ "http://identifiers.org/reactome/REACT_29358",
+ "http://identifiers.org/reactome/REACT_389573",
+ "http://identifiers.org/reactome/REACT_139836",
+ "http://identifiers.org/reactome/REACT_211579",
+ "http://identifiers.org/seed.compound/cpd00002",
+ "http://identifiers.org/unipathway.compound/UPC00002"
+ ]
+ }
+ ]
+ },
"name": "ATP"
},
{
- "annotation": {
- "bigg.metabolite": "dhap",
- "biocyc": "DIHYDROXY-ACETONE-PHOSPHATE",
- "cas": [
- "57-04-5"
- ],
- "chebi": [
- "CHEBI:14341",
- "CHEBI:57642",
- "CHEBI:14342",
- "CHEBI:16108",
- "CHEBI:5454",
- "CHEBI:24355",
- "CHEBI:39571"
- ],
- "hmdb": [
- "HMDB01473",
- "HMDB11735"
- ],
- "kegg.compound": "C00111",
- "pubchem.substance": "3411",
- "reactome": [
- "REACT_188451",
- "REACT_75970",
- "REACT_390404"
- ],
- "seed.compound": "cpd00095",
- "unipathway.compound": "UPC00111"
- },
"charge": -2,
"compartment": "c",
"formula": "C3H5O6P",
- "id": "dhap_c",
+ "id": "M_dhap_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/dhap",
+ "http://identifiers.org/biocyc/DIHYDROXY-ACETONE-PHOSPHATE",
+ "http://identifiers.org/cas/57-04-5",
+ "http://identifiers.org/cas/57-04-5",
+ "http://identifiers.org/chebi/CHEBI:14341",
+ "http://identifiers.org/chebi/CHEBI:57642",
+ "http://identifiers.org/chebi/CHEBI:14342",
+ "http://identifiers.org/chebi/CHEBI:16108",
+ "http://identifiers.org/chebi/CHEBI:5454",
+ "http://identifiers.org/chebi/CHEBI:24355",
+ "http://identifiers.org/chebi/CHEBI:39571",
+ "http://identifiers.org/hmdb/HMDB01473",
+ "http://identifiers.org/hmdb/HMDB11735",
+ "http://identifiers.org/kegg.compound/C00111",
+ "http://identifiers.org/pubchem.substance/3411",
+ "http://identifiers.org/reactome/REACT_188451",
+ "http://identifiers.org/reactome/REACT_75970",
+ "http://identifiers.org/reactome/REACT_390404",
+ "http://identifiers.org/seed.compound/cpd00095",
+ "http://identifiers.org/unipathway.compound/UPC00111"
+ ]
+ }
+ ]
+ },
"name": "Dihydroxyacetone phosphate"
},
{
- "annotation": {
- "bigg.metabolite": "f6p",
- "biocyc": "FRUCTOSE-6P",
- "cas": [
- "643-13-0"
- ],
- "chebi": [
- "CHEBI:57634",
- "CHEBI:12352",
- "CHEBI:45804",
- "CHEBI:61527",
- "CHEBI:61553",
- "CHEBI:10375",
- "CHEBI:16084",
- "CHEBI:42378",
- "CHEBI:22768"
- ],
- "hmdb": "HMDB03971",
- "kegg.compound": [
- "C05345",
- "C00085"
- ],
- "pubchem.substance": "3385",
- "seed.compound": "cpd00072",
- "unipathway.compound": [
- "UPC05345",
- "UPC00085"
- ]
- },
"charge": -2,
"compartment": "c",
"formula": "C6H11O9P",
- "id": "f6p_c",
+ "id": "M_f6p_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/f6p",
+ "http://identifiers.org/biocyc/FRUCTOSE-6P",
+ "http://identifiers.org/cas/643-13-0",
+ "http://identifiers.org/cas/643-13-0",
+ "http://identifiers.org/chebi/CHEBI:57634",
+ "http://identifiers.org/chebi/CHEBI:12352",
+ "http://identifiers.org/chebi/CHEBI:45804",
+ "http://identifiers.org/chebi/CHEBI:61527",
+ "http://identifiers.org/chebi/CHEBI:61553",
+ "http://identifiers.org/chebi/CHEBI:10375",
+ "http://identifiers.org/chebi/CHEBI:16084",
+ "http://identifiers.org/chebi/CHEBI:42378",
+ "http://identifiers.org/chebi/CHEBI:22768",
+ "http://identifiers.org/hmdb/HMDB03971",
+ "http://identifiers.org/kegg.compound/C05345",
+ "http://identifiers.org/kegg.compound/C00085",
+ "http://identifiers.org/pubchem.substance/3385",
+ "http://identifiers.org/seed.compound/cpd00072",
+ "http://identifiers.org/unipathway.compound/UPC05345",
+ "http://identifiers.org/unipathway.compound/UPC00085"
+ ]
+ }
+ ]
+ },
"name": "D-Fructose 6-phosphate"
},
{
- "annotation": {
- "bigg.metabolite": "fdp",
- "biocyc": "FRUCTOSE-16-DIPHOSPHATE",
- "cas": [
- "488-69-7"
- ],
- "chebi": [
- "CHEBI:32968",
- "CHEBI:49299",
- "CHEBI:42553",
- "CHEBI:32966",
- "CHEBI:37736",
- "CHEBI:28013",
- "CHEBI:32967",
- "CHEBI:41014",
- "CHEBI:22767",
- "CHEBI:10374",
- "CHEBI:40595",
- "CHEBI:40591"
- ],
- "kegg.compound": [
- "C05378",
- "C00354"
- ],
- "pubchem.substance": "3647",
- "seed.compound": "cpd00290",
- "unipathway.compound": "UPC00354"
- },
"charge": -4,
"compartment": "c",
"formula": "C6H10O12P2",
- "id": "fdp_c",
+ "id": "M_fdp_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/fdp",
+ "http://identifiers.org/biocyc/FRUCTOSE-16-DIPHOSPHATE",
+ "http://identifiers.org/cas/488-69-7",
+ "http://identifiers.org/cas/488-69-7",
+ "http://identifiers.org/chebi/CHEBI:32968",
+ "http://identifiers.org/chebi/CHEBI:49299",
+ "http://identifiers.org/chebi/CHEBI:42553",
+ "http://identifiers.org/chebi/CHEBI:32966",
+ "http://identifiers.org/chebi/CHEBI:37736",
+ "http://identifiers.org/chebi/CHEBI:28013",
+ "http://identifiers.org/chebi/CHEBI:32967",
+ "http://identifiers.org/chebi/CHEBI:41014",
+ "http://identifiers.org/chebi/CHEBI:22767",
+ "http://identifiers.org/chebi/CHEBI:10374",
+ "http://identifiers.org/chebi/CHEBI:40595",
+ "http://identifiers.org/chebi/CHEBI:40591",
+ "http://identifiers.org/kegg.compound/C05378",
+ "http://identifiers.org/kegg.compound/C00354",
+ "http://identifiers.org/pubchem.substance/3647",
+ "http://identifiers.org/seed.compound/cpd00290",
+ "http://identifiers.org/unipathway.compound/UPC00354"
+ ]
+ }
+ ]
+ },
"name": "D-Fructose 1,6-bisphosphate"
},
{
- "annotation": {
- "bigg.metabolite": "g3p",
- "cas": [
- "142-10-9"
- ],
- "chebi": [
- "CHEBI:17138",
- "CHEBI:14333",
- "CHEBI:5446",
- "CHEBI:58027"
- ],
- "hmdb": "HMDB01112",
- "kegg.compound": [
- "C00661",
- "C00118"
- ],
- "pubchem.substance": "3930",
- "seed.compound": "cpd00102",
- "unipathway.compound": [
- "UPC00661",
- "UPC00118"
- ]
- },
"charge": -2,
"compartment": "c",
"formula": "C3H5O6P",
- "id": "g3p_c",
+ "id": "M_g3p_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/g3p",
+ "http://identifiers.org/cas/142-10-9",
+ "http://identifiers.org/cas/142-10-9",
+ "http://identifiers.org/chebi/CHEBI:17138",
+ "http://identifiers.org/chebi/CHEBI:14333",
+ "http://identifiers.org/chebi/CHEBI:5446",
+ "http://identifiers.org/chebi/CHEBI:58027",
+ "http://identifiers.org/hmdb/HMDB01112",
+ "http://identifiers.org/kegg.compound/C00661",
+ "http://identifiers.org/kegg.compound/C00118",
+ "http://identifiers.org/pubchem.substance/3930",
+ "http://identifiers.org/seed.compound/cpd00102",
+ "http://identifiers.org/unipathway.compound/UPC00661",
+ "http://identifiers.org/unipathway.compound/UPC00118"
+ ]
+ }
+ ]
+ },
"name": "Glyceraldehyde 3-phosphate"
},
{
- "annotation": {
- "bigg.metabolite": "g6p",
- "biocyc": [
- "D-glucose-6-phosphate",
- "GLC-6-P"
- ],
- "cas": [
- "56-73-5"
- ],
- "chebi": [
- "CHEBI:10399",
- "CHEBI:22797",
- "CHEBI:41041",
- "CHEBI:17719",
- "CHEBI:4170",
- "CHEBI:61548",
- "CHEBI:58247",
- "CHEBI:12375"
- ],
- "hmdb": [
- "HMDB03498",
- "HMDB06793",
- "HMDB01401",
- "HMDB01549"
- ],
- "kegg.compound": [
- "C00092",
- "C01172"
- ],
- "pubchem.substance": "3392",
- "reactome": "REACT_1629756",
- "seed.compound": "cpd00079",
- "unipathway.compound": "UPC00092"
- },
"charge": -2,
"compartment": "c",
"formula": "C6H11O9P",
- "id": "g6p_c",
+ "id": "M_g6p_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/g6p",
+ "http://identifiers.org/biocyc/D-glucose-6-phosphate",
+ "http://identifiers.org/biocyc/GLC-6-P",
+ "http://identifiers.org/cas/56-73-5",
+ "http://identifiers.org/cas/56-73-5",
+ "http://identifiers.org/chebi/CHEBI:10399",
+ "http://identifiers.org/chebi/CHEBI:22797",
+ "http://identifiers.org/chebi/CHEBI:41041",
+ "http://identifiers.org/chebi/CHEBI:17719",
+ "http://identifiers.org/chebi/CHEBI:4170",
+ "http://identifiers.org/chebi/CHEBI:61548",
+ "http://identifiers.org/chebi/CHEBI:58247",
+ "http://identifiers.org/chebi/CHEBI:12375",
+ "http://identifiers.org/hmdb/HMDB03498",
+ "http://identifiers.org/hmdb/HMDB06793",
+ "http://identifiers.org/hmdb/HMDB01401",
+ "http://identifiers.org/hmdb/HMDB01549",
+ "http://identifiers.org/kegg.compound/C00092",
+ "http://identifiers.org/kegg.compound/C01172",
+ "http://identifiers.org/pubchem.substance/3392",
+ "http://identifiers.org/reactome/REACT_1629756",
+ "http://identifiers.org/seed.compound/cpd00079",
+ "http://identifiers.org/unipathway.compound/UPC00092"
+ ]
+ }
+ ]
+ },
"name": "D-Glucose 6-phosphate"
},
{
- "annotation": {
- "bigg.metabolite": "glc__D",
- "cas": [
- "50-99-7"
- ],
- "kegg.compound": "C00031",
- "pubchem.substance": "3333"
- },
"charge": 0,
"compartment": "e",
"formula": "C6H12O6",
- "id": "glc__D_e",
+ "id": "M_glc__D_e",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/glc__D",
+ "http://identifiers.org/cas/50-99-7",
+ "http://identifiers.org/cas/50-99-7",
+ "http://identifiers.org/kegg.compound/C00031",
+ "http://identifiers.org/pubchem.substance/3333"
+ ]
+ }
+ ]
+ },
"name": "D-Glucose"
},
{
- "annotation": {
- "bigg.metabolite": "h2o",
- "biocyc": [
- "WATER",
- "OH",
- "OXONIUM"
- ],
- "cas": [
- "7732-18-5"
- ],
- "chebi": [
- "CHEBI:15377",
- "CHEBI:13365",
- "CHEBI:41979",
- "CHEBI:16234",
- "CHEBI:36385",
- "CHEBI:42857",
- "CHEBI:27313",
- "CHEBI:44819",
- "CHEBI:29373",
- "CHEBI:10743",
- "CHEBI:5594",
- "CHEBI:29356",
- "CHEBI:53442",
- "CHEBI:29375",
- "CHEBI:29374",
- "CHEBI:13419",
- "CHEBI:43228",
- "CHEBI:44292",
- "CHEBI:13352",
- "CHEBI:41981",
- "CHEBI:29412",
- "CHEBI:42043",
- "CHEBI:33811",
- "CHEBI:33813",
- "CHEBI:35511",
- "CHEBI:5585",
- "CHEBI:44641",
- "CHEBI:44701"
- ],
- "hmdb": [
- "HMDB01039",
- "HMDB02111"
- ],
- "kegg.compound": [
- "C01328",
- "C00001",
- "C18714",
- "C18712"
- ],
- "kegg.drug": [
- "D00001",
- "D06322",
- "D03703"
- ],
- "pubchem.substance": "3303",
- "reactome": [
- "REACT_947593",
- "REACT_189422",
- "REACT_141343",
- "REACT_113518",
- "REACT_1605715",
- "REACT_109276",
- "REACT_113521",
- "REACT_113519",
- "REACT_2022884",
- "REACT_351603",
- "REACT_29356"
- ],
- "seed.compound": [
- "cpd15275",
- "cpd00001"
- ],
- "unipathway.compound": [
- "UPC00001",
- "UPC01328"
- ]
- },
"charge": 0,
"compartment": "c",
"formula": "H2O",
- "id": "h2o_c",
+ "id": "M_h2o_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/h2o",
+ "http://identifiers.org/biocyc/WATER",
+ "http://identifiers.org/biocyc/OH",
+ "http://identifiers.org/biocyc/OXONIUM",
+ "http://identifiers.org/cas/7732-18-5",
+ "http://identifiers.org/cas/7732-18-5",
+ "http://identifiers.org/chebi/CHEBI:15377",
+ "http://identifiers.org/chebi/CHEBI:13365",
+ "http://identifiers.org/chebi/CHEBI:41979",
+ "http://identifiers.org/chebi/CHEBI:16234",
+ "http://identifiers.org/chebi/CHEBI:36385",
+ "http://identifiers.org/chebi/CHEBI:42857",
+ "http://identifiers.org/chebi/CHEBI:27313",
+ "http://identifiers.org/chebi/CHEBI:44819",
+ "http://identifiers.org/chebi/CHEBI:29373",
+ "http://identifiers.org/chebi/CHEBI:10743",
+ "http://identifiers.org/chebi/CHEBI:5594",
+ "http://identifiers.org/chebi/CHEBI:29356",
+ "http://identifiers.org/chebi/CHEBI:53442",
+ "http://identifiers.org/chebi/CHEBI:29375",
+ "http://identifiers.org/chebi/CHEBI:29374",
+ "http://identifiers.org/chebi/CHEBI:13419",
+ "http://identifiers.org/chebi/CHEBI:43228",
+ "http://identifiers.org/chebi/CHEBI:44292",
+ "http://identifiers.org/chebi/CHEBI:13352",
+ "http://identifiers.org/chebi/CHEBI:41981",
+ "http://identifiers.org/chebi/CHEBI:29412",
+ "http://identifiers.org/chebi/CHEBI:42043",
+ "http://identifiers.org/chebi/CHEBI:33811",
+ "http://identifiers.org/chebi/CHEBI:33813",
+ "http://identifiers.org/chebi/CHEBI:35511",
+ "http://identifiers.org/chebi/CHEBI:5585",
+ "http://identifiers.org/chebi/CHEBI:44641",
+ "http://identifiers.org/chebi/CHEBI:44701",
+ "http://identifiers.org/hmdb/HMDB01039",
+ "http://identifiers.org/hmdb/HMDB02111",
+ "http://identifiers.org/kegg.compound/C01328",
+ "http://identifiers.org/kegg.compound/C00001",
+ "http://identifiers.org/kegg.compound/C18714",
+ "http://identifiers.org/kegg.compound/C18712",
+ "http://identifiers.org/kegg.drug/D00001",
+ "http://identifiers.org/kegg.drug/D06322",
+ "http://identifiers.org/kegg.drug/D03703",
+ "http://identifiers.org/pubchem.substance/3303",
+ "http://identifiers.org/reactome/REACT_947593",
+ "http://identifiers.org/reactome/REACT_189422",
+ "http://identifiers.org/reactome/REACT_141343",
+ "http://identifiers.org/reactome/REACT_113518",
+ "http://identifiers.org/reactome/REACT_1605715",
+ "http://identifiers.org/reactome/REACT_109276",
+ "http://identifiers.org/reactome/REACT_113521",
+ "http://identifiers.org/reactome/REACT_113519",
+ "http://identifiers.org/reactome/REACT_2022884",
+ "http://identifiers.org/reactome/REACT_351603",
+ "http://identifiers.org/reactome/REACT_29356",
+ "http://identifiers.org/seed.compound/cpd15275",
+ "http://identifiers.org/seed.compound/cpd00001",
+ "http://identifiers.org/unipathway.compound/UPC00001",
+ "http://identifiers.org/unipathway.compound/UPC01328"
+ ]
+ }
+ ]
+ },
"name": "H2O"
},
{
- "annotation": {
- "bigg.metabolite": "h2o",
- "biocyc": [
- "WATER",
- "OH",
- "OXONIUM"
- ],
- "cas": [
- "7732-18-5"
- ],
- "chebi": [
- "CHEBI:15377",
- "CHEBI:13365",
- "CHEBI:41979",
- "CHEBI:16234",
- "CHEBI:36385",
- "CHEBI:42857",
- "CHEBI:27313",
- "CHEBI:44819",
- "CHEBI:29373",
- "CHEBI:10743",
- "CHEBI:5594",
- "CHEBI:29356",
- "CHEBI:53442",
- "CHEBI:29375",
- "CHEBI:29374",
- "CHEBI:13419",
- "CHEBI:43228",
- "CHEBI:44292",
- "CHEBI:13352",
- "CHEBI:41981",
- "CHEBI:29412",
- "CHEBI:42043",
- "CHEBI:33811",
- "CHEBI:33813",
- "CHEBI:35511",
- "CHEBI:5585",
- "CHEBI:44641",
- "CHEBI:44701"
- ],
- "hmdb": [
- "HMDB01039",
- "HMDB02111"
- ],
- "kegg.compound": [
- "C01328",
- "C00001",
- "C18714",
- "C18712"
- ],
- "kegg.drug": [
- "D00001",
- "D06322",
- "D03703"
- ],
- "pubchem.substance": "3303",
- "reactome": [
- "REACT_947593",
- "REACT_189422",
- "REACT_141343",
- "REACT_113518",
- "REACT_1605715",
- "REACT_109276",
- "REACT_113521",
- "REACT_113519",
- "REACT_2022884",
- "REACT_351603",
- "REACT_29356"
- ],
- "seed.compound": [
- "cpd15275",
- "cpd00001"
- ],
- "unipathway.compound": [
- "UPC00001",
- "UPC01328"
- ]
- },
"charge": 0,
"compartment": "e",
"formula": "H2O",
- "id": "h2o_e",
+ "id": "M_h2o_e",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/h2o",
+ "http://identifiers.org/biocyc/WATER",
+ "http://identifiers.org/biocyc/OH",
+ "http://identifiers.org/biocyc/OXONIUM",
+ "http://identifiers.org/cas/7732-18-5",
+ "http://identifiers.org/cas/7732-18-5",
+ "http://identifiers.org/chebi/CHEBI:15377",
+ "http://identifiers.org/chebi/CHEBI:13365",
+ "http://identifiers.org/chebi/CHEBI:41979",
+ "http://identifiers.org/chebi/CHEBI:16234",
+ "http://identifiers.org/chebi/CHEBI:36385",
+ "http://identifiers.org/chebi/CHEBI:42857",
+ "http://identifiers.org/chebi/CHEBI:27313",
+ "http://identifiers.org/chebi/CHEBI:44819",
+ "http://identifiers.org/chebi/CHEBI:29373",
+ "http://identifiers.org/chebi/CHEBI:10743",
+ "http://identifiers.org/chebi/CHEBI:5594",
+ "http://identifiers.org/chebi/CHEBI:29356",
+ "http://identifiers.org/chebi/CHEBI:53442",
+ "http://identifiers.org/chebi/CHEBI:29375",
+ "http://identifiers.org/chebi/CHEBI:29374",
+ "http://identifiers.org/chebi/CHEBI:13419",
+ "http://identifiers.org/chebi/CHEBI:43228",
+ "http://identifiers.org/chebi/CHEBI:44292",
+ "http://identifiers.org/chebi/CHEBI:13352",
+ "http://identifiers.org/chebi/CHEBI:41981",
+ "http://identifiers.org/chebi/CHEBI:29412",
+ "http://identifiers.org/chebi/CHEBI:42043",
+ "http://identifiers.org/chebi/CHEBI:33811",
+ "http://identifiers.org/chebi/CHEBI:33813",
+ "http://identifiers.org/chebi/CHEBI:35511",
+ "http://identifiers.org/chebi/CHEBI:5585",
+ "http://identifiers.org/chebi/CHEBI:44641",
+ "http://identifiers.org/chebi/CHEBI:44701",
+ "http://identifiers.org/hmdb/HMDB01039",
+ "http://identifiers.org/hmdb/HMDB02111",
+ "http://identifiers.org/kegg.compound/C01328",
+ "http://identifiers.org/kegg.compound/C00001",
+ "http://identifiers.org/kegg.compound/C18714",
+ "http://identifiers.org/kegg.compound/C18712",
+ "http://identifiers.org/kegg.drug/D00001",
+ "http://identifiers.org/kegg.drug/D06322",
+ "http://identifiers.org/kegg.drug/D03703",
+ "http://identifiers.org/pubchem.substance/3303",
+ "http://identifiers.org/reactome/REACT_947593",
+ "http://identifiers.org/reactome/REACT_189422",
+ "http://identifiers.org/reactome/REACT_141343",
+ "http://identifiers.org/reactome/REACT_113518",
+ "http://identifiers.org/reactome/REACT_1605715",
+ "http://identifiers.org/reactome/REACT_109276",
+ "http://identifiers.org/reactome/REACT_113521",
+ "http://identifiers.org/reactome/REACT_113519",
+ "http://identifiers.org/reactome/REACT_2022884",
+ "http://identifiers.org/reactome/REACT_351603",
+ "http://identifiers.org/reactome/REACT_29356",
+ "http://identifiers.org/seed.compound/cpd15275",
+ "http://identifiers.org/seed.compound/cpd00001",
+ "http://identifiers.org/unipathway.compound/UPC00001",
+ "http://identifiers.org/unipathway.compound/UPC01328"
+ ]
+ }
+ ]
+ },
"name": "H2O"
},
{
- "annotation": {
- "bigg.metabolite": "h",
- "biocyc": "PROTON",
- "cas": [
- "12408-02-5"
- ],
- "chebi": [
- "CHEBI:24636",
- "CHEBI:15378",
- "CHEBI:10744",
- "CHEBI:13357",
- "CHEBI:5584"
- ],
- "kegg.compound": "C00080",
- "pubchem.substance": "3380",
- "reactome": [
- "REACT_194688",
- "REACT_425978",
- "REACT_193465",
- "REACT_374900",
- "REACT_74722",
- "REACT_425999",
- "REACT_428040",
- "REACT_163953",
- "REACT_372511",
- "REACT_2000349",
- "REACT_70106",
- "REACT_1470067",
- "REACT_113529",
- "REACT_425969",
- "REACT_428548",
- "REACT_156540",
- "REACT_1614597",
- "REACT_351626",
- "REACT_427899"
- ],
- "seed.compound": "cpd00067",
- "unipathway.compound": "UPC00080"
- },
"charge": 1,
"compartment": "c",
"formula": "H",
- "id": "h_c",
+ "id": "M_h_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/h",
+ "http://identifiers.org/biocyc/PROTON",
+ "http://identifiers.org/cas/12408-02-5",
+ "http://identifiers.org/cas/12408-02-5",
+ "http://identifiers.org/chebi/CHEBI:24636",
+ "http://identifiers.org/chebi/CHEBI:15378",
+ "http://identifiers.org/chebi/CHEBI:10744",
+ "http://identifiers.org/chebi/CHEBI:13357",
+ "http://identifiers.org/chebi/CHEBI:5584",
+ "http://identifiers.org/kegg.compound/C00080",
+ "http://identifiers.org/pubchem.substance/3380",
+ "http://identifiers.org/reactome/REACT_194688",
+ "http://identifiers.org/reactome/REACT_425978",
+ "http://identifiers.org/reactome/REACT_193465",
+ "http://identifiers.org/reactome/REACT_374900",
+ "http://identifiers.org/reactome/REACT_74722",
+ "http://identifiers.org/reactome/REACT_425999",
+ "http://identifiers.org/reactome/REACT_428040",
+ "http://identifiers.org/reactome/REACT_163953",
+ "http://identifiers.org/reactome/REACT_372511",
+ "http://identifiers.org/reactome/REACT_2000349",
+ "http://identifiers.org/reactome/REACT_70106",
+ "http://identifiers.org/reactome/REACT_1470067",
+ "http://identifiers.org/reactome/REACT_113529",
+ "http://identifiers.org/reactome/REACT_425969",
+ "http://identifiers.org/reactome/REACT_428548",
+ "http://identifiers.org/reactome/REACT_156540",
+ "http://identifiers.org/reactome/REACT_1614597",
+ "http://identifiers.org/reactome/REACT_351626",
+ "http://identifiers.org/reactome/REACT_427899",
+ "http://identifiers.org/seed.compound/cpd00067",
+ "http://identifiers.org/unipathway.compound/UPC00080"
+ ]
+ }
+ ]
+ },
"name": "H+"
},
{
- "annotation": {
- "bigg.metabolite": "h",
- "biocyc": "PROTON",
- "cas": [
- "12408-02-5"
- ],
- "chebi": [
- "CHEBI:24636",
- "CHEBI:15378",
- "CHEBI:10744",
- "CHEBI:13357",
- "CHEBI:5584"
- ],
- "kegg.compound": "C00080",
- "pubchem.substance": "3380",
- "reactome": [
- "REACT_194688",
- "REACT_425978",
- "REACT_193465",
- "REACT_374900",
- "REACT_74722",
- "REACT_425999",
- "REACT_428040",
- "REACT_163953",
- "REACT_372511",
- "REACT_2000349",
- "REACT_70106",
- "REACT_1470067",
- "REACT_113529",
- "REACT_425969",
- "REACT_428548",
- "REACT_156540",
- "REACT_1614597",
- "REACT_351626",
- "REACT_427899"
- ],
- "seed.compound": "cpd00067",
- "unipathway.compound": "UPC00080"
- },
"charge": 1,
"compartment": "e",
"formula": "H",
- "id": "h_e",
+ "id": "M_h_e",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/h",
+ "http://identifiers.org/biocyc/PROTON",
+ "http://identifiers.org/cas/12408-02-5",
+ "http://identifiers.org/cas/12408-02-5",
+ "http://identifiers.org/chebi/CHEBI:24636",
+ "http://identifiers.org/chebi/CHEBI:15378",
+ "http://identifiers.org/chebi/CHEBI:10744",
+ "http://identifiers.org/chebi/CHEBI:13357",
+ "http://identifiers.org/chebi/CHEBI:5584",
+ "http://identifiers.org/kegg.compound/C00080",
+ "http://identifiers.org/pubchem.substance/3380",
+ "http://identifiers.org/reactome/REACT_194688",
+ "http://identifiers.org/reactome/REACT_425978",
+ "http://identifiers.org/reactome/REACT_193465",
+ "http://identifiers.org/reactome/REACT_374900",
+ "http://identifiers.org/reactome/REACT_74722",
+ "http://identifiers.org/reactome/REACT_425999",
+ "http://identifiers.org/reactome/REACT_428040",
+ "http://identifiers.org/reactome/REACT_163953",
+ "http://identifiers.org/reactome/REACT_372511",
+ "http://identifiers.org/reactome/REACT_2000349",
+ "http://identifiers.org/reactome/REACT_70106",
+ "http://identifiers.org/reactome/REACT_1470067",
+ "http://identifiers.org/reactome/REACT_113529",
+ "http://identifiers.org/reactome/REACT_425969",
+ "http://identifiers.org/reactome/REACT_428548",
+ "http://identifiers.org/reactome/REACT_156540",
+ "http://identifiers.org/reactome/REACT_1614597",
+ "http://identifiers.org/reactome/REACT_351626",
+ "http://identifiers.org/reactome/REACT_427899",
+ "http://identifiers.org/seed.compound/cpd00067",
+ "http://identifiers.org/unipathway.compound/UPC00080"
+ ]
+ }
+ ]
+ },
"name": "H+"
},
{
- "annotation": {
- "bigg.metabolite": "lac__D",
- "biocyc": "META:D-LACTATE",
- "chebi": [
- "CHEBI:11001",
- "CHEBI:16004",
- "CHEBI:18684",
- "CHEBI:341",
- "CHEBI:42105",
- "CHEBI:42111",
- "CHEBI:43701"
- ],
- "hmdb": [
- "HMDB00171",
- "HMDB01311"
- ],
- "kegg.compound": "C00256",
- "metanetx.chemical": "MNXM285",
- "seed.compound": "cpd00221"
- },
"charge": -1,
"compartment": "c",
"formula": "C3H5O3",
- "id": "lac__D_c",
+ "id": "M_lac__D_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/lac__D",
+ "http://identifiers.org/biocyc/META:D-LACTATE",
+ "http://identifiers.org/chebi/CHEBI:11001",
+ "http://identifiers.org/chebi/CHEBI:16004",
+ "http://identifiers.org/chebi/CHEBI:18684",
+ "http://identifiers.org/chebi/CHEBI:341",
+ "http://identifiers.org/chebi/CHEBI:42105",
+ "http://identifiers.org/chebi/CHEBI:42111",
+ "http://identifiers.org/chebi/CHEBI:43701",
+ "http://identifiers.org/hmdb/HMDB00171",
+ "http://identifiers.org/hmdb/HMDB01311",
+ "http://identifiers.org/kegg.compound/C00256",
+ "http://identifiers.org/metanetx.chemical/MNXM285",
+ "http://identifiers.org/seed.compound/cpd00221"
+ ]
+ }
+ ]
+ },
"name": "D-Lactate"
},
{
- "annotation": {
- "bigg.metabolite": "lac__D",
- "biocyc": "META:D-LACTATE",
- "chebi": [
- "CHEBI:11001",
- "CHEBI:16004",
- "CHEBI:18684",
- "CHEBI:341",
- "CHEBI:42105",
- "CHEBI:42111",
- "CHEBI:43701"
- ],
- "hmdb": [
- "HMDB00171",
- "HMDB01311"
- ],
- "kegg.compound": "C00256",
- "metanetx.chemical": "MNXM285",
- "seed.compound": "cpd00221"
- },
"charge": -1,
"compartment": "e",
"formula": "C3H5O3",
- "id": "lac__D_e",
+ "id": "M_lac__D_e",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/lac__D",
+ "http://identifiers.org/biocyc/META:D-LACTATE",
+ "http://identifiers.org/chebi/CHEBI:11001",
+ "http://identifiers.org/chebi/CHEBI:16004",
+ "http://identifiers.org/chebi/CHEBI:18684",
+ "http://identifiers.org/chebi/CHEBI:341",
+ "http://identifiers.org/chebi/CHEBI:42105",
+ "http://identifiers.org/chebi/CHEBI:42111",
+ "http://identifiers.org/chebi/CHEBI:43701",
+ "http://identifiers.org/hmdb/HMDB00171",
+ "http://identifiers.org/hmdb/HMDB01311",
+ "http://identifiers.org/kegg.compound/C00256",
+ "http://identifiers.org/metanetx.chemical/MNXM285",
+ "http://identifiers.org/seed.compound/cpd00221"
+ ]
+ }
+ ]
+ },
"name": "D-Lactate"
},
{
- "annotation": {
- "bigg.metabolite": "nad",
- "biocyc": "NAD",
- "cas": [
- "53-84-9"
- ],
- "chebi": [
- "CHEBI:21901",
- "CHEBI:7422",
- "CHEBI:44214",
- "CHEBI:15846",
- "CHEBI:13394",
- "CHEBI:13393",
- "CHEBI:44215",
- "CHEBI:13389",
- "CHEBI:57540",
- "CHEBI:44281"
- ],
- "hmdb": "HMDB00902",
- "kegg.compound": "C00003",
- "kegg.drug": "D00002",
- "pubchem.substance": "3305",
- "reactome": [
- "REACT_192307",
- "REACT_29360",
- "REACT_427523",
- "REACT_194653",
- "REACT_113526"
- ],
- "seed.compound": "cpd00003",
- "unipathway.compound": "UPC00003"
- },
"charge": -1,
"compartment": "c",
"formula": "C21H26N7O14P2",
- "id": "nad_c",
+ "id": "M_nad_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/nad",
+ "http://identifiers.org/biocyc/NAD",
+ "http://identifiers.org/cas/53-84-9",
+ "http://identifiers.org/cas/53-84-9",
+ "http://identifiers.org/chebi/CHEBI:21901",
+ "http://identifiers.org/chebi/CHEBI:7422",
+ "http://identifiers.org/chebi/CHEBI:44214",
+ "http://identifiers.org/chebi/CHEBI:15846",
+ "http://identifiers.org/chebi/CHEBI:13394",
+ "http://identifiers.org/chebi/CHEBI:13393",
+ "http://identifiers.org/chebi/CHEBI:44215",
+ "http://identifiers.org/chebi/CHEBI:13389",
+ "http://identifiers.org/chebi/CHEBI:57540",
+ "http://identifiers.org/chebi/CHEBI:44281",
+ "http://identifiers.org/hmdb/HMDB00902",
+ "http://identifiers.org/kegg.compound/C00003",
+ "http://identifiers.org/kegg.drug/D00002",
+ "http://identifiers.org/pubchem.substance/3305",
+ "http://identifiers.org/reactome/REACT_192307",
+ "http://identifiers.org/reactome/REACT_29360",
+ "http://identifiers.org/reactome/REACT_427523",
+ "http://identifiers.org/reactome/REACT_194653",
+ "http://identifiers.org/reactome/REACT_113526",
+ "http://identifiers.org/seed.compound/cpd00003",
+ "http://identifiers.org/unipathway.compound/UPC00003"
+ ]
+ }
+ ]
+ },
"name": "Nicotinamide adenine dinucleotide"
},
{
- "annotation": {
- "bigg.metabolite": "nadh",
- "biocyc": "NADH",
- "cas": [
- "58-68-4"
- ],
- "chebi": [
- "CHEBI:13395",
- "CHEBI:21902",
- "CHEBI:16908",
- "CHEBI:7423",
- "CHEBI:44216",
- "CHEBI:57945",
- "CHEBI:13396"
- ],
- "hmdb": "HMDB01487",
- "kegg.compound": "C00004",
- "pubchem.substance": "3306",
- "reactome": [
- "REACT_192305",
- "REACT_73473",
- "REACT_194697",
- "REACT_29362"
- ],
- "seed.compound": "cpd00004",
- "unipathway.compound": "UPC00004"
- },
"charge": -2,
"compartment": "c",
"formula": "C21H27N7O14P2",
- "id": "nadh_c",
+ "id": "M_nadh_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/nadh",
+ "http://identifiers.org/biocyc/NADH",
+ "http://identifiers.org/cas/58-68-4",
+ "http://identifiers.org/cas/58-68-4",
+ "http://identifiers.org/chebi/CHEBI:13395",
+ "http://identifiers.org/chebi/CHEBI:21902",
+ "http://identifiers.org/chebi/CHEBI:16908",
+ "http://identifiers.org/chebi/CHEBI:7423",
+ "http://identifiers.org/chebi/CHEBI:44216",
+ "http://identifiers.org/chebi/CHEBI:57945",
+ "http://identifiers.org/chebi/CHEBI:13396",
+ "http://identifiers.org/hmdb/HMDB01487",
+ "http://identifiers.org/kegg.compound/C00004",
+ "http://identifiers.org/pubchem.substance/3306",
+ "http://identifiers.org/reactome/REACT_192305",
+ "http://identifiers.org/reactome/REACT_73473",
+ "http://identifiers.org/reactome/REACT_194697",
+ "http://identifiers.org/reactome/REACT_29362",
+ "http://identifiers.org/seed.compound/cpd00004",
+ "http://identifiers.org/unipathway.compound/UPC00004"
+ ]
+ }
+ ]
+ },
"name": "Nicotinamide adenine dinucleotide - reduced"
},
{
- "annotation": {
- "bigg.metabolite": "pep",
- "biocyc": "PHOSPHO-ENOL-PYRUVATE",
- "cas": [
- "138-08-9"
- ],
- "chebi": [
- "CHEBI:44897",
- "CHEBI:44894",
- "CHEBI:14812",
- "CHEBI:8147",
- "CHEBI:26055",
- "CHEBI:26054",
- "CHEBI:58702",
- "CHEBI:18021"
- ],
- "hmdb": "HMDB00263",
- "kegg.compound": "C00074",
- "pubchem.substance": "3374",
- "reactome": [
- "REACT_29492",
- "REACT_372364"
- ],
- "seed.compound": "cpd00061",
- "unipathway.compound": "UPC00074"
- },
"charge": -3,
"compartment": "c",
"formula": "C3H2O6P",
- "id": "pep_c",
+ "id": "M_pep_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/pep",
+ "http://identifiers.org/biocyc/PHOSPHO-ENOL-PYRUVATE",
+ "http://identifiers.org/cas/138-08-9",
+ "http://identifiers.org/cas/138-08-9",
+ "http://identifiers.org/chebi/CHEBI:44897",
+ "http://identifiers.org/chebi/CHEBI:44894",
+ "http://identifiers.org/chebi/CHEBI:14812",
+ "http://identifiers.org/chebi/CHEBI:8147",
+ "http://identifiers.org/chebi/CHEBI:26055",
+ "http://identifiers.org/chebi/CHEBI:26054",
+ "http://identifiers.org/chebi/CHEBI:58702",
+ "http://identifiers.org/chebi/CHEBI:18021",
+ "http://identifiers.org/hmdb/HMDB00263",
+ "http://identifiers.org/kegg.compound/C00074",
+ "http://identifiers.org/pubchem.substance/3374",
+ "http://identifiers.org/reactome/REACT_29492",
+ "http://identifiers.org/reactome/REACT_372364",
+ "http://identifiers.org/seed.compound/cpd00061",
+ "http://identifiers.org/unipathway.compound/UPC00074"
+ ]
+ }
+ ]
+ },
"name": "Phosphoenolpyruvate"
},
{
- "annotation": {
- "bigg.metabolite": "pi",
- "biocyc": [
- "Pi",
- "PHOSPHATE-GROUP",
- "CPD0-1421"
- ],
- "cas": [
- "14265-44-2"
- ],
- "chebi": [
- "CHEBI:37583",
- "CHEBI:7793",
- "CHEBI:37585",
- "CHEBI:34683",
- "CHEBI:14791",
- "CHEBI:34855",
- "CHEBI:29137",
- "CHEBI:29139",
- "CHEBI:63036",
- "CHEBI:26020",
- "CHEBI:39739",
- "CHEBI:32597",
- "CHEBI:32596",
- "CHEBI:43474",
- "CHEBI:63051",
- "CHEBI:43470",
- "CHEBI:9679",
- "CHEBI:35433",
- "CHEBI:4496",
- "CHEBI:45024",
- "CHEBI:18367",
- "CHEBI:26078",
- "CHEBI:39745",
- "CHEBI:24838"
- ],
- "hmdb": "HMDB02142",
- "kegg.compound": [
- "C13556",
- "C13558",
- "C00009"
- ],
- "kegg.drug": "D05467",
- "pubchem.substance": "3311",
- "reactome": [
- "REACT_947590",
- "REACT_109277",
- "REACT_113548",
- "REACT_2255331",
- "REACT_29372",
- "REACT_113550",
- "REACT_113551"
- ],
- "seed.compound": [
- "cpd09464",
- "cpd09463",
- "cpd00009"
- ],
- "unipathway.compound": "UPC00009"
- },
"charge": -2,
"compartment": "c",
"formula": "HO4P",
- "id": "pi_c",
+ "id": "M_pi_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/pi",
+ "http://identifiers.org/biocyc/Pi",
+ "http://identifiers.org/biocyc/PHOSPHATE-GROUP",
+ "http://identifiers.org/biocyc/CPD0-1421",
+ "http://identifiers.org/cas/14265-44-2",
+ "http://identifiers.org/cas/14265-44-2",
+ "http://identifiers.org/chebi/CHEBI:37583",
+ "http://identifiers.org/chebi/CHEBI:7793",
+ "http://identifiers.org/chebi/CHEBI:37585",
+ "http://identifiers.org/chebi/CHEBI:34683",
+ "http://identifiers.org/chebi/CHEBI:14791",
+ "http://identifiers.org/chebi/CHEBI:34855",
+ "http://identifiers.org/chebi/CHEBI:29137",
+ "http://identifiers.org/chebi/CHEBI:29139",
+ "http://identifiers.org/chebi/CHEBI:63036",
+ "http://identifiers.org/chebi/CHEBI:26020",
+ "http://identifiers.org/chebi/CHEBI:39739",
+ "http://identifiers.org/chebi/CHEBI:32597",
+ "http://identifiers.org/chebi/CHEBI:32596",
+ "http://identifiers.org/chebi/CHEBI:43474",
+ "http://identifiers.org/chebi/CHEBI:63051",
+ "http://identifiers.org/chebi/CHEBI:43470",
+ "http://identifiers.org/chebi/CHEBI:9679",
+ "http://identifiers.org/chebi/CHEBI:35433",
+ "http://identifiers.org/chebi/CHEBI:4496",
+ "http://identifiers.org/chebi/CHEBI:45024",
+ "http://identifiers.org/chebi/CHEBI:18367",
+ "http://identifiers.org/chebi/CHEBI:26078",
+ "http://identifiers.org/chebi/CHEBI:39745",
+ "http://identifiers.org/chebi/CHEBI:24838",
+ "http://identifiers.org/hmdb/HMDB02142",
+ "http://identifiers.org/kegg.compound/C13556",
+ "http://identifiers.org/kegg.compound/C13558",
+ "http://identifiers.org/kegg.compound/C00009",
+ "http://identifiers.org/kegg.drug/D05467",
+ "http://identifiers.org/pubchem.substance/3311",
+ "http://identifiers.org/reactome/REACT_947590",
+ "http://identifiers.org/reactome/REACT_109277",
+ "http://identifiers.org/reactome/REACT_113548",
+ "http://identifiers.org/reactome/REACT_2255331",
+ "http://identifiers.org/reactome/REACT_29372",
+ "http://identifiers.org/reactome/REACT_113550",
+ "http://identifiers.org/reactome/REACT_113551",
+ "http://identifiers.org/seed.compound/cpd09464",
+ "http://identifiers.org/seed.compound/cpd09463",
+ "http://identifiers.org/seed.compound/cpd00009",
+ "http://identifiers.org/unipathway.compound/UPC00009"
+ ]
+ }
+ ]
+ },
"name": "Phosphate"
},
{
- "annotation": {
- "bigg.metabolite": "pi",
- "biocyc": [
- "Pi",
- "PHOSPHATE-GROUP",
- "CPD0-1421"
- ],
- "cas": [
- "14265-44-2"
- ],
- "chebi": [
- "CHEBI:37583",
- "CHEBI:7793",
- "CHEBI:37585",
- "CHEBI:34683",
- "CHEBI:14791",
- "CHEBI:34855",
- "CHEBI:29137",
- "CHEBI:29139",
- "CHEBI:63036",
- "CHEBI:26020",
- "CHEBI:39739",
- "CHEBI:32597",
- "CHEBI:32596",
- "CHEBI:43474",
- "CHEBI:63051",
- "CHEBI:43470",
- "CHEBI:9679",
- "CHEBI:35433",
- "CHEBI:4496",
- "CHEBI:45024",
- "CHEBI:18367",
- "CHEBI:26078",
- "CHEBI:39745",
- "CHEBI:24838"
- ],
- "hmdb": "HMDB02142",
- "kegg.compound": [
- "C13556",
- "C13558",
- "C00009"
- ],
- "kegg.drug": "D05467",
- "pubchem.substance": "3311",
- "reactome": [
- "REACT_947590",
- "REACT_109277",
- "REACT_113548",
- "REACT_2255331",
- "REACT_29372",
- "REACT_113550",
- "REACT_113551"
- ],
- "seed.compound": [
- "cpd09464",
- "cpd09463",
- "cpd00009"
- ],
- "unipathway.compound": "UPC00009"
- },
"charge": -2,
"compartment": "e",
"formula": "HO4P",
- "id": "pi_e",
+ "id": "M_pi_e",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/pi",
+ "http://identifiers.org/biocyc/Pi",
+ "http://identifiers.org/biocyc/PHOSPHATE-GROUP",
+ "http://identifiers.org/biocyc/CPD0-1421",
+ "http://identifiers.org/cas/14265-44-2",
+ "http://identifiers.org/cas/14265-44-2",
+ "http://identifiers.org/chebi/CHEBI:37583",
+ "http://identifiers.org/chebi/CHEBI:7793",
+ "http://identifiers.org/chebi/CHEBI:37585",
+ "http://identifiers.org/chebi/CHEBI:34683",
+ "http://identifiers.org/chebi/CHEBI:14791",
+ "http://identifiers.org/chebi/CHEBI:34855",
+ "http://identifiers.org/chebi/CHEBI:29137",
+ "http://identifiers.org/chebi/CHEBI:29139",
+ "http://identifiers.org/chebi/CHEBI:63036",
+ "http://identifiers.org/chebi/CHEBI:26020",
+ "http://identifiers.org/chebi/CHEBI:39739",
+ "http://identifiers.org/chebi/CHEBI:32597",
+ "http://identifiers.org/chebi/CHEBI:32596",
+ "http://identifiers.org/chebi/CHEBI:43474",
+ "http://identifiers.org/chebi/CHEBI:63051",
+ "http://identifiers.org/chebi/CHEBI:43470",
+ "http://identifiers.org/chebi/CHEBI:9679",
+ "http://identifiers.org/chebi/CHEBI:35433",
+ "http://identifiers.org/chebi/CHEBI:4496",
+ "http://identifiers.org/chebi/CHEBI:45024",
+ "http://identifiers.org/chebi/CHEBI:18367",
+ "http://identifiers.org/chebi/CHEBI:26078",
+ "http://identifiers.org/chebi/CHEBI:39745",
+ "http://identifiers.org/chebi/CHEBI:24838",
+ "http://identifiers.org/hmdb/HMDB02142",
+ "http://identifiers.org/kegg.compound/C13556",
+ "http://identifiers.org/kegg.compound/C13558",
+ "http://identifiers.org/kegg.compound/C00009",
+ "http://identifiers.org/kegg.drug/D05467",
+ "http://identifiers.org/pubchem.substance/3311",
+ "http://identifiers.org/reactome/REACT_947590",
+ "http://identifiers.org/reactome/REACT_109277",
+ "http://identifiers.org/reactome/REACT_113548",
+ "http://identifiers.org/reactome/REACT_2255331",
+ "http://identifiers.org/reactome/REACT_29372",
+ "http://identifiers.org/reactome/REACT_113550",
+ "http://identifiers.org/reactome/REACT_113551",
+ "http://identifiers.org/seed.compound/cpd09464",
+ "http://identifiers.org/seed.compound/cpd09463",
+ "http://identifiers.org/seed.compound/cpd00009",
+ "http://identifiers.org/unipathway.compound/UPC00009"
+ ]
+ }
+ ]
+ },
"name": "Phosphate"
},
{
- "annotation": {
- "bigg.metabolite": "pyr",
- "biocyc": "PYRUVATE",
- "cas": [
- "127-17-3"
- ],
- "chebi": [
- "CHEBI:15361",
- "CHEBI:14987",
- "CHEBI:8685",
- "CHEBI:32816",
- "CHEBI:45253",
- "CHEBI:26466",
- "CHEBI:26462"
- ],
- "hmdb": "HMDB00243",
- "kegg.compound": "C00022",
- "lipidmaps": "LMFA01060077",
- "pubchem.substance": "3324",
- "reactome": [
- "REACT_113557",
- "REACT_389680",
- "REACT_29398"
- ],
- "seed.compound": "cpd00020",
- "unipathway.compound": "UPC00022"
- },
"charge": -1,
"compartment": "c",
"formula": "C3H3O3",
- "id": "pyr_c",
+ "id": "M_pyr_c",
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/pyr",
+ "http://identifiers.org/biocyc/PYRUVATE",
+ "http://identifiers.org/cas/127-17-3",
+ "http://identifiers.org/cas/127-17-3",
+ "http://identifiers.org/chebi/CHEBI:15361",
+ "http://identifiers.org/chebi/CHEBI:14987",
+ "http://identifiers.org/chebi/CHEBI:8685",
+ "http://identifiers.org/chebi/CHEBI:32816",
+ "http://identifiers.org/chebi/CHEBI:45253",
+ "http://identifiers.org/chebi/CHEBI:26466",
+ "http://identifiers.org/chebi/CHEBI:26462",
+ "http://identifiers.org/hmdb/HMDB00243",
+ "http://identifiers.org/kegg.compound/C00022",
+ "http://identifiers.org/lipidmaps/LMFA01060077",
+ "http://identifiers.org/pubchem.substance/3324",
+ "http://identifiers.org/reactome/REACT_113557",
+ "http://identifiers.org/reactome/REACT_389680",
+ "http://identifiers.org/reactome/REACT_29398",
+ "http://identifiers.org/seed.compound/cpd00020",
+ "http://identifiers.org/unipathway.compound/UPC00022"
+ ]
+ }
+ ]
+ },
"name": "Pyruvate"
}
],
"reactions": [
{
- "annotation": {
- "bigg.reaction": "ATPM"
- },
"gene_reaction_rule": "",
- "id": "ATPM",
+ "id": "R_ATPM",
"lower_bound": 8.39,
"metabolites": {
- "adp_c": 1.0,
- "atp_c": -1.0,
- "h2o_c": -1.0,
- "h_c": 1.0,
- "pi_c": 1.0
+ "M_adp_c": 1.0,
+ "M_atp_c": -1.0,
+ "M_h2o_c": -1.0,
+ "M_h_c": 1.0,
+ "M_pi_c": 1.0
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/ATPM"
+ ]
+ }
+ ]
},
"name": "ATP maintenance requirement",
"objective_coefficient": 1.0,
@@ -1126,266 +1172,376 @@
},
{
"gene_reaction_rule": "",
- "id": "D_LACt2",
+ "id": "R_D_LACt2",
"lower_bound": -1000.0,
"metabolites": {},
"name": "",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "ENO"
- },
"gene_reaction_rule": "b2779",
- "id": "ENO",
+ "id": "R_ENO",
"lower_bound": -1000.0,
"metabolites": {
- "2pg_c": -1.0,
- "h2o_c": 1.0,
- "pep_c": 1.0
+ "M_2pg_c": -1.0,
+ "M_h2o_c": 1.0,
+ "M_pep_c": 1.0
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/ENO"
+ ]
+ }
+ ]
},
"name": "enolase",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "glc",
- "sbo": "SBO:0000627"
- },
"gene_reaction_rule": "",
- "id": "EX_glc__D_e",
+ "id": "R_EX_glc__D_e",
"lower_bound": -10.0,
"metabolites": {
- "glc__D_e": -1.0
+ "M_glc__D_e": -1.0
+ },
+ "metadata": {
+ "sbo": "SBO:0000627",
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/glc"
+ ]
+ }
+ ]
},
"name": "D-Glucose exchange",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "h",
- "sbo": "SBO:0000627"
- },
"gene_reaction_rule": "",
- "id": "EX_h_e",
+ "id": "R_EX_h_e",
"lower_bound": -1000.0,
"metabolites": {
- "h_e": -1.0
+ "M_h_e": -1.0
+ },
+ "metadata": {
+ "sbo": "SBO:0000627",
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/h"
+ ]
+ }
+ ]
},
"name": "H+ exchange",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "lac__D",
- "sbo": "SBO:0000627"
- },
"gene_reaction_rule": "",
- "id": "EX_lac__D_e",
+ "id": "R_EX_lac__D_e",
"lower_bound": 0.0,
"metabolites": {
- "lac__D_e": -1.0
+ "M_lac__D_e": -1.0
+ },
+ "metadata": {
+ "sbo": "SBO:0000627",
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/lac__D"
+ ]
+ }
+ ]
},
"name": "D-lactate exchange",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "FBA"
- },
"gene_reaction_rule": "b1773 or b2097 or b2925",
- "id": "FBA",
+ "id": "R_FBA",
"lower_bound": -1000.0,
"metabolites": {
- "dhap_c": 1.0,
- "fdp_c": -1.0,
- "g3p_c": 1.0
+ "M_dhap_c": 1.0,
+ "M_fdp_c": -1.0,
+ "M_g3p_c": 1.0
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/FBA"
+ ]
+ }
+ ]
},
"name": "fructose-bisphosphate aldolase",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "GAPD"
- },
"gene_reaction_rule": "b1779",
- "id": "GAPD",
+ "id": "R_GAPD",
"lower_bound": -1000.0,
"metabolites": {
- "13dpg_c": 1.0,
- "g3p_c": -1.0,
- "h_c": 1.0,
- "nad_c": -1.0,
- "nadh_c": 1.0,
- "pi_c": -1.0
+ "M_13dpg_c": 1.0,
+ "M_g3p_c": -1.0,
+ "M_h_c": 1.0,
+ "M_nad_c": -1.0,
+ "M_nadh_c": 1.0,
+ "M_pi_c": -1.0
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/GAPD"
+ ]
+ }
+ ]
},
"name": "glyceraldehyde-3-phosphate dehydrogenase",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "GLCpts"
- },
"gene_reaction_rule": "(b2415 and b2417 and b1101 and b2416) or (b2415 and b2417 and b1621 and b2416) or (b2415 and b1818 and b1817 and b1819 and b2416)",
- "id": "GLCpts",
+ "id": "R_GLCpts",
"lower_bound": 0.0,
"metabolites": {
- "g6p_c": 1.0,
- "glc__D_e": -1.0,
- "pep_c": -1.0,
- "pyr_c": 1.0
+ "M_g6p_c": 1.0,
+ "M_glc__D_e": -1.0,
+ "M_pep_c": -1.0,
+ "M_pyr_c": 1.0
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/GLCpts"
+ ]
+ }
+ ]
},
"name": "D-glucose transport via PEP:Pyr PTS",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "H2Ot"
- },
"gene_reaction_rule": "b0875 or s0001",
- "id": "H2Ot",
+ "id": "R_H2Ot",
"lower_bound": -1000.0,
"metabolites": {
- "h2o_c": 1.0,
- "h2o_e": -1.0
+ "M_h2o_c": 1.0,
+ "M_h2o_e": -1.0
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/H2Ot"
+ ]
+ }
+ ]
},
"name": "R H2O transport via - diffusion",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "LDH_D",
- "biocyc": "META:DLACTDEHYDROGNAD-RXN",
- "ec-code": "1.1.1.28",
- "kegg.reaction": "R00704",
- "metanetx.reaction": "MNXR101037",
- "rhea": [
- "16369",
- "16370",
- "16371",
- "16372"
- ],
- "sbo": "SBO:0000375"
- },
"gene_reaction_rule": "b2133 or b1380",
- "id": "LDH_D",
+ "id": "R_LDH_D",
"lower_bound": -1000.0,
"metabolites": {
- "h_c": 1.0,
- "lac__D_c": -1.0,
- "nad_c": -1.0,
- "nadh_c": 1.0,
- "pyr_c": 1.0
+ "M_h_c": 1.0,
+ "M_lac__D_c": -1.0,
+ "M_nad_c": -1.0,
+ "M_nadh_c": 1.0,
+ "M_pyr_c": 1.0
+ },
+ "metadata": {
+ "sbo": "SBO:0000375",
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/LDH_D",
+ "http://identifiers.org/biocyc/META:DLACTDEHYDROGNAD-RXN",
+ "http://identifiers.org/ec-code/1.1.1.28",
+ "http://identifiers.org/kegg.reaction/R00704",
+ "http://identifiers.org/metanetx.reaction/MNXR101037",
+ "http://identifiers.org/rhea/16369",
+ "http://identifiers.org/rhea/16370",
+ "http://identifiers.org/rhea/16371",
+ "http://identifiers.org/rhea/16372"
+ ]
+ }
+ ]
},
"name": "D-lactate dehydrogenase",
"subsystem": "Pyruvate Metabolism",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "PFK"
- },
"gene_reaction_rule": "b3916 or b1723",
- "id": "PFK",
+ "id": "R_PFK",
"lower_bound": 0.0,
"metabolites": {
- "adp_c": 1.0,
- "atp_c": -1.0,
- "f6p_c": -1.0,
- "fdp_c": 1.0,
- "h_c": 1.0
+ "M_adp_c": 1.0,
+ "M_atp_c": -1.0,
+ "M_f6p_c": -1.0,
+ "M_fdp_c": 1.0,
+ "M_h_c": 1.0
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PFK"
+ ]
+ }
+ ]
},
"name": "phosphofructokinase",
"objective_coefficient": 1.0,
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "PGI"
- },
"gene_reaction_rule": "b4025",
- "id": "PGI",
+ "id": "R_PGI",
"lower_bound": -1000.0,
"metabolites": {
- "f6p_c": 1.0,
- "g6p_c": -1.0
+ "M_f6p_c": 1.0,
+ "M_g6p_c": -1.0
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PGI"
+ ]
+ }
+ ]
},
"name": "glucose-6-phosphate isomerase",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "PGK"
- },
"gene_reaction_rule": "b2926",
- "id": "PGK",
+ "id": "R_PGK",
"lower_bound": -1000.0,
"metabolites": {
- "13dpg_c": 1.0,
- "3pg_c": -1.0,
- "adp_c": 1.0,
- "atp_c": -1.0
+ "M_13dpg_c": 1.0,
+ "M_3pg_c": -1.0,
+ "M_adp_c": 1.0,
+ "M_atp_c": -1.0
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PGK"
+ ]
+ }
+ ]
},
"name": "phosphoglycerate kinase",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "PGM"
- },
"gene_reaction_rule": "b4395 or b3612 or b0755",
- "id": "PGM",
+ "id": "R_PGM",
"lower_bound": -1000.0,
"metabolites": {
- "2pg_c": -1.0,
- "3pg_c": 1.0
+ "M_2pg_c": -1.0,
+ "M_3pg_c": 1.0
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PGM"
+ ]
+ }
+ ]
},
"name": "phosphoglycerate mutase",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "PIt2r"
- },
"gene_reaction_rule": "b2987 or b3493",
- "id": "PIt2r",
+ "id": "R_PIt2r",
"lower_bound": -1000.0,
"metabolites": {
- "h_c": 1.0,
- "h_e": -1.0,
- "pi_c": 1.0,
- "pi_e": -1.0
+ "M_h_c": 1.0,
+ "M_h_e": -1.0,
+ "M_pi_c": 1.0,
+ "M_pi_e": -1.0
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PIt2r"
+ ]
+ }
+ ]
},
"name": "R phosphate reversible transport via - symport",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "PYK"
- },
"gene_reaction_rule": "b1854 or b1676",
- "id": "PYK",
+ "id": "R_PYK",
"lower_bound": 0.0,
"metabolites": {
- "adp_c": -1.0,
- "atp_c": 1.0,
- "h_c": -1.0,
- "pep_c": -1.0,
- "pyr_c": 1.0
+ "M_adp_c": -1.0,
+ "M_atp_c": 1.0,
+ "M_h_c": -1.0,
+ "M_pep_c": -1.0,
+ "M_pyr_c": 1.0
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PYK"
+ ]
+ }
+ ]
},
"name": "pyruvate kinase",
"upper_bound": 1000.0
},
{
- "annotation": {
- "bigg.reaction": "TPI"
- },
"gene_reaction_rule": "b3919",
- "id": "TPI",
+ "id": "R_TPI",
"lower_bound": -1000.0,
"metabolites": {
- "dhap_c": -1.0,
- "g3p_c": 1.0
+ "M_dhap_c": -1.0,
+ "M_g3p_c": 1.0
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_is",
+ "resources": [
+ "http://identifiers.org/bigg.reaction/TPI"
+ ]
+ }
+ ]
},
"name": "triose-phosphate isomerase",
"upper_bound": 1000.0
diff --git a/src/cobra/data/mini.mat b/src/cobra/data/mini.mat
index 9f46abd4c..b3ade4f10 100644
Binary files a/src/cobra/data/mini.mat and b/src/cobra/data/mini.mat differ
diff --git a/src/cobra/data/mini.yml b/src/cobra/data/mini.yml
index cd9a28a41..72aced4e4 100644
--- a/src/cobra/data/mini.yml
+++ b/src/cobra/data/mini.yml
@@ -1,1168 +1,1233 @@
!!omap
- metabolites:
- !!omap
- - id: 13dpg_c
+ - id: M_13dpg_c
- name: 3-Phospho-D-glyceroyl phosphate
- compartment: c
- charge: -4
- formula: C3H4O10P2
- - annotation: !!omap
- - bigg.metabolite: 13dpg
- - biocyc: DPG
- - chebi:
- - CHEBI:16001
- - CHEBI:1658
- - CHEBI:20189
- - CHEBI:57604
- - CHEBI:11881
- - hmdb: HMDB01270
- - kegg.compound: C00236
- - pubchem.substance: '3535'
- - reactome: REACT_29800
- - seed.compound: cpd00203
- - unipathway.compound: UPC00236
- - !!omap
- - id: 2pg_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/13dpg
+ - http://identifiers.org/biocyc/DPG
+ - http://identifiers.org/chebi/CHEBI:16001
+ - http://identifiers.org/chebi/CHEBI:1658
+ - http://identifiers.org/chebi/CHEBI:20189
+ - http://identifiers.org/chebi/CHEBI:57604
+ - http://identifiers.org/chebi/CHEBI:11881
+ - http://identifiers.org/hmdb/HMDB01270
+ - http://identifiers.org/kegg.compound/C00236
+ - http://identifiers.org/pubchem.substance/3535
+ - http://identifiers.org/reactome/REACT_29800
+ - http://identifiers.org/seed.compound/cpd00203
+ - http://identifiers.org/unipathway.compound/UPC00236
+ - !!omap
+ - id: M_2pg_c
- name: D-Glycerate 2-phosphate
- compartment: c
- charge: -3
- formula: C3H4O7P
- - annotation: !!omap
- - bigg.metabolite: 2pg
- - biocyc: 2-PG
- - chebi:
- - CHEBI:1267
- - CHEBI:58289
- - CHEBI:17835
- - CHEBI:21028
- - CHEBI:11651
- - CHEBI:12986
- - CHEBI:24344
- - CHEBI:39868
- - hmdb:
- - HMDB03391
- - HMDB00362
- - kegg.compound: C00631
- - pubchem.substance: '3904'
- - reactome: REACT_30485
- - seed.compound: cpd00482
- - unipathway.compound: UPC00631
- - !!omap
- - id: 3pg_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/2pg
+ - http://identifiers.org/biocyc/2-PG
+ - http://identifiers.org/chebi/CHEBI:1267
+ - http://identifiers.org/chebi/CHEBI:58289
+ - http://identifiers.org/chebi/CHEBI:17835
+ - http://identifiers.org/chebi/CHEBI:21028
+ - http://identifiers.org/chebi/CHEBI:11651
+ - http://identifiers.org/chebi/CHEBI:12986
+ - http://identifiers.org/chebi/CHEBI:24344
+ - http://identifiers.org/chebi/CHEBI:39868
+ - http://identifiers.org/hmdb/HMDB03391
+ - http://identifiers.org/hmdb/HMDB00362
+ - http://identifiers.org/kegg.compound/C00631
+ - http://identifiers.org/pubchem.substance/3904
+ - http://identifiers.org/reactome/REACT_30485
+ - http://identifiers.org/seed.compound/cpd00482
+ - http://identifiers.org/unipathway.compound/UPC00631
+ - !!omap
+ - id: M_3pg_c
- name: 3-Phospho-D-glycerate
- compartment: c
- charge: -3
- formula: C3H4O7P
- - annotation: !!omap
- - bigg.metabolite: 3pg
- - biocyc: G3P
- - chebi:
- - CHEBI:40016
- - CHEBI:58272
- - CHEBI:57998
- - CHEBI:11879
- - CHEBI:1657
- - CHEBI:1659
- - CHEBI:17050
- - CHEBI:21029
- - CHEBI:11882
- - CHEBI:11880
- - CHEBI:12987
- - CHEBI:17794
- - CHEBI:24345
- - hmdb: HMDB00807
- - kegg.compound:
- - C00197
- - C00597
- - pubchem.substance: '3497'
- - reactome: REACT_29728
- - seed.compound: cpd00169
- - unipathway.compound:
- - UPC00597
- - UPC00197
- - !!omap
- - id: adp_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/3pg
+ - http://identifiers.org/biocyc/G3P
+ - http://identifiers.org/chebi/CHEBI:40016
+ - http://identifiers.org/chebi/CHEBI:58272
+ - http://identifiers.org/chebi/CHEBI:57998
+ - http://identifiers.org/chebi/CHEBI:11879
+ - http://identifiers.org/chebi/CHEBI:1657
+ - http://identifiers.org/chebi/CHEBI:1659
+ - http://identifiers.org/chebi/CHEBI:17050
+ - http://identifiers.org/chebi/CHEBI:21029
+ - http://identifiers.org/chebi/CHEBI:11882
+ - http://identifiers.org/chebi/CHEBI:11880
+ - http://identifiers.org/chebi/CHEBI:12987
+ - http://identifiers.org/chebi/CHEBI:17794
+ - http://identifiers.org/chebi/CHEBI:24345
+ - http://identifiers.org/hmdb/HMDB00807
+ - http://identifiers.org/kegg.compound/C00197
+ - http://identifiers.org/kegg.compound/C00597
+ - http://identifiers.org/pubchem.substance/3497
+ - http://identifiers.org/reactome/REACT_29728
+ - http://identifiers.org/seed.compound/cpd00169
+ - http://identifiers.org/unipathway.compound/UPC00597
+ - http://identifiers.org/unipathway.compound/UPC00197
+ - !!omap
+ - id: M_adp_c
- name: ADP
- compartment: c
- charge: -3
- formula: C10H12N5O10P2
- - annotation: !!omap
- - bigg.metabolite: adp
- - biocyc:
- - ADP
- - ADP-GROUP
- - cas:
- - 58-64-0
- - chebi:
- - CHEBI:13222
- - CHEBI:16761
- - CHEBI:2342
- - CHEBI:22244
- - CHEBI:40553
- - CHEBI:456216
- - hmdb: HMDB01341
- - kegg.compound: C00008
- - kegg.glycan: G11113
- - pubchem.substance: '3310'
- - reactome:
- - REACT_190072
- - REACT_481002
- - REACT_211606
- - REACT_429160
- - REACT_29370
- - REACT_196180
- - REACT_113581
- - REACT_113582
- - REACT_114564
- - REACT_114565
- - REACT_429153
- - seed.compound: cpd00008
- - unipathway.compound: UPC00008
- - !!omap
- - id: atp_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/adp
+ - http://identifiers.org/biocyc/ADP
+ - http://identifiers.org/biocyc/ADP-GROUP
+ - http://identifiers.org/cas/58-64-0
+ - http://identifiers.org/cas/58-64-0
+ - http://identifiers.org/chebi/CHEBI:13222
+ - http://identifiers.org/chebi/CHEBI:16761
+ - http://identifiers.org/chebi/CHEBI:2342
+ - http://identifiers.org/chebi/CHEBI:22244
+ - http://identifiers.org/chebi/CHEBI:40553
+ - http://identifiers.org/chebi/CHEBI:456216
+ - http://identifiers.org/hmdb/HMDB01341
+ - http://identifiers.org/kegg.compound/C00008
+ - http://identifiers.org/kegg.glycan/G11113
+ - http://identifiers.org/pubchem.substance/3310
+ - http://identifiers.org/reactome/REACT_190072
+ - http://identifiers.org/reactome/REACT_481002
+ - http://identifiers.org/reactome/REACT_211606
+ - http://identifiers.org/reactome/REACT_429160
+ - http://identifiers.org/reactome/REACT_29370
+ - http://identifiers.org/reactome/REACT_196180
+ - http://identifiers.org/reactome/REACT_113581
+ - http://identifiers.org/reactome/REACT_113582
+ - http://identifiers.org/reactome/REACT_114564
+ - http://identifiers.org/reactome/REACT_114565
+ - http://identifiers.org/reactome/REACT_429153
+ - http://identifiers.org/seed.compound/cpd00008
+ - http://identifiers.org/unipathway.compound/UPC00008
+ - !!omap
+ - id: M_atp_c
- name: ATP
- compartment: c
- charge: -4
- formula: C10H12N5O13P3
- - annotation: !!omap
- - bigg.metabolite: atp
- - biocyc: ATP
- - cas:
- - 56-65-5
- - chebi:
- - CHEBI:40938
- - CHEBI:15422
- - CHEBI:57299
- - CHEBI:13236
- - CHEBI:10789
- - CHEBI:30616
- - CHEBI:22249
- - CHEBI:10841
- - CHEBI:2359
- - hmdb: HMDB00538
- - kegg.compound: C00002
- - kegg.drug: D08646
- - pubchem.substance: '3304'
- - reactome:
- - REACT_190078
- - REACT_113592
- - REACT_113593
- - REACT_114570
- - REACT_29358
- - REACT_389573
- - REACT_139836
- - REACT_211579
- - seed.compound: cpd00002
- - unipathway.compound: UPC00002
- - !!omap
- - id: dhap_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/atp
+ - http://identifiers.org/biocyc/ATP
+ - http://identifiers.org/cas/56-65-5
+ - http://identifiers.org/cas/56-65-5
+ - http://identifiers.org/chebi/CHEBI:40938
+ - http://identifiers.org/chebi/CHEBI:15422
+ - http://identifiers.org/chebi/CHEBI:57299
+ - http://identifiers.org/chebi/CHEBI:13236
+ - http://identifiers.org/chebi/CHEBI:10789
+ - http://identifiers.org/chebi/CHEBI:30616
+ - http://identifiers.org/chebi/CHEBI:22249
+ - http://identifiers.org/chebi/CHEBI:10841
+ - http://identifiers.org/chebi/CHEBI:2359
+ - http://identifiers.org/hmdb/HMDB00538
+ - http://identifiers.org/kegg.compound/C00002
+ - http://identifiers.org/kegg.drug/D08646
+ - http://identifiers.org/pubchem.substance/3304
+ - http://identifiers.org/reactome/REACT_190078
+ - http://identifiers.org/reactome/REACT_113592
+ - http://identifiers.org/reactome/REACT_113593
+ - http://identifiers.org/reactome/REACT_114570
+ - http://identifiers.org/reactome/REACT_29358
+ - http://identifiers.org/reactome/REACT_389573
+ - http://identifiers.org/reactome/REACT_139836
+ - http://identifiers.org/reactome/REACT_211579
+ - http://identifiers.org/seed.compound/cpd00002
+ - http://identifiers.org/unipathway.compound/UPC00002
+ - !!omap
+ - id: M_dhap_c
- name: Dihydroxyacetone phosphate
- compartment: c
- charge: -2
- formula: C3H5O6P
- - annotation: !!omap
- - bigg.metabolite: dhap
- - biocyc: DIHYDROXY-ACETONE-PHOSPHATE
- - cas:
- - 57-04-5
- - chebi:
- - CHEBI:14341
- - CHEBI:57642
- - CHEBI:14342
- - CHEBI:16108
- - CHEBI:5454
- - CHEBI:24355
- - CHEBI:39571
- - hmdb:
- - HMDB01473
- - HMDB11735
- - kegg.compound: C00111
- - pubchem.substance: '3411'
- - reactome:
- - REACT_188451
- - REACT_75970
- - REACT_390404
- - seed.compound: cpd00095
- - unipathway.compound: UPC00111
- - !!omap
- - id: f6p_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/dhap
+ - http://identifiers.org/biocyc/DIHYDROXY-ACETONE-PHOSPHATE
+ - http://identifiers.org/cas/57-04-5
+ - http://identifiers.org/cas/57-04-5
+ - http://identifiers.org/chebi/CHEBI:14341
+ - http://identifiers.org/chebi/CHEBI:57642
+ - http://identifiers.org/chebi/CHEBI:14342
+ - http://identifiers.org/chebi/CHEBI:16108
+ - http://identifiers.org/chebi/CHEBI:5454
+ - http://identifiers.org/chebi/CHEBI:24355
+ - http://identifiers.org/chebi/CHEBI:39571
+ - http://identifiers.org/hmdb/HMDB01473
+ - http://identifiers.org/hmdb/HMDB11735
+ - http://identifiers.org/kegg.compound/C00111
+ - http://identifiers.org/pubchem.substance/3411
+ - http://identifiers.org/reactome/REACT_188451
+ - http://identifiers.org/reactome/REACT_75970
+ - http://identifiers.org/reactome/REACT_390404
+ - http://identifiers.org/seed.compound/cpd00095
+ - http://identifiers.org/unipathway.compound/UPC00111
+ - !!omap
+ - id: M_f6p_c
- name: D-Fructose 6-phosphate
- compartment: c
- charge: -2
- formula: C6H11O9P
- - annotation: !!omap
- - bigg.metabolite: f6p
- - biocyc: FRUCTOSE-6P
- - cas:
- - 643-13-0
- - chebi:
- - CHEBI:57634
- - CHEBI:12352
- - CHEBI:45804
- - CHEBI:61527
- - CHEBI:61553
- - CHEBI:10375
- - CHEBI:16084
- - CHEBI:42378
- - CHEBI:22768
- - hmdb: HMDB03971
- - kegg.compound:
- - C05345
- - C00085
- - pubchem.substance: '3385'
- - seed.compound: cpd00072
- - unipathway.compound:
- - UPC05345
- - UPC00085
- - !!omap
- - id: fdp_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/f6p
+ - http://identifiers.org/biocyc/FRUCTOSE-6P
+ - http://identifiers.org/cas/643-13-0
+ - http://identifiers.org/cas/643-13-0
+ - http://identifiers.org/chebi/CHEBI:57634
+ - http://identifiers.org/chebi/CHEBI:12352
+ - http://identifiers.org/chebi/CHEBI:45804
+ - http://identifiers.org/chebi/CHEBI:61527
+ - http://identifiers.org/chebi/CHEBI:61553
+ - http://identifiers.org/chebi/CHEBI:10375
+ - http://identifiers.org/chebi/CHEBI:16084
+ - http://identifiers.org/chebi/CHEBI:42378
+ - http://identifiers.org/chebi/CHEBI:22768
+ - http://identifiers.org/hmdb/HMDB03971
+ - http://identifiers.org/kegg.compound/C05345
+ - http://identifiers.org/kegg.compound/C00085
+ - http://identifiers.org/pubchem.substance/3385
+ - http://identifiers.org/seed.compound/cpd00072
+ - http://identifiers.org/unipathway.compound/UPC05345
+ - http://identifiers.org/unipathway.compound/UPC00085
+ - !!omap
+ - id: M_fdp_c
- name: D-Fructose 1,6-bisphosphate
- compartment: c
- charge: -4
- formula: C6H10O12P2
- - annotation: !!omap
- - bigg.metabolite: fdp
- - biocyc: FRUCTOSE-16-DIPHOSPHATE
- - cas:
- - 488-69-7
- - chebi:
- - CHEBI:32968
- - CHEBI:49299
- - CHEBI:42553
- - CHEBI:32966
- - CHEBI:37736
- - CHEBI:28013
- - CHEBI:32967
- - CHEBI:41014
- - CHEBI:22767
- - CHEBI:10374
- - CHEBI:40595
- - CHEBI:40591
- - kegg.compound:
- - C05378
- - C00354
- - pubchem.substance: '3647'
- - seed.compound: cpd00290
- - unipathway.compound: UPC00354
- - !!omap
- - id: g3p_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/fdp
+ - http://identifiers.org/biocyc/FRUCTOSE-16-DIPHOSPHATE
+ - http://identifiers.org/cas/488-69-7
+ - http://identifiers.org/cas/488-69-7
+ - http://identifiers.org/chebi/CHEBI:32968
+ - http://identifiers.org/chebi/CHEBI:49299
+ - http://identifiers.org/chebi/CHEBI:42553
+ - http://identifiers.org/chebi/CHEBI:32966
+ - http://identifiers.org/chebi/CHEBI:37736
+ - http://identifiers.org/chebi/CHEBI:28013
+ - http://identifiers.org/chebi/CHEBI:32967
+ - http://identifiers.org/chebi/CHEBI:41014
+ - http://identifiers.org/chebi/CHEBI:22767
+ - http://identifiers.org/chebi/CHEBI:10374
+ - http://identifiers.org/chebi/CHEBI:40595
+ - http://identifiers.org/chebi/CHEBI:40591
+ - http://identifiers.org/kegg.compound/C05378
+ - http://identifiers.org/kegg.compound/C00354
+ - http://identifiers.org/pubchem.substance/3647
+ - http://identifiers.org/seed.compound/cpd00290
+ - http://identifiers.org/unipathway.compound/UPC00354
+ - !!omap
+ - id: M_g3p_c
- name: Glyceraldehyde 3-phosphate
- compartment: c
- charge: -2
- formula: C3H5O6P
- - annotation: !!omap
- - bigg.metabolite: g3p
- - cas:
- - 142-10-9
- - chebi:
- - CHEBI:17138
- - CHEBI:14333
- - CHEBI:5446
- - CHEBI:58027
- - hmdb: HMDB01112
- - kegg.compound:
- - C00661
- - C00118
- - pubchem.substance: '3930'
- - seed.compound: cpd00102
- - unipathway.compound:
- - UPC00661
- - UPC00118
- - !!omap
- - id: g6p_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/g3p
+ - http://identifiers.org/cas/142-10-9
+ - http://identifiers.org/cas/142-10-9
+ - http://identifiers.org/chebi/CHEBI:17138
+ - http://identifiers.org/chebi/CHEBI:14333
+ - http://identifiers.org/chebi/CHEBI:5446
+ - http://identifiers.org/chebi/CHEBI:58027
+ - http://identifiers.org/hmdb/HMDB01112
+ - http://identifiers.org/kegg.compound/C00661
+ - http://identifiers.org/kegg.compound/C00118
+ - http://identifiers.org/pubchem.substance/3930
+ - http://identifiers.org/seed.compound/cpd00102
+ - http://identifiers.org/unipathway.compound/UPC00661
+ - http://identifiers.org/unipathway.compound/UPC00118
+ - !!omap
+ - id: M_g6p_c
- name: D-Glucose 6-phosphate
- compartment: c
- charge: -2
- formula: C6H11O9P
- - annotation: !!omap
- - bigg.metabolite: g6p
- - biocyc:
- - D-glucose-6-phosphate
- - GLC-6-P
- - cas:
- - 56-73-5
- - chebi:
- - CHEBI:10399
- - CHEBI:22797
- - CHEBI:41041
- - CHEBI:17719
- - CHEBI:4170
- - CHEBI:61548
- - CHEBI:58247
- - CHEBI:12375
- - hmdb:
- - HMDB03498
- - HMDB06793
- - HMDB01401
- - HMDB01549
- - kegg.compound:
- - C00092
- - C01172
- - pubchem.substance: '3392'
- - reactome: REACT_1629756
- - seed.compound: cpd00079
- - unipathway.compound: UPC00092
- - !!omap
- - id: glc__D_e
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/g6p
+ - http://identifiers.org/biocyc/D-glucose-6-phosphate
+ - http://identifiers.org/biocyc/GLC-6-P
+ - http://identifiers.org/cas/56-73-5
+ - http://identifiers.org/cas/56-73-5
+ - http://identifiers.org/chebi/CHEBI:10399
+ - http://identifiers.org/chebi/CHEBI:22797
+ - http://identifiers.org/chebi/CHEBI:41041
+ - http://identifiers.org/chebi/CHEBI:17719
+ - http://identifiers.org/chebi/CHEBI:4170
+ - http://identifiers.org/chebi/CHEBI:61548
+ - http://identifiers.org/chebi/CHEBI:58247
+ - http://identifiers.org/chebi/CHEBI:12375
+ - http://identifiers.org/hmdb/HMDB03498
+ - http://identifiers.org/hmdb/HMDB06793
+ - http://identifiers.org/hmdb/HMDB01401
+ - http://identifiers.org/hmdb/HMDB01549
+ - http://identifiers.org/kegg.compound/C00092
+ - http://identifiers.org/kegg.compound/C01172
+ - http://identifiers.org/pubchem.substance/3392
+ - http://identifiers.org/reactome/REACT_1629756
+ - http://identifiers.org/seed.compound/cpd00079
+ - http://identifiers.org/unipathway.compound/UPC00092
+ - !!omap
+ - id: M_glc__D_e
- name: D-Glucose
- compartment: e
- charge: 0
- formula: C6H12O6
- - annotation: !!omap
- - bigg.metabolite: glc__D
- - cas:
- - 50-99-7
- - kegg.compound: C00031
- - pubchem.substance: '3333'
- - !!omap
- - id: h2o_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/glc__D
+ - http://identifiers.org/cas/50-99-7
+ - http://identifiers.org/cas/50-99-7
+ - http://identifiers.org/kegg.compound/C00031
+ - http://identifiers.org/pubchem.substance/3333
+ - !!omap
+ - id: M_h2o_c
- name: H2O
- compartment: c
- charge: 0
- formula: H2O
- - annotation: !!omap
- - bigg.metabolite: h2o
- - biocyc:
- - WATER
- - OH
- - OXONIUM
- - cas:
- - 7732-18-5
- - chebi:
- - CHEBI:15377
- - CHEBI:13365
- - CHEBI:41979
- - CHEBI:16234
- - CHEBI:36385
- - CHEBI:42857
- - CHEBI:27313
- - CHEBI:44819
- - CHEBI:29373
- - CHEBI:10743
- - CHEBI:5594
- - CHEBI:29356
- - CHEBI:53442
- - CHEBI:29375
- - CHEBI:29374
- - CHEBI:13419
- - CHEBI:43228
- - CHEBI:44292
- - CHEBI:13352
- - CHEBI:41981
- - CHEBI:29412
- - CHEBI:42043
- - CHEBI:33811
- - CHEBI:33813
- - CHEBI:35511
- - CHEBI:5585
- - CHEBI:44641
- - CHEBI:44701
- - hmdb:
- - HMDB01039
- - HMDB02111
- - kegg.compound:
- - C01328
- - C00001
- - C18714
- - C18712
- - kegg.drug:
- - D00001
- - D06322
- - D03703
- - pubchem.substance: '3303'
- - reactome:
- - REACT_947593
- - REACT_189422
- - REACT_141343
- - REACT_113518
- - REACT_1605715
- - REACT_109276
- - REACT_113521
- - REACT_113519
- - REACT_2022884
- - REACT_351603
- - REACT_29356
- - seed.compound:
- - cpd15275
- - cpd00001
- - unipathway.compound:
- - UPC00001
- - UPC01328
- - !!omap
- - id: h2o_e
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/h2o
+ - http://identifiers.org/biocyc/WATER
+ - http://identifiers.org/biocyc/OH
+ - http://identifiers.org/biocyc/OXONIUM
+ - http://identifiers.org/cas/7732-18-5
+ - http://identifiers.org/cas/7732-18-5
+ - http://identifiers.org/chebi/CHEBI:15377
+ - http://identifiers.org/chebi/CHEBI:13365
+ - http://identifiers.org/chebi/CHEBI:41979
+ - http://identifiers.org/chebi/CHEBI:16234
+ - http://identifiers.org/chebi/CHEBI:36385
+ - http://identifiers.org/chebi/CHEBI:42857
+ - http://identifiers.org/chebi/CHEBI:27313
+ - http://identifiers.org/chebi/CHEBI:44819
+ - http://identifiers.org/chebi/CHEBI:29373
+ - http://identifiers.org/chebi/CHEBI:10743
+ - http://identifiers.org/chebi/CHEBI:5594
+ - http://identifiers.org/chebi/CHEBI:29356
+ - http://identifiers.org/chebi/CHEBI:53442
+ - http://identifiers.org/chebi/CHEBI:29375
+ - http://identifiers.org/chebi/CHEBI:29374
+ - http://identifiers.org/chebi/CHEBI:13419
+ - http://identifiers.org/chebi/CHEBI:43228
+ - http://identifiers.org/chebi/CHEBI:44292
+ - http://identifiers.org/chebi/CHEBI:13352
+ - http://identifiers.org/chebi/CHEBI:41981
+ - http://identifiers.org/chebi/CHEBI:29412
+ - http://identifiers.org/chebi/CHEBI:42043
+ - http://identifiers.org/chebi/CHEBI:33811
+ - http://identifiers.org/chebi/CHEBI:33813
+ - http://identifiers.org/chebi/CHEBI:35511
+ - http://identifiers.org/chebi/CHEBI:5585
+ - http://identifiers.org/chebi/CHEBI:44641
+ - http://identifiers.org/chebi/CHEBI:44701
+ - http://identifiers.org/hmdb/HMDB01039
+ - http://identifiers.org/hmdb/HMDB02111
+ - http://identifiers.org/kegg.compound/C01328
+ - http://identifiers.org/kegg.compound/C00001
+ - http://identifiers.org/kegg.compound/C18714
+ - http://identifiers.org/kegg.compound/C18712
+ - http://identifiers.org/kegg.drug/D00001
+ - http://identifiers.org/kegg.drug/D06322
+ - http://identifiers.org/kegg.drug/D03703
+ - http://identifiers.org/pubchem.substance/3303
+ - http://identifiers.org/reactome/REACT_947593
+ - http://identifiers.org/reactome/REACT_189422
+ - http://identifiers.org/reactome/REACT_141343
+ - http://identifiers.org/reactome/REACT_113518
+ - http://identifiers.org/reactome/REACT_1605715
+ - http://identifiers.org/reactome/REACT_109276
+ - http://identifiers.org/reactome/REACT_113521
+ - http://identifiers.org/reactome/REACT_113519
+ - http://identifiers.org/reactome/REACT_2022884
+ - http://identifiers.org/reactome/REACT_351603
+ - http://identifiers.org/reactome/REACT_29356
+ - http://identifiers.org/seed.compound/cpd15275
+ - http://identifiers.org/seed.compound/cpd00001
+ - http://identifiers.org/unipathway.compound/UPC00001
+ - http://identifiers.org/unipathway.compound/UPC01328
+ - !!omap
+ - id: M_h2o_e
- name: H2O
- compartment: e
- charge: 0
- formula: H2O
- - annotation: !!omap
- - bigg.metabolite: h2o
- - biocyc:
- - WATER
- - OH
- - OXONIUM
- - cas:
- - 7732-18-5
- - chebi:
- - CHEBI:15377
- - CHEBI:13365
- - CHEBI:41979
- - CHEBI:16234
- - CHEBI:36385
- - CHEBI:42857
- - CHEBI:27313
- - CHEBI:44819
- - CHEBI:29373
- - CHEBI:10743
- - CHEBI:5594
- - CHEBI:29356
- - CHEBI:53442
- - CHEBI:29375
- - CHEBI:29374
- - CHEBI:13419
- - CHEBI:43228
- - CHEBI:44292
- - CHEBI:13352
- - CHEBI:41981
- - CHEBI:29412
- - CHEBI:42043
- - CHEBI:33811
- - CHEBI:33813
- - CHEBI:35511
- - CHEBI:5585
- - CHEBI:44641
- - CHEBI:44701
- - hmdb:
- - HMDB01039
- - HMDB02111
- - kegg.compound:
- - C01328
- - C00001
- - C18714
- - C18712
- - kegg.drug:
- - D00001
- - D06322
- - D03703
- - pubchem.substance: '3303'
- - reactome:
- - REACT_947593
- - REACT_189422
- - REACT_141343
- - REACT_113518
- - REACT_1605715
- - REACT_109276
- - REACT_113521
- - REACT_113519
- - REACT_2022884
- - REACT_351603
- - REACT_29356
- - seed.compound:
- - cpd15275
- - cpd00001
- - unipathway.compound:
- - UPC00001
- - UPC01328
- - !!omap
- - id: h_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/h2o
+ - http://identifiers.org/biocyc/WATER
+ - http://identifiers.org/biocyc/OH
+ - http://identifiers.org/biocyc/OXONIUM
+ - http://identifiers.org/cas/7732-18-5
+ - http://identifiers.org/cas/7732-18-5
+ - http://identifiers.org/chebi/CHEBI:15377
+ - http://identifiers.org/chebi/CHEBI:13365
+ - http://identifiers.org/chebi/CHEBI:41979
+ - http://identifiers.org/chebi/CHEBI:16234
+ - http://identifiers.org/chebi/CHEBI:36385
+ - http://identifiers.org/chebi/CHEBI:42857
+ - http://identifiers.org/chebi/CHEBI:27313
+ - http://identifiers.org/chebi/CHEBI:44819
+ - http://identifiers.org/chebi/CHEBI:29373
+ - http://identifiers.org/chebi/CHEBI:10743
+ - http://identifiers.org/chebi/CHEBI:5594
+ - http://identifiers.org/chebi/CHEBI:29356
+ - http://identifiers.org/chebi/CHEBI:53442
+ - http://identifiers.org/chebi/CHEBI:29375
+ - http://identifiers.org/chebi/CHEBI:29374
+ - http://identifiers.org/chebi/CHEBI:13419
+ - http://identifiers.org/chebi/CHEBI:43228
+ - http://identifiers.org/chebi/CHEBI:44292
+ - http://identifiers.org/chebi/CHEBI:13352
+ - http://identifiers.org/chebi/CHEBI:41981
+ - http://identifiers.org/chebi/CHEBI:29412
+ - http://identifiers.org/chebi/CHEBI:42043
+ - http://identifiers.org/chebi/CHEBI:33811
+ - http://identifiers.org/chebi/CHEBI:33813
+ - http://identifiers.org/chebi/CHEBI:35511
+ - http://identifiers.org/chebi/CHEBI:5585
+ - http://identifiers.org/chebi/CHEBI:44641
+ - http://identifiers.org/chebi/CHEBI:44701
+ - http://identifiers.org/hmdb/HMDB01039
+ - http://identifiers.org/hmdb/HMDB02111
+ - http://identifiers.org/kegg.compound/C01328
+ - http://identifiers.org/kegg.compound/C00001
+ - http://identifiers.org/kegg.compound/C18714
+ - http://identifiers.org/kegg.compound/C18712
+ - http://identifiers.org/kegg.drug/D00001
+ - http://identifiers.org/kegg.drug/D06322
+ - http://identifiers.org/kegg.drug/D03703
+ - http://identifiers.org/pubchem.substance/3303
+ - http://identifiers.org/reactome/REACT_947593
+ - http://identifiers.org/reactome/REACT_189422
+ - http://identifiers.org/reactome/REACT_141343
+ - http://identifiers.org/reactome/REACT_113518
+ - http://identifiers.org/reactome/REACT_1605715
+ - http://identifiers.org/reactome/REACT_109276
+ - http://identifiers.org/reactome/REACT_113521
+ - http://identifiers.org/reactome/REACT_113519
+ - http://identifiers.org/reactome/REACT_2022884
+ - http://identifiers.org/reactome/REACT_351603
+ - http://identifiers.org/reactome/REACT_29356
+ - http://identifiers.org/seed.compound/cpd15275
+ - http://identifiers.org/seed.compound/cpd00001
+ - http://identifiers.org/unipathway.compound/UPC00001
+ - http://identifiers.org/unipathway.compound/UPC01328
+ - !!omap
+ - id: M_h_c
- name: H+
- compartment: c
- charge: 1
- formula: H
- - annotation: !!omap
- - bigg.metabolite: h
- - biocyc: PROTON
- - cas:
- - 12408-02-5
- - chebi:
- - CHEBI:24636
- - CHEBI:15378
- - CHEBI:10744
- - CHEBI:13357
- - CHEBI:5584
- - kegg.compound: C00080
- - pubchem.substance: '3380'
- - reactome:
- - REACT_194688
- - REACT_425978
- - REACT_193465
- - REACT_374900
- - REACT_74722
- - REACT_425999
- - REACT_428040
- - REACT_163953
- - REACT_372511
- - REACT_2000349
- - REACT_70106
- - REACT_1470067
- - REACT_113529
- - REACT_425969
- - REACT_428548
- - REACT_156540
- - REACT_1614597
- - REACT_351626
- - REACT_427899
- - seed.compound: cpd00067
- - unipathway.compound: UPC00080
- - !!omap
- - id: h_e
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/h
+ - http://identifiers.org/biocyc/PROTON
+ - http://identifiers.org/cas/12408-02-5
+ - http://identifiers.org/cas/12408-02-5
+ - http://identifiers.org/chebi/CHEBI:24636
+ - http://identifiers.org/chebi/CHEBI:15378
+ - http://identifiers.org/chebi/CHEBI:10744
+ - http://identifiers.org/chebi/CHEBI:13357
+ - http://identifiers.org/chebi/CHEBI:5584
+ - http://identifiers.org/kegg.compound/C00080
+ - http://identifiers.org/pubchem.substance/3380
+ - http://identifiers.org/reactome/REACT_194688
+ - http://identifiers.org/reactome/REACT_425978
+ - http://identifiers.org/reactome/REACT_193465
+ - http://identifiers.org/reactome/REACT_374900
+ - http://identifiers.org/reactome/REACT_74722
+ - http://identifiers.org/reactome/REACT_425999
+ - http://identifiers.org/reactome/REACT_428040
+ - http://identifiers.org/reactome/REACT_163953
+ - http://identifiers.org/reactome/REACT_372511
+ - http://identifiers.org/reactome/REACT_2000349
+ - http://identifiers.org/reactome/REACT_70106
+ - http://identifiers.org/reactome/REACT_1470067
+ - http://identifiers.org/reactome/REACT_113529
+ - http://identifiers.org/reactome/REACT_425969
+ - http://identifiers.org/reactome/REACT_428548
+ - http://identifiers.org/reactome/REACT_156540
+ - http://identifiers.org/reactome/REACT_1614597
+ - http://identifiers.org/reactome/REACT_351626
+ - http://identifiers.org/reactome/REACT_427899
+ - http://identifiers.org/seed.compound/cpd00067
+ - http://identifiers.org/unipathway.compound/UPC00080
+ - !!omap
+ - id: M_h_e
- name: H+
- compartment: e
- charge: 1
- formula: H
- - annotation: !!omap
- - bigg.metabolite: h
- - biocyc: PROTON
- - cas:
- - 12408-02-5
- - chebi:
- - CHEBI:24636
- - CHEBI:15378
- - CHEBI:10744
- - CHEBI:13357
- - CHEBI:5584
- - kegg.compound: C00080
- - pubchem.substance: '3380'
- - reactome:
- - REACT_194688
- - REACT_425978
- - REACT_193465
- - REACT_374900
- - REACT_74722
- - REACT_425999
- - REACT_428040
- - REACT_163953
- - REACT_372511
- - REACT_2000349
- - REACT_70106
- - REACT_1470067
- - REACT_113529
- - REACT_425969
- - REACT_428548
- - REACT_156540
- - REACT_1614597
- - REACT_351626
- - REACT_427899
- - seed.compound: cpd00067
- - unipathway.compound: UPC00080
- - !!omap
- - id: lac__D_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/h
+ - http://identifiers.org/biocyc/PROTON
+ - http://identifiers.org/cas/12408-02-5
+ - http://identifiers.org/cas/12408-02-5
+ - http://identifiers.org/chebi/CHEBI:24636
+ - http://identifiers.org/chebi/CHEBI:15378
+ - http://identifiers.org/chebi/CHEBI:10744
+ - http://identifiers.org/chebi/CHEBI:13357
+ - http://identifiers.org/chebi/CHEBI:5584
+ - http://identifiers.org/kegg.compound/C00080
+ - http://identifiers.org/pubchem.substance/3380
+ - http://identifiers.org/reactome/REACT_194688
+ - http://identifiers.org/reactome/REACT_425978
+ - http://identifiers.org/reactome/REACT_193465
+ - http://identifiers.org/reactome/REACT_374900
+ - http://identifiers.org/reactome/REACT_74722
+ - http://identifiers.org/reactome/REACT_425999
+ - http://identifiers.org/reactome/REACT_428040
+ - http://identifiers.org/reactome/REACT_163953
+ - http://identifiers.org/reactome/REACT_372511
+ - http://identifiers.org/reactome/REACT_2000349
+ - http://identifiers.org/reactome/REACT_70106
+ - http://identifiers.org/reactome/REACT_1470067
+ - http://identifiers.org/reactome/REACT_113529
+ - http://identifiers.org/reactome/REACT_425969
+ - http://identifiers.org/reactome/REACT_428548
+ - http://identifiers.org/reactome/REACT_156540
+ - http://identifiers.org/reactome/REACT_1614597
+ - http://identifiers.org/reactome/REACT_351626
+ - http://identifiers.org/reactome/REACT_427899
+ - http://identifiers.org/seed.compound/cpd00067
+ - http://identifiers.org/unipathway.compound/UPC00080
+ - !!omap
+ - id: M_lac__D_c
- name: D-Lactate
- compartment: c
- charge: -1
- formula: C3H5O3
- - annotation: !!omap
- - bigg.metabolite: lac__D
- - biocyc: META:D-LACTATE
- - chebi:
- - CHEBI:11001
- - CHEBI:16004
- - CHEBI:18684
- - CHEBI:341
- - CHEBI:42105
- - CHEBI:42111
- - CHEBI:43701
- - hmdb:
- - HMDB00171
- - HMDB01311
- - kegg.compound: C00256
- - metanetx.chemical: MNXM285
- - seed.compound: cpd00221
- - !!omap
- - id: lac__D_e
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/lac__D
+ - http://identifiers.org/biocyc/META:D-LACTATE
+ - http://identifiers.org/chebi/CHEBI:11001
+ - http://identifiers.org/chebi/CHEBI:16004
+ - http://identifiers.org/chebi/CHEBI:18684
+ - http://identifiers.org/chebi/CHEBI:341
+ - http://identifiers.org/chebi/CHEBI:42105
+ - http://identifiers.org/chebi/CHEBI:42111
+ - http://identifiers.org/chebi/CHEBI:43701
+ - http://identifiers.org/hmdb/HMDB00171
+ - http://identifiers.org/hmdb/HMDB01311
+ - http://identifiers.org/kegg.compound/C00256
+ - http://identifiers.org/metanetx.chemical/MNXM285
+ - http://identifiers.org/seed.compound/cpd00221
+ - !!omap
+ - id: M_lac__D_e
- name: D-Lactate
- compartment: e
- charge: -1
- formula: C3H5O3
- - annotation: !!omap
- - bigg.metabolite: lac__D
- - biocyc: META:D-LACTATE
- - chebi:
- - CHEBI:11001
- - CHEBI:16004
- - CHEBI:18684
- - CHEBI:341
- - CHEBI:42105
- - CHEBI:42111
- - CHEBI:43701
- - hmdb:
- - HMDB00171
- - HMDB01311
- - kegg.compound: C00256
- - metanetx.chemical: MNXM285
- - seed.compound: cpd00221
- - !!omap
- - id: nad_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/lac__D
+ - http://identifiers.org/biocyc/META:D-LACTATE
+ - http://identifiers.org/chebi/CHEBI:11001
+ - http://identifiers.org/chebi/CHEBI:16004
+ - http://identifiers.org/chebi/CHEBI:18684
+ - http://identifiers.org/chebi/CHEBI:341
+ - http://identifiers.org/chebi/CHEBI:42105
+ - http://identifiers.org/chebi/CHEBI:42111
+ - http://identifiers.org/chebi/CHEBI:43701
+ - http://identifiers.org/hmdb/HMDB00171
+ - http://identifiers.org/hmdb/HMDB01311
+ - http://identifiers.org/kegg.compound/C00256
+ - http://identifiers.org/metanetx.chemical/MNXM285
+ - http://identifiers.org/seed.compound/cpd00221
+ - !!omap
+ - id: M_nad_c
- name: Nicotinamide adenine dinucleotide
- compartment: c
- charge: -1
- formula: C21H26N7O14P2
- - annotation: !!omap
- - bigg.metabolite: nad
- - biocyc: NAD
- - cas:
- - 53-84-9
- - chebi:
- - CHEBI:21901
- - CHEBI:7422
- - CHEBI:44214
- - CHEBI:15846
- - CHEBI:13394
- - CHEBI:13393
- - CHEBI:44215
- - CHEBI:13389
- - CHEBI:57540
- - CHEBI:44281
- - hmdb: HMDB00902
- - kegg.compound: C00003
- - kegg.drug: D00002
- - pubchem.substance: '3305'
- - reactome:
- - REACT_192307
- - REACT_29360
- - REACT_427523
- - REACT_194653
- - REACT_113526
- - seed.compound: cpd00003
- - unipathway.compound: UPC00003
- - !!omap
- - id: nadh_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/nad
+ - http://identifiers.org/biocyc/NAD
+ - http://identifiers.org/cas/53-84-9
+ - http://identifiers.org/cas/53-84-9
+ - http://identifiers.org/chebi/CHEBI:21901
+ - http://identifiers.org/chebi/CHEBI:7422
+ - http://identifiers.org/chebi/CHEBI:44214
+ - http://identifiers.org/chebi/CHEBI:15846
+ - http://identifiers.org/chebi/CHEBI:13394
+ - http://identifiers.org/chebi/CHEBI:13393
+ - http://identifiers.org/chebi/CHEBI:44215
+ - http://identifiers.org/chebi/CHEBI:13389
+ - http://identifiers.org/chebi/CHEBI:57540
+ - http://identifiers.org/chebi/CHEBI:44281
+ - http://identifiers.org/hmdb/HMDB00902
+ - http://identifiers.org/kegg.compound/C00003
+ - http://identifiers.org/kegg.drug/D00002
+ - http://identifiers.org/pubchem.substance/3305
+ - http://identifiers.org/reactome/REACT_192307
+ - http://identifiers.org/reactome/REACT_29360
+ - http://identifiers.org/reactome/REACT_427523
+ - http://identifiers.org/reactome/REACT_194653
+ - http://identifiers.org/reactome/REACT_113526
+ - http://identifiers.org/seed.compound/cpd00003
+ - http://identifiers.org/unipathway.compound/UPC00003
+ - !!omap
+ - id: M_nadh_c
- name: Nicotinamide adenine dinucleotide - reduced
- compartment: c
- charge: -2
- formula: C21H27N7O14P2
- - annotation: !!omap
- - bigg.metabolite: nadh
- - biocyc: NADH
- - cas:
- - 58-68-4
- - chebi:
- - CHEBI:13395
- - CHEBI:21902
- - CHEBI:16908
- - CHEBI:7423
- - CHEBI:44216
- - CHEBI:57945
- - CHEBI:13396
- - hmdb: HMDB01487
- - kegg.compound: C00004
- - pubchem.substance: '3306'
- - reactome:
- - REACT_192305
- - REACT_73473
- - REACT_194697
- - REACT_29362
- - seed.compound: cpd00004
- - unipathway.compound: UPC00004
- - !!omap
- - id: pep_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/nadh
+ - http://identifiers.org/biocyc/NADH
+ - http://identifiers.org/cas/58-68-4
+ - http://identifiers.org/cas/58-68-4
+ - http://identifiers.org/chebi/CHEBI:13395
+ - http://identifiers.org/chebi/CHEBI:21902
+ - http://identifiers.org/chebi/CHEBI:16908
+ - http://identifiers.org/chebi/CHEBI:7423
+ - http://identifiers.org/chebi/CHEBI:44216
+ - http://identifiers.org/chebi/CHEBI:57945
+ - http://identifiers.org/chebi/CHEBI:13396
+ - http://identifiers.org/hmdb/HMDB01487
+ - http://identifiers.org/kegg.compound/C00004
+ - http://identifiers.org/pubchem.substance/3306
+ - http://identifiers.org/reactome/REACT_192305
+ - http://identifiers.org/reactome/REACT_73473
+ - http://identifiers.org/reactome/REACT_194697
+ - http://identifiers.org/reactome/REACT_29362
+ - http://identifiers.org/seed.compound/cpd00004
+ - http://identifiers.org/unipathway.compound/UPC00004
+ - !!omap
+ - id: M_pep_c
- name: Phosphoenolpyruvate
- compartment: c
- charge: -3
- formula: C3H2O6P
- - annotation: !!omap
- - bigg.metabolite: pep
- - biocyc: PHOSPHO-ENOL-PYRUVATE
- - cas:
- - 138-08-9
- - chebi:
- - CHEBI:44897
- - CHEBI:44894
- - CHEBI:14812
- - CHEBI:8147
- - CHEBI:26055
- - CHEBI:26054
- - CHEBI:58702
- - CHEBI:18021
- - hmdb: HMDB00263
- - kegg.compound: C00074
- - pubchem.substance: '3374'
- - reactome:
- - REACT_29492
- - REACT_372364
- - seed.compound: cpd00061
- - unipathway.compound: UPC00074
- - !!omap
- - id: pi_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/pep
+ - http://identifiers.org/biocyc/PHOSPHO-ENOL-PYRUVATE
+ - http://identifiers.org/cas/138-08-9
+ - http://identifiers.org/cas/138-08-9
+ - http://identifiers.org/chebi/CHEBI:44897
+ - http://identifiers.org/chebi/CHEBI:44894
+ - http://identifiers.org/chebi/CHEBI:14812
+ - http://identifiers.org/chebi/CHEBI:8147
+ - http://identifiers.org/chebi/CHEBI:26055
+ - http://identifiers.org/chebi/CHEBI:26054
+ - http://identifiers.org/chebi/CHEBI:58702
+ - http://identifiers.org/chebi/CHEBI:18021
+ - http://identifiers.org/hmdb/HMDB00263
+ - http://identifiers.org/kegg.compound/C00074
+ - http://identifiers.org/pubchem.substance/3374
+ - http://identifiers.org/reactome/REACT_29492
+ - http://identifiers.org/reactome/REACT_372364
+ - http://identifiers.org/seed.compound/cpd00061
+ - http://identifiers.org/unipathway.compound/UPC00074
+ - !!omap
+ - id: M_pi_c
- name: Phosphate
- compartment: c
- charge: -2
- formula: HO4P
- - annotation: !!omap
- - bigg.metabolite: pi
- - biocyc:
- - Pi
- - PHOSPHATE-GROUP
- - CPD0-1421
- - cas:
- - 14265-44-2
- - chebi:
- - CHEBI:37583
- - CHEBI:7793
- - CHEBI:37585
- - CHEBI:34683
- - CHEBI:14791
- - CHEBI:34855
- - CHEBI:29137
- - CHEBI:29139
- - CHEBI:63036
- - CHEBI:26020
- - CHEBI:39739
- - CHEBI:32597
- - CHEBI:32596
- - CHEBI:43474
- - CHEBI:63051
- - CHEBI:43470
- - CHEBI:9679
- - CHEBI:35433
- - CHEBI:4496
- - CHEBI:45024
- - CHEBI:18367
- - CHEBI:26078
- - CHEBI:39745
- - CHEBI:24838
- - hmdb: HMDB02142
- - kegg.compound:
- - C13556
- - C13558
- - C00009
- - kegg.drug: D05467
- - pubchem.substance: '3311'
- - reactome:
- - REACT_947590
- - REACT_109277
- - REACT_113548
- - REACT_2255331
- - REACT_29372
- - REACT_113550
- - REACT_113551
- - seed.compound:
- - cpd09464
- - cpd09463
- - cpd00009
- - unipathway.compound: UPC00009
- - !!omap
- - id: pi_e
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/pi
+ - http://identifiers.org/biocyc/Pi
+ - http://identifiers.org/biocyc/PHOSPHATE-GROUP
+ - http://identifiers.org/biocyc/CPD0-1421
+ - http://identifiers.org/cas/14265-44-2
+ - http://identifiers.org/cas/14265-44-2
+ - http://identifiers.org/chebi/CHEBI:37583
+ - http://identifiers.org/chebi/CHEBI:7793
+ - http://identifiers.org/chebi/CHEBI:37585
+ - http://identifiers.org/chebi/CHEBI:34683
+ - http://identifiers.org/chebi/CHEBI:14791
+ - http://identifiers.org/chebi/CHEBI:34855
+ - http://identifiers.org/chebi/CHEBI:29137
+ - http://identifiers.org/chebi/CHEBI:29139
+ - http://identifiers.org/chebi/CHEBI:63036
+ - http://identifiers.org/chebi/CHEBI:26020
+ - http://identifiers.org/chebi/CHEBI:39739
+ - http://identifiers.org/chebi/CHEBI:32597
+ - http://identifiers.org/chebi/CHEBI:32596
+ - http://identifiers.org/chebi/CHEBI:43474
+ - http://identifiers.org/chebi/CHEBI:63051
+ - http://identifiers.org/chebi/CHEBI:43470
+ - http://identifiers.org/chebi/CHEBI:9679
+ - http://identifiers.org/chebi/CHEBI:35433
+ - http://identifiers.org/chebi/CHEBI:4496
+ - http://identifiers.org/chebi/CHEBI:45024
+ - http://identifiers.org/chebi/CHEBI:18367
+ - http://identifiers.org/chebi/CHEBI:26078
+ - http://identifiers.org/chebi/CHEBI:39745
+ - http://identifiers.org/chebi/CHEBI:24838
+ - http://identifiers.org/hmdb/HMDB02142
+ - http://identifiers.org/kegg.compound/C13556
+ - http://identifiers.org/kegg.compound/C13558
+ - http://identifiers.org/kegg.compound/C00009
+ - http://identifiers.org/kegg.drug/D05467
+ - http://identifiers.org/pubchem.substance/3311
+ - http://identifiers.org/reactome/REACT_947590
+ - http://identifiers.org/reactome/REACT_109277
+ - http://identifiers.org/reactome/REACT_113548
+ - http://identifiers.org/reactome/REACT_2255331
+ - http://identifiers.org/reactome/REACT_29372
+ - http://identifiers.org/reactome/REACT_113550
+ - http://identifiers.org/reactome/REACT_113551
+ - http://identifiers.org/seed.compound/cpd09464
+ - http://identifiers.org/seed.compound/cpd09463
+ - http://identifiers.org/seed.compound/cpd00009
+ - http://identifiers.org/unipathway.compound/UPC00009
+ - !!omap
+ - id: M_pi_e
- name: Phosphate
- compartment: e
- charge: -2
- formula: HO4P
- - annotation: !!omap
- - bigg.metabolite: pi
- - biocyc:
- - Pi
- - PHOSPHATE-GROUP
- - CPD0-1421
- - cas:
- - 14265-44-2
- - chebi:
- - CHEBI:37583
- - CHEBI:7793
- - CHEBI:37585
- - CHEBI:34683
- - CHEBI:14791
- - CHEBI:34855
- - CHEBI:29137
- - CHEBI:29139
- - CHEBI:63036
- - CHEBI:26020
- - CHEBI:39739
- - CHEBI:32597
- - CHEBI:32596
- - CHEBI:43474
- - CHEBI:63051
- - CHEBI:43470
- - CHEBI:9679
- - CHEBI:35433
- - CHEBI:4496
- - CHEBI:45024
- - CHEBI:18367
- - CHEBI:26078
- - CHEBI:39745
- - CHEBI:24838
- - hmdb: HMDB02142
- - kegg.compound:
- - C13556
- - C13558
- - C00009
- - kegg.drug: D05467
- - pubchem.substance: '3311'
- - reactome:
- - REACT_947590
- - REACT_109277
- - REACT_113548
- - REACT_2255331
- - REACT_29372
- - REACT_113550
- - REACT_113551
- - seed.compound:
- - cpd09464
- - cpd09463
- - cpd00009
- - unipathway.compound: UPC00009
- - !!omap
- - id: pyr_c
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/pi
+ - http://identifiers.org/biocyc/Pi
+ - http://identifiers.org/biocyc/PHOSPHATE-GROUP
+ - http://identifiers.org/biocyc/CPD0-1421
+ - http://identifiers.org/cas/14265-44-2
+ - http://identifiers.org/cas/14265-44-2
+ - http://identifiers.org/chebi/CHEBI:37583
+ - http://identifiers.org/chebi/CHEBI:7793
+ - http://identifiers.org/chebi/CHEBI:37585
+ - http://identifiers.org/chebi/CHEBI:34683
+ - http://identifiers.org/chebi/CHEBI:14791
+ - http://identifiers.org/chebi/CHEBI:34855
+ - http://identifiers.org/chebi/CHEBI:29137
+ - http://identifiers.org/chebi/CHEBI:29139
+ - http://identifiers.org/chebi/CHEBI:63036
+ - http://identifiers.org/chebi/CHEBI:26020
+ - http://identifiers.org/chebi/CHEBI:39739
+ - http://identifiers.org/chebi/CHEBI:32597
+ - http://identifiers.org/chebi/CHEBI:32596
+ - http://identifiers.org/chebi/CHEBI:43474
+ - http://identifiers.org/chebi/CHEBI:63051
+ - http://identifiers.org/chebi/CHEBI:43470
+ - http://identifiers.org/chebi/CHEBI:9679
+ - http://identifiers.org/chebi/CHEBI:35433
+ - http://identifiers.org/chebi/CHEBI:4496
+ - http://identifiers.org/chebi/CHEBI:45024
+ - http://identifiers.org/chebi/CHEBI:18367
+ - http://identifiers.org/chebi/CHEBI:26078
+ - http://identifiers.org/chebi/CHEBI:39745
+ - http://identifiers.org/chebi/CHEBI:24838
+ - http://identifiers.org/hmdb/HMDB02142
+ - http://identifiers.org/kegg.compound/C13556
+ - http://identifiers.org/kegg.compound/C13558
+ - http://identifiers.org/kegg.compound/C00009
+ - http://identifiers.org/kegg.drug/D05467
+ - http://identifiers.org/pubchem.substance/3311
+ - http://identifiers.org/reactome/REACT_947590
+ - http://identifiers.org/reactome/REACT_109277
+ - http://identifiers.org/reactome/REACT_113548
+ - http://identifiers.org/reactome/REACT_2255331
+ - http://identifiers.org/reactome/REACT_29372
+ - http://identifiers.org/reactome/REACT_113550
+ - http://identifiers.org/reactome/REACT_113551
+ - http://identifiers.org/seed.compound/cpd09464
+ - http://identifiers.org/seed.compound/cpd09463
+ - http://identifiers.org/seed.compound/cpd00009
+ - http://identifiers.org/unipathway.compound/UPC00009
+ - !!omap
+ - id: M_pyr_c
- name: Pyruvate
- compartment: c
- charge: -1
- formula: C3H3O3
- - annotation: !!omap
- - bigg.metabolite: pyr
- - biocyc: PYRUVATE
- - cas:
- - 127-17-3
- - chebi:
- - CHEBI:15361
- - CHEBI:14987
- - CHEBI:8685
- - CHEBI:32816
- - CHEBI:45253
- - CHEBI:26466
- - CHEBI:26462
- - hmdb: HMDB00243
- - kegg.compound: C00022
- - lipidmaps: LMFA01060077
- - pubchem.substance: '3324'
- - reactome:
- - REACT_113557
- - REACT_389680
- - REACT_29398
- - seed.compound: cpd00020
- - unipathway.compound: UPC00022
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.metabolite/pyr
+ - http://identifiers.org/biocyc/PYRUVATE
+ - http://identifiers.org/cas/127-17-3
+ - http://identifiers.org/cas/127-17-3
+ - http://identifiers.org/chebi/CHEBI:15361
+ - http://identifiers.org/chebi/CHEBI:14987
+ - http://identifiers.org/chebi/CHEBI:8685
+ - http://identifiers.org/chebi/CHEBI:32816
+ - http://identifiers.org/chebi/CHEBI:45253
+ - http://identifiers.org/chebi/CHEBI:26466
+ - http://identifiers.org/chebi/CHEBI:26462
+ - http://identifiers.org/hmdb/HMDB00243
+ - http://identifiers.org/kegg.compound/C00022
+ - http://identifiers.org/lipidmaps/LMFA01060077
+ - http://identifiers.org/pubchem.substance/3324
+ - http://identifiers.org/reactome/REACT_113557
+ - http://identifiers.org/reactome/REACT_389680
+ - http://identifiers.org/reactome/REACT_29398
+ - http://identifiers.org/seed.compound/cpd00020
+ - http://identifiers.org/unipathway.compound/UPC00022
- reactions:
- !!omap
- - id: ATPM
+ - id: R_ATPM
- name: ATP maintenance requirement
- - metabolites: !!omap
- - adp_c: 1.0
- - atp_c: -1.0
- - h2o_c: -1.0
- - h_c: 1.0
- - pi_c: 1.0
- lower_bound: 8.39
- upper_bound: 1000.0
- gene_reaction_rule: ''
+ - metabolites: !!omap
+ - M_atp_c: -1.0
+ - M_h2o_c: -1.0
+ - M_adp_c: 1.0
+ - M_h_c: 1.0
+ - M_pi_c: 1.0
- objective_coefficient: 1.0
- - annotation: !!omap
- - bigg.reaction: ATPM
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/ATPM
- !!omap
- - id: D_LACt2
+ - id: R_D_LACt2
- name: ''
- - metabolites: !!omap []
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: ''
+ - metabolites: !!omap []
- !!omap
- - id: ENO
+ - id: R_ENO
- name: enolase
- - metabolites: !!omap
- - 2pg_c: -1.0
- - h2o_c: 1.0
- - pep_c: 1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b2779
- - annotation: !!omap
- - bigg.reaction: ENO
- - !!omap
- - id: EX_glc__D_e
- - name: D-Glucose exchange
- metabolites: !!omap
- - glc__D_e: -1.0
+ - M_2pg_c: -1.0
+ - M_pep_c: 1.0
+ - M_h2o_c: 1.0
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/ENO
+ - !!omap
+ - id: R_EX_glc__D_e
+ - name: D-Glucose exchange
- lower_bound: -10.0
- upper_bound: 1000.0
- gene_reaction_rule: ''
- - annotation: !!omap
- - bigg.reaction: glc
+ - metabolites: !!omap
+ - M_glc__D_e: -1.0
+ - metadata: !!omap
- sbo: SBO:0000627
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/glc
- !!omap
- - id: EX_h_e
+ - id: R_EX_h_e
- name: H+ exchange
- - metabolites: !!omap
- - h_e: -1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: ''
- - annotation: !!omap
- - bigg.reaction: h
+ - metabolites: !!omap
+ - M_h_e: -1.0
+ - metadata: !!omap
- sbo: SBO:0000627
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/h
- !!omap
- - id: EX_lac__D_e
+ - id: R_EX_lac__D_e
- name: D-lactate exchange
- - metabolites: !!omap
- - lac__D_e: -1.0
- lower_bound: 0.0
- upper_bound: 1000.0
- gene_reaction_rule: ''
- - annotation: !!omap
- - bigg.reaction: lac__D
+ - metabolites: !!omap
+ - M_lac__D_e: -1.0
+ - metadata: !!omap
- sbo: SBO:0000627
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/lac__D
- !!omap
- - id: FBA
+ - id: R_FBA
- name: fructose-bisphosphate aldolase
- - metabolites: !!omap
- - dhap_c: 1.0
- - fdp_c: -1.0
- - g3p_c: 1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b1773 or b2097 or b2925
- - annotation: !!omap
- - bigg.reaction: FBA
- - !!omap
- - id: GAPD
- - name: glyceraldehyde-3-phosphate dehydrogenase
- metabolites: !!omap
- - 13dpg_c: 1.0
- - g3p_c: -1.0
- - h_c: 1.0
- - nad_c: -1.0
- - nadh_c: 1.0
- - pi_c: -1.0
+ - M_fdp_c: -1.0
+ - M_dhap_c: 1.0
+ - M_g3p_c: 1.0
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/FBA
+ - !!omap
+ - id: R_GAPD
+ - name: glyceraldehyde-3-phosphate dehydrogenase
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b1779
- - annotation: !!omap
- - bigg.reaction: GAPD
- - !!omap
- - id: GLCpts
- - name: D-glucose transport via PEP:Pyr PTS
- metabolites: !!omap
- - g6p_c: 1.0
- - glc__D_e: -1.0
- - pep_c: -1.0
- - pyr_c: 1.0
+ - M_nad_c: -1.0
+ - M_13dpg_c: 1.0
+ - M_nadh_c: 1.0
+ - M_g3p_c: -1.0
+ - M_pi_c: -1.0
+ - M_h_c: 1.0
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/GAPD
+ - !!omap
+ - id: R_GLCpts
+ - name: D-glucose transport via PEP:Pyr PTS
- lower_bound: 0.0
- upper_bound: 1000.0
- gene_reaction_rule: (b2415 and b2417 and b1101 and b2416) or (b2415 and b2417
and b1621 and b2416) or (b2415 and b1818 and b1817 and b1819 and b2416)
- - annotation: !!omap
- - bigg.reaction: GLCpts
- - !!omap
- - id: H2Ot
- - name: R H2O transport via - diffusion
- metabolites: !!omap
- - h2o_c: 1.0
- - h2o_e: -1.0
+ - M_g6p_c: 1.0
+ - M_pyr_c: 1.0
+ - M_glc__D_e: -1.0
+ - M_pep_c: -1.0
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/GLCpts
+ - !!omap
+ - id: R_H2Ot
+ - name: R H2O transport via - diffusion
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b0875 or s0001
- - annotation: !!omap
- - bigg.reaction: H2Ot
- - !!omap
- - id: LDH_D
- - name: D-lactate dehydrogenase
- metabolites: !!omap
- - h_c: 1.0
- - lac__D_c: -1.0
- - nad_c: -1.0
- - nadh_c: 1.0
- - pyr_c: 1.0
+ - M_h2o_e: -1.0
+ - M_h2o_c: 1.0
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/H2Ot
+ - !!omap
+ - id: R_LDH_D
+ - name: D-lactate dehydrogenase
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b2133 or b1380
+ - metabolites: !!omap
+ - M_lac__D_c: -1.0
+ - M_nad_c: -1.0
+ - M_h_c: 1.0
+ - M_nadh_c: 1.0
+ - M_pyr_c: 1.0
- subsystem: Pyruvate Metabolism
- - annotation: !!omap
- - bigg.reaction: LDH_D
- - biocyc: META:DLACTDEHYDROGNAD-RXN
- - ec-code: 1.1.1.28
- - kegg.reaction: R00704
- - metanetx.reaction: MNXR101037
- - rhea:
- - '16369'
- - '16370'
- - '16371'
- - '16372'
+ - metadata: !!omap
- sbo: SBO:0000375
- - !!omap
- - id: PFK
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/LDH_D
+ - http://identifiers.org/biocyc/META:DLACTDEHYDROGNAD-RXN
+ - http://identifiers.org/ec-code/1.1.1.28
+ - http://identifiers.org/kegg.reaction/R00704
+ - http://identifiers.org/metanetx.reaction/MNXR101037
+ - http://identifiers.org/rhea/16369
+ - http://identifiers.org/rhea/16370
+ - http://identifiers.org/rhea/16371
+ - http://identifiers.org/rhea/16372
+ - !!omap
+ - id: R_PFK
- name: phosphofructokinase
- - metabolites: !!omap
- - adp_c: 1.0
- - atp_c: -1.0
- - f6p_c: -1.0
- - fdp_c: 1.0
- - h_c: 1.0
- lower_bound: 0.0
- upper_bound: 1000.0
- gene_reaction_rule: b3916 or b1723
+ - metabolites: !!omap
+ - M_f6p_c: -1.0
+ - M_atp_c: -1.0
+ - M_adp_c: 1.0
+ - M_fdp_c: 1.0
+ - M_h_c: 1.0
- objective_coefficient: 1.0
- - annotation: !!omap
- - bigg.reaction: PFK
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/PFK
- !!omap
- - id: PGI
+ - id: R_PGI
- name: glucose-6-phosphate isomerase
- - metabolites: !!omap
- - f6p_c: 1.0
- - g6p_c: -1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b4025
- - annotation: !!omap
- - bigg.reaction: PGI
- - !!omap
- - id: PGK
- - name: phosphoglycerate kinase
- metabolites: !!omap
- - 13dpg_c: 1.0
- - 3pg_c: -1.0
- - adp_c: 1.0
- - atp_c: -1.0
+ - M_g6p_c: -1.0
+ - M_f6p_c: 1.0
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/PGI
+ - !!omap
+ - id: R_PGK
+ - name: phosphoglycerate kinase
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b2926
- - annotation: !!omap
- - bigg.reaction: PGK
- - !!omap
- - id: PGM
- - name: phosphoglycerate mutase
- metabolites: !!omap
- - 2pg_c: -1.0
- - 3pg_c: 1.0
+ - M_3pg_c: -1.0
+ - M_atp_c: -1.0
+ - M_13dpg_c: 1.0
+ - M_adp_c: 1.0
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/PGK
+ - !!omap
+ - id: R_PGM
+ - name: phosphoglycerate mutase
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b4395 or b3612 or b0755
- - annotation: !!omap
- - bigg.reaction: PGM
- - !!omap
- - id: PIt2r
- - name: R phosphate reversible transport via - symport
- metabolites: !!omap
- - h_c: 1.0
- - h_e: -1.0
- - pi_c: 1.0
- - pi_e: -1.0
+ - M_2pg_c: -1.0
+ - M_3pg_c: 1.0
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/PGM
+ - !!omap
+ - id: R_PIt2r
+ - name: R phosphate reversible transport via - symport
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b2987 or b3493
- - annotation: !!omap
- - bigg.reaction: PIt2r
- - !!omap
- - id: PYK
- - name: pyruvate kinase
- metabolites: !!omap
- - adp_c: -1.0
- - atp_c: 1.0
- - h_c: -1.0
- - pep_c: -1.0
- - pyr_c: 1.0
+ - M_pi_e: -1.0
+ - M_h_e: -1.0
+ - M_h_c: 1.0
+ - M_pi_c: 1.0
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/PIt2r
+ - !!omap
+ - id: R_PYK
+ - name: pyruvate kinase
- lower_bound: 0.0
- upper_bound: 1000.0
- gene_reaction_rule: b1854 or b1676
- - annotation: !!omap
- - bigg.reaction: PYK
- - !!omap
- - id: TPI
- - name: triose-phosphate isomerase
- metabolites: !!omap
- - dhap_c: -1.0
- - g3p_c: 1.0
+ - M_adp_c: -1.0
+ - M_h_c: -1.0
+ - M_pep_c: -1.0
+ - M_atp_c: 1.0
+ - M_pyr_c: 1.0
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/PYK
+ - !!omap
+ - id: R_TPI
+ - name: triose-phosphate isomerase
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b3919
- - annotation: !!omap
- - bigg.reaction: TPI
+ - metabolites: !!omap
+ - M_dhap_c: -1.0
+ - M_g3p_c: 1.0
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - http://identifiers.org/bigg.reaction/TPI
- genes:
- !!omap
- - id: b0755
+ - id: G_b0755
- name: gpmA
- !!omap
- - id: b0875
+ - id: G_b0875
- name: aqpZ
- !!omap
- - id: b1101
+ - id: G_b1101
- name: ptsG
- !!omap
- - id: b1380
+ - id: G_b1380
- name: ldhA
- !!omap
- - id: b1621
+ - id: G_b1621
- name: malX
- !!omap
- - id: b1676
+ - id: G_b1676
- name: pykF
- - annotation: !!omap
- - ncbiprotein:
- - '1208453'
- - '1652654'
- - !!omap
- - id: b1723
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - https://identifiers.org/ncbiprotein:1208453
+ - https://identifiers.org/ncbiprotein:1652654
+ - !!omap
+ - id: G_b1723
- name: pfkB
- !!omap
- - id: b1773
+ - id: G_b1773
- name: ydjI
- !!omap
- - id: b1779
+ - id: G_b1779
- name: gapA
- !!omap
- - id: b1817
+ - id: G_b1817
- name: manX
- !!omap
- - id: b1818
+ - id: G_b1818
- name: manY
- !!omap
- - id: b1819
+ - id: G_b1819
- name: manZ
- !!omap
- - id: b1854
+ - id: G_b1854
- name: pykA
- !!omap
- - id: b2097
+ - id: G_b2097
- name: fbaB
- !!omap
- - id: b2133
+ - id: G_b2133
- name: dld
- !!omap
- - id: b2415
+ - id: G_b2415
- name: ptsH
- !!omap
- - id: b2416
+ - id: G_b2416
- name: ptsI
- !!omap
- - id: b2417
+ - id: G_b2417
- name: crr
- !!omap
- - id: b2779
+ - id: G_b2779
- name: eno
- - annotation: !!omap
- - ncbiprotein: '1653839'
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - https://identifiers.org/ncbiprotein:1653839
- !!omap
- - id: b2925
+ - id: G_b2925
- name: fbaA
- !!omap
- - id: b2926
+ - id: G_b2926
- name: pgk
- - annotation: !!omap
- - ncbiprotein: '1653609'
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - https://identifiers.org/ncbiprotein:1653609
- !!omap
- - id: b2987
+ - id: G_b2987
- name: pitB
- !!omap
- - id: b3493
+ - id: G_b3493
- name: pitA
- !!omap
- - id: b3612
+ - id: G_b3612
- name: gpmM
- !!omap
- - id: b3916
+ - id: G_b3916
- name: pfkA
- - annotation: !!omap
- - ncbiprotein:
- - '1006614'
- - '1651919'
- - !!omap
- - id: b3919
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - https://identifiers.org/ncbiprotein:1006614
+ - https://identifiers.org/ncbiprotein:1651919
+ - !!omap
+ - id: G_b3919
- name: tpiA
- !!omap
- - id: b4025
+ - id: G_b4025
- name: pgi
- - annotation: !!omap
- - ncbiprotein: '1653253'
+ - metadata: !!omap
+ - standardized:
+ - qualifier: bqb_is
+ resources:
+ - https://identifiers.org/ncbiprotein:1653253
- !!omap
- - id: b4395
+ - id: G_b4395
- name: ytjC
- !!omap
- - id: s0001
+ - id: G_s0001
- name: G_s0001
+- groups: []
- id: mini_textbook
- compartments: !!omap
- c: cytosol
diff --git a/src/cobra/data/mini_cobra.xml b/src/cobra/data/mini_cobra.xml
index bc0d31f38..0cbf9dfed 100644
--- a/src/cobra/data/mini_cobra.xml
+++ b/src/cobra/data/mini_cobra.xml
@@ -1,5 +1,5 @@
-
+
@@ -21,19 +21,19 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -46,23 +46,23 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -75,29 +75,29 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -110,33 +110,34 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -149,32 +150,33 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -187,25 +189,26 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -218,25 +221,26 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -249,26 +253,27 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -281,19 +286,20 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -306,28 +312,29 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -340,10 +347,11 @@
-
-
-
-
+
+
+
+
+
@@ -356,64 +364,65 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -426,64 +435,65 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -496,37 +506,38 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -539,37 +550,38 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -582,20 +594,20 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -608,20 +620,20 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -634,30 +646,31 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -670,25 +683,26 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -701,24 +715,25 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -731,52 +746,53 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -789,52 +805,53 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -847,25 +864,26 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -883,13 +901,13 @@
-
+
-
+
@@ -905,14 +923,14 @@
-
-
+
+
-
+
@@ -929,13 +947,13 @@
-
+
-
+
@@ -945,13 +963,13 @@
-
+
-
+
@@ -961,13 +979,13 @@
-
+
-
+
@@ -977,13 +995,13 @@
-
+
-
+
@@ -1004,13 +1022,13 @@
-
+
-
+
@@ -1030,13 +1048,13 @@
-
+
-
+
@@ -1074,13 +1092,13 @@
-
+
-
+
@@ -1099,21 +1117,21 @@
-
+
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
@@ -1135,13 +1153,13 @@
-
+
-
+
@@ -1163,13 +1181,13 @@
-
+
-
+
@@ -1185,13 +1203,13 @@
-
+
-
+
@@ -1209,13 +1227,13 @@
-
+
-
+
@@ -1235,13 +1253,13 @@
-
+
-
+
@@ -1262,13 +1280,13 @@
-
+
-
+
@@ -1290,13 +1308,13 @@
-
+
-
+
@@ -1322,97 +1340,97 @@
-
-
-
-
-
+
+
+
+
+
-
-
+
+
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
-
+
-
+
-
+
-
-
-
+
+
+
-
-
+
+
-
+
-
+
-
-
+
+
diff --git a/src/cobra/flux_analysis/reaction.py b/src/cobra/flux_analysis/reaction.py
index d3f146d4a..ebc8a1e9a 100644
--- a/src/cobra/flux_analysis/reaction.py
+++ b/src/cobra/flux_analysis/reaction.py
@@ -58,13 +58,14 @@ def assess(
if m.slim_optimize(error_value=0.0) >= flux_coefficient_cutoff:
return True
else:
- results = {}
- results["precursors"] = assess_component(
- model, reaction, "reactants", flux_coefficient_cutoff
- )
- results["products"] = assess_component(
- model, reaction, "products", flux_coefficient_cutoff
- )
+ results = {
+ "precursors": assess_component(
+ model, reaction, "reactants", flux_coefficient_cutoff
+ ),
+ "products": assess_component(
+ model, reaction, "products", flux_coefficient_cutoff
+ ),
+ }
return results
diff --git a/src/cobra/io/__init__.py b/src/cobra/io/__init__.py
index f81680c1c..db169903a 100644
--- a/src/cobra/io/__init__.py
+++ b/src/cobra/io/__init__.py
@@ -1,8 +1,14 @@
"""Provide functions for loading and saving metabolic models."""
from cobra.io.dict import model_from_dict, model_to_dict
-from cobra.io.json import from_json, load_json_model, save_json_model, to_json
-from cobra.io.mat import load_matlab_model, save_matlab_model
+from cobra.io.json import (
+ from_json,
+ load_json_model,
+ save_json_model,
+ to_json,
+ validate_json_model,
+)
+from cobra.io.mat import load_matlab_model, save_matlab_model, create_mat_dict
from cobra.io.sbml import read_sbml_model, write_sbml_model, validate_sbml_model
from cobra.io.yaml import from_yaml, load_yaml_model, save_yaml_model, to_yaml
from cobra.io.web import AbstractModelRepository, BiGGModels, BioModels, load_model
diff --git a/src/cobra/io/dict.py b/src/cobra/io/dict.py
index 362471a91..a1b013186 100644
--- a/src/cobra/io/dict.py
+++ b/src/cobra/io/dict.py
@@ -1,12 +1,25 @@
"""Provide functions for cobrapy objects to generic Python objects and vice-versa."""
-from collections import OrderedDict
-from operator import attrgetter, itemgetter
-from typing import TYPE_CHECKING, Dict, List, Sequence, Set, Union
+import itertools
+from collections import OrderedDict, defaultdict
+from typing import TYPE_CHECKING, Dict, List, Sequence, Set, Tuple, Union
import numpy as np
-from ..core import Gene, Metabolite, Model, Reaction
+from ..core import Gene, Group, Metabolite, Model, Reaction
+from ..core.metadata import Metadata
+from ..core.metadata.resource import parse_identifiers_uri
+from ..io.sbml import (
+ F_GENE,
+ F_GENE_REV,
+ F_GROUP,
+ F_GROUP_REV,
+ F_REACTION,
+ F_REACTION_REV,
+ F_REPLACE,
+ F_SPECIE,
+ F_SPECIE_REV,
+)
from ..util.solver import set_objective
@@ -16,7 +29,6 @@
_REQUIRED_REACTION_ATTRIBUTES = [
"id",
"name",
- "metabolites",
"lower_bound",
"upper_bound",
"gene_reaction_rule",
@@ -25,13 +37,15 @@
"objective_coefficient",
"subsystem",
"notes",
- "annotation",
+ # "annotation",
+ "metadata",
]
_OPTIONAL_REACTION_ATTRIBUTES = {
"objective_coefficient": 0,
"subsystem": "",
"notes": {},
- "annotation": {},
+ # "annotation": {},
+ "metadata": {},
}
_REQUIRED_METABOLITE_ATTRIBUTES = ["id", "name", "compartment"]
@@ -40,33 +54,68 @@
"formula",
"_bound",
"notes",
- "annotation",
+ # "annotation",
+ "metadata",
]
_OPTIONAL_METABOLITE_ATTRIBUTES = {
"charge": None,
"formula": None,
"_bound": 0,
"notes": {},
- "annotation": {},
+ # "annotation": {},
+ "metadata": {},
}
_REQUIRED_GENE_ATTRIBUTES = ["id", "name"]
-_ORDERED_OPTIONAL_GENE_KEYS = ["notes", "annotation"]
+_ORDERED_OPTIONAL_GENE_KEYS = ["notes", "metadata"]
_OPTIONAL_GENE_ATTRIBUTES = {
"notes": {},
- "annotation": {},
+ # "annotation": {},
+ "metadata": {},
}
-_ORDERED_OPTIONAL_MODEL_KEYS = ["name", "compartments", "notes", "annotation"]
+_REQUIRED_GROUP_ATTRIBUTES = ["id", "kind", "members"]
+_ORDERED_OPTIONAL_GROUP_KEYS = ["name", "notes", "metadata"]
+_OPTIONAL_GROUP_ATTRIBUTES = {
+ "name": "",
+ "notes": {},
+ # "annotation": {},
+ "metadata": {},
+}
+
+_ORDERED_OPTIONAL_MODEL_KEYS = [
+ "name",
+ "compartments",
+ "notes",
+ # "annotation",
+ "metadata",
+]
_OPTIONAL_MODEL_ATTRIBUTES = {
"name": None,
# "description": None, should not actually be included
"compartments": [],
"notes": {},
- "annotation": {},
+ # "annotation": {},
+ "metadata": {},
}
+def flatten(list_of_lists: Union[List, Tuple]) -> List:
+ """Flatten lists of lists.
+
+ Parameters
+ ----------
+ list_of_lists: List or Tuple
+ List or Tuple of lists or tuples to flatten.
+
+ Returns
+ -------
+ list: flattened list
+
+ """
+ return list(itertools.chain.from_iterable(list_of_lists))
+
+
def _fix_type(
value: Union[str, float, bool, Set, Dict],
) -> Union[str, float, bool, List, OrderedDict]:
@@ -94,6 +143,8 @@ def _fix_type(
return list(value)
if isinstance(value, dict):
return OrderedDict((key, value[key]) for key in sorted(value))
+ if isinstance(value, Metadata):
+ return OrderedDict(value.to_dict())
# handle legacy Formula type
if value.__class__.__name__ == "Formula":
return str(value)
@@ -131,19 +182,85 @@ def _update_optional(
"""
for key in ordered_keys:
default = optional_attribute_dict[key]
- value = getattr(cobra_object, key)
+ value = getattr(cobra_object, key, None)
if value is None or value == default:
continue
new_dict[key] = _fix_type(value)
-def _metabolite_to_dict(metabolite: Metabolite) -> OrderedDict:
+def _fix_id_from_dict(
+ _id_to_fix: str,
+ _class_to_fix_to: str,
+ f_replace: dict = F_REPLACE, # noqa: W0102
+):
+ if f_replace is None:
+ f_replace = {}
+ if not f_replace:
+ return _id_to_fix
+ if _class_to_fix_to == "Metabolite":
+ return F_REPLACE[F_SPECIE](_id_to_fix)
+ elif _class_to_fix_to == "Reaction":
+ return F_REPLACE[F_REACTION](_id_to_fix)
+ elif _class_to_fix_to == "Gene":
+ return F_REPLACE[F_GENE](_id_to_fix)
+ elif _class_to_fix_to == "Group":
+ return F_REPLACE[F_GROUP](_id_to_fix)
+
+
+def _fix_value_from_dict(_key: str, _value_to_fix: Union[Dict, List, str]):
+ if _key == "metadata":
+ # New style annotations for json v2.
+ _value_to_fix = Metadata.from_dict(_value_to_fix)
+ elif _key == "annotation":
+ # Old style annotations for json v1.
+ # if annotation is in the form of list of list, modify the format
+ # https://github.com/opencobra/cobrapy/issues/736
+ if isinstance(_value_to_fix, list) and isinstance(_value_to_fix[0], list):
+ _value_to_fix = flatten(_value_to_fix)
+ anno_dict = defaultdict(list)
+ if isinstance(_value_to_fix, list):
+ for item in _value_to_fix:
+ if (identifier_match := parse_identifiers_uri(item)) is not None:
+ provider, identifier, _provider, _uri = identifier_match
+ anno_dict[provider].append(identifier)
+ _value_to_fix = anno_dict
+ # metadata = Metadata()
+ # old_style_interface = SimplifiedAnnotationInterface(metadata)
+ # old_style_interface.add(_value_to_fix)
+ # _value_to_fix = metadata
+ elif _key == "lower_bound" or _key == "upper_bound":
+ _value_to_fix = float(_value_to_fix)
+
+ return _value_to_fix
+
+
+def _get_by_id(
+ _id: str, _object_to_get: str, model: Model
+) -> Union[Gene, Metabolite, Group, Reaction]:
+ if _object_to_get == "Reaction":
+ return model.reactions.get_by_id(_id)
+ elif _object_to_get == "Metabolite":
+ return model.metabolites.get_by_id(_id)
+ elif _object_to_get == "Group":
+ return model.groups.get_by_id(_id)
+ elif _object_to_get == "Gene":
+ return model.genes.get_by_id(_id)
+
+
+def _metabolite_to_dict(
+ metabolite: Metabolite, f_replace: dict = F_REPLACE # noqa: W0102
+) -> OrderedDict:
"""Convert a cobra Metabolite object to dictionary.
Parameters
----------
metabolite : cobra.Metabolite
The cobra.Metabolite to convert to dictionary.
+ f_replace : dict of replacement functions for id replacement
+ Dictionary of replacement functions for gene, specie, and reaction.
+ By default, the following id changes are performed on import:
+ clip G_ from genes, clip M_ from species, clip R_ from reactions
+ If no replacements should be performed, set f_replace={} or None
Returns
-------
@@ -155,9 +272,15 @@ def _metabolite_to_dict(metabolite: Metabolite) -> OrderedDict:
_metabolite_from_dict : Convert a dictionary to cobra Metabolite object.
"""
+ if f_replace is None:
+ f_replace = {}
+
new_metabolite = OrderedDict()
for key in _REQUIRED_METABOLITE_ATTRIBUTES:
- new_metabolite[key] = _fix_type(getattr(metabolite, key))
+ if key == "id" and f_replace and F_SPECIE_REV in f_replace:
+ new_metabolite[key] = _fix_type(f_replace[F_SPECIE_REV](metabolite.id))
+ else:
+ new_metabolite[key] = _fix_type(getattr(metabolite, key))
_update_optional(
metabolite,
new_metabolite,
@@ -167,7 +290,9 @@ def _metabolite_to_dict(metabolite: Metabolite) -> OrderedDict:
return new_metabolite
-def _metabolite_from_dict(metabolite: Dict) -> Metabolite:
+def _metabolite_from_dict(
+ metabolite: Dict, f_replace: dict = F_REPLACE # noqa: W0102
+) -> Metabolite:
"""Convert a dictionary to cobra Metabolite object.
Parameters
@@ -184,9 +309,17 @@ def _metabolite_from_dict(metabolite: Dict) -> Metabolite:
_metabolite_to_dict : Convert a cobra Metabolite object to dictionary.
"""
- new_metabolite = Metabolite()
- for k, v in metabolite.items():
- setattr(new_metabolite, k, v)
+ if f_replace is None:
+ f_replace = {}
+
+ new_metabolite = Metabolite(
+ _fix_id_from_dict(metabolite["id"], "Metabolite", f_replace)
+ )
+ [
+ setattr(new_metabolite, k, _fix_value_from_dict(k, v))
+ for k, v in metabolite.items()
+ if k != "id"
+ ]
return new_metabolite
@@ -210,14 +343,17 @@ def _gene_to_dict(gene: Gene) -> OrderedDict:
"""
new_gene = OrderedDict()
for key in _REQUIRED_GENE_ATTRIBUTES:
- new_gene[key] = _fix_type(getattr(gene, key))
+ if key == "id":
+ new_gene[key] = _fix_type(F_REPLACE["F_GENE_REV"](gene.id))
+ else:
+ new_gene[key] = _fix_type(getattr(gene, key))
_update_optional(
gene, new_gene, _OPTIONAL_GENE_ATTRIBUTES, _ORDERED_OPTIONAL_GENE_KEYS
)
return new_gene
-def gene_from_dict(gene: Dict) -> Gene:
+def gene_from_dict(gene: Dict, f_replace: dict = F_REPLACE) -> Gene: # noqa: W0102
"""Convert a dictionary to cobra Gene object.
Parameters
@@ -235,9 +371,15 @@ def gene_from_dict(gene: Dict) -> Gene:
_gene_to_dict : Convert a cobra Gene object to a dictionary.
"""
- new_gene = Gene(gene["id"])
- for k, v in gene.items():
- setattr(new_gene, k, v)
+ if f_replace is None:
+ f_replace = {}
+
+ new_gene = Gene(_fix_id_from_dict(gene["id"], "Gene", f_replace))
+ [
+ setattr(new_gene, k, _fix_value_from_dict(k, v))
+ for k, v in gene.items()
+ if k != "id"
+ ]
return new_gene
@@ -261,22 +403,22 @@ def _reaction_to_dict(reaction: Reaction) -> OrderedDict:
"""
new_reaction = OrderedDict()
for key in _REQUIRED_REACTION_ATTRIBUTES:
- if key != "metabolites":
- if key == "lower_bound" and (
- np.isnan(reaction.lower_bound) or np.isinf(reaction.lower_bound)
- ):
- new_reaction[key] = str(_fix_type(getattr(reaction, key)))
- elif key == "upper_bound" and (
- np.isnan(reaction.upper_bound) or np.isinf(reaction.upper_bound)
- ):
- new_reaction[key] = str(_fix_type(getattr(reaction, key)))
- else:
- new_reaction[key] = _fix_type(getattr(reaction, key))
- continue
- mets = OrderedDict()
- for met in sorted(reaction.metabolites, key=attrgetter("id")):
- mets[str(met)] = reaction.metabolites[met]
- new_reaction["metabolites"] = mets
+ if key == "id":
+ new_reaction[key] = _fix_type(F_REPLACE[F_REACTION_REV](reaction.id))
+ elif (key == "lower_bound" or key == "upper_bound") and not np.isfinite(
+ getattr(reaction, key)
+ ):
+ new_reaction[key] = str(_fix_type(getattr(reaction, key)))
+ else:
+ new_reaction[key] = _fix_type(getattr(reaction, key))
+ if F_REPLACE and F_SPECIE_REV in F_REPLACE:
+ mets = {
+ F_REPLACE[F_SPECIE_REV](met.id): stoic
+ for met, stoic in reaction.metabolites.items()
+ }
+ else:
+ mets = {met.id: stoic for met, stoic in reaction.metabolites.items()}
+ new_reaction["metabolites"] = OrderedDict(mets)
_update_optional(
reaction,
new_reaction,
@@ -286,7 +428,9 @@ def _reaction_to_dict(reaction: Reaction) -> OrderedDict:
return new_reaction
-def _reaction_from_dict(reaction: Dict, model: Model) -> Reaction:
+def _reaction_from_dict(
+ reaction: Dict, model: Model, f_replace: Dict = F_REPLACE # noqa: W0102
+) -> Reaction:
"""Convert a dictionary to a cobra Reaction object.
Parameters
@@ -306,26 +450,131 @@ def _reaction_from_dict(reaction: Dict, model: Model) -> Reaction:
_reaction_to_dict : Convert a cobra Reaction object to a dictionary.
"""
- new_reaction = Reaction()
- for k, v in reaction.items():
- if k in {"objective_coefficient", "reversibility", "reaction"}:
- continue
- elif k == "metabolites":
- new_reaction.add_metabolites(
- OrderedDict(
- (model.metabolites.get_by_id(str(met)), coeff)
- for met, coeff in v.items()
- )
+ if f_replace is None:
+ f_replace = {}
+
+ new_reaction = Reaction(_fix_id_from_dict(reaction["id"], "Reaction", f_replace))
+ [
+ setattr(new_reaction, k, _fix_value_from_dict(k, v))
+ for k, v in reaction.items()
+ if k
+ not in {
+ "id",
+ "objective_coefficient",
+ "reversibility",
+ "reaction",
+ "metabolites",
+ }
+ ]
+
+ new_reaction.add_metabolites(
+ OrderedDict(
+ (
+ model.metabolites.get_by_id(
+ _fix_id_from_dict(str(met), "Metabolite", f_replace)
+ ),
+ coeff,
)
- else:
- if k == "lower_bound" or k == "upper_bound":
- setattr(new_reaction, k, float(v))
- else:
- setattr(new_reaction, k, v)
+ for met, coeff in reaction.get("metabolites", {}).items()
+ )
+ )
return new_reaction
-def model_to_dict(model: Model, sort: bool = False) -> OrderedDict:
+def _group_to_dict(group: "Group") -> Dict:
+ """Convert a cobra Group object to a dictionary.
+
+ Parameters
+ ----------
+ group : cobra.Group
+ The cobra.Group to convert to a dictionary.
+
+ Returns
+ -------
+ dict
+ A dictionary representing the cobra.Group object.
+
+ See Also
+ --------
+ _group_from_dict : Convert a dictionary to a cobra Group object.
+
+ """
+
+ new_group = OrderedDict()
+ for key in _REQUIRED_GROUP_ATTRIBUTES:
+ if key != "members":
+ if key == "id":
+ new_group[key] = _fix_type(F_REPLACE[F_GROUP_REV](group.id))
+ else:
+ new_group[key] = _fix_type(getattr(group, key))
+ continue
+ members = []
+ for member in group.members:
+ idRef = member.id
+ if isinstance(member, Reaction):
+ idRef = F_REPLACE[F_REACTION_REV](member.id)
+ elif isinstance(member, Gene):
+ idRef = F_REPLACE[F_GENE_REV](member.id)
+ elif isinstance(member, Metabolite):
+ idRef = F_REPLACE[F_SPECIE_REV](member.id)
+ elif isinstance(member, Group):
+ idRef = F_REPLACE[F_GROUP_REV](member.id)
+ json_member = {"idRef": idRef, "type": type(member).__name__}
+ members.append(json_member)
+ new_group["members"] = members
+ _update_optional(
+ group, new_group, _OPTIONAL_GROUP_ATTRIBUTES, _ORDERED_OPTIONAL_GROUP_KEYS
+ )
+ return new_group
+
+
+def _group_from_dict(
+ group: Dict, model: Model, f_replace=F_REPLACE # noqa: W0102
+) -> Group:
+ """Convert a dictionary to a cobra Group object.
+
+ Parameters
+ ----------
+ group : dict
+ The dictionary to convert to cobra.Group .
+ model : cobra.Model
+ The model to which the group should associate with.
+
+ Returns
+ -------
+ cobra.Group
+ The converted cobra.Group object.
+
+ See Also
+ --------
+ _group_to_dict : Convert a cobra Group object to a dictionary.
+
+ """
+
+ if f_replace is None:
+ f_replace = {}
+
+ new_group = Group(_fix_id_from_dict(group["id"], "Group"))
+ [
+ setattr(new_group, k, _fix_value_from_dict(k, v))
+ for k, v in group.items()
+ if k not in {"id", "members"}
+ ]
+ cobra_members = [
+ _get_by_id(
+ _fix_id_from_dict(member["idRef"], member["type"], f_replace),
+ member["type"],
+ model,
+ )
+ for member in group["members"]
+ ]
+ new_group.add_members(cobra_members)
+ return new_group
+
+
+def model_to_dict(
+ model: Model, sort: bool = False, f_replace: dict = F_REPLACE # noqa: W0102
+) -> OrderedDict:
"""Convert a cobra Model to a dictionary.
Parameters
@@ -335,6 +584,11 @@ def model_to_dict(model: Model, sort: bool = False) -> OrderedDict:
sort : bool, optional
Whether to sort the metabolites, reactions, and genes or maintain the
order defined in the model (default False).
+ f_replace : dict of replacement functions for id replacement
+ Dictionary of replacement functions for gene, specie, and reaction.
+ By default, the following id changes are performed on import:
+ clip G_ from genes, clip M_ from species, clip R_ from reactions
+ If no replacements should be performed, set f_replace={} or None
Returns
-------
@@ -349,19 +603,29 @@ def model_to_dict(model: Model, sort: bool = False) -> OrderedDict:
model_from_dict : Convert a dictionary to a cobra Model.
"""
+ if f_replace is None:
+ f_replace = {}
+
obj = OrderedDict()
obj["metabolites"] = list(map(_metabolite_to_dict, model.metabolites))
obj["reactions"] = list(map(_reaction_to_dict, model.reactions))
obj["genes"] = list(map(_gene_to_dict, model.genes))
+ obj["groups"] = list(map(_group_to_dict, model.groups))
+
+ # sbml meta info
+ if hasattr(model, "_sbml"):
+ obj["sbml_info"] = OrderedDict(
+ {key: _fix_type(value) for key, value in model._sbml.items()}
+ )
obj["id"] = model.id
_update_optional(
model, obj, _OPTIONAL_MODEL_ATTRIBUTES, _ORDERED_OPTIONAL_MODEL_KEYS
)
if sort:
- get_id = itemgetter("id")
- obj["metabolites"].sort(key=get_id)
- obj["reactions"].sort(key=get_id)
- obj["genes"].sort(key=get_id)
+ obj["metabolites"].sort(key=lambda x: x["id"])
+ obj["reactions"].sort(key=lambda x: x["id"])
+ obj["genes"].sort(key=lambda x: x["id"])
+ obj["groups"].sort(key=lambda x: x["id"])
return obj
@@ -408,11 +672,24 @@ def model_from_dict(obj: Dict) -> Model:
rxn for rxn in obj["reactions"] if rxn.get("objective_coefficient", 0) != 0
]
coefficients = {
- model.reactions.get_by_id(rxn["id"]): rxn["objective_coefficient"]
+ model.reactions.get_by_id(F_REPLACE["F_REACTION"](rxn["id"])): rxn[
+ "objective_coefficient"
+ ]
for rxn in objective_reactions
}
+ if "groups" in obj:
+ model.add_groups([_group_from_dict(group, model) for group in obj["groups"]])
set_objective(model, coefficients)
- for k, v in obj.items():
- if k in {"id", "name", "notes", "compartments", "annotation"}:
- setattr(model, k, v)
+
+ # sbml meta info
+ if "sbml_info" in obj:
+ meta = {k: _fix_value_from_dict(k, v) for k, v in obj["sbml_info"].items()}
+ model._sbml = meta
+
+ [
+ setattr(model, k, _fix_value_from_dict(k, v))
+ for k, v in obj.items()
+ if k in {"id", "name", "compartments", "metadata", "notes"}
+ ]
+
return model
diff --git a/src/cobra/io/json.py b/src/cobra/io/json.py
index 83347219b..5a3978fff 100644
--- a/src/cobra/io/json.py
+++ b/src/cobra/io/json.py
@@ -2,7 +2,12 @@
import json
from pathlib import Path
-from typing import IO, TYPE_CHECKING, Any, Union
+from typing import IO, TYPE_CHECKING, Any, Iterable, TextIO, Union
+
+import jsonschema
+from importlib_resources import files
+
+from cobra import io as cio
from .dict import model_from_dict, model_to_dict
@@ -14,6 +19,25 @@
JSON_SPEC = "1"
+def _validator_for_json_schema(schema_version):
+ if schema_version == 1:
+ schema_filename = "schema_v1.json"
+ elif schema_version == 2:
+ schema_filename = "schema_v2.json"
+ else:
+ raise ValueError(
+ f"Only v1 and v2 of JSON schema are available. JSON "
+ f"schema v{schema_version} is not supported."
+ )
+ with files(cio).joinpath(schema_filename).open("r") as handle:
+ schema = json.load(handle)
+
+ # TODO: Should the validator be picked by schema?
+ # Something like validators.validator_for
+ validator = jsonschema.Draft7Validator(schema)
+ return validator
+
+
def to_json(model: "Model", sort: bool = False, **kwargs: Any) -> str:
"""Return the model as a JSON string.
@@ -77,7 +101,7 @@ def save_json_model(
----------
model : cobra.Model
The cobra model to represent.
- filename : str or file-like
+ filename : str or file-like or Path
File path or descriptor that the JSON representation should be
written to.
sort : bool, optional
@@ -127,7 +151,7 @@ def load_json_model(filename: Union[str, Path, IO]) -> "Model":
Parameters
----------
- filename : str or file-like
+ filename : str or file-like or Path
File path or descriptor that contains the JSON document describing the
cobra model.
@@ -146,3 +170,35 @@ def load_json_model(filename: Union[str, Path, IO]) -> "Model":
return model_from_dict(json.load(file_handle))
else:
return model_from_dict(json.load(filename))
+
+
+def validate_json_model(
+ filename: Union[str, Path, bytes, TextIO], json_schema_version: int = 1
+) -> Iterable[Any]:
+ """
+ Validate a model in json format against the schema with given version.
+
+ Parameters
+ ----------
+ filename : str or file-like
+ File path or descriptor that contains the JSON document describing the
+ cobra model.
+ json_schema_version : int {1, 2}
+ the version of schema to be used for validation.
+ Currently we have v1 and v2 only and v2 is under development
+ Returns
+ -------
+ errors : Iterable
+ The iterable of errors encountered while validating
+ """
+ validator = _validator_for_json_schema(schema_version=json_schema_version)
+ try:
+ if isinstance(filename, (str, Path)):
+ with open(filename, "r") as file_handle:
+ errors = validator.iter_errors(json.load(file_handle))
+ else:
+ errors = validator.iter_errors(json.load(filename))
+ except OSError:
+ errors = validator.iter_errors(json.loads(filename))
+
+ return list(errors)
diff --git a/src/cobra/io/mat.py b/src/cobra/io/mat.py
index 2a67d5ec8..23b71434b 100644
--- a/src/cobra/io/mat.py
+++ b/src/cobra/io/mat.py
@@ -924,7 +924,7 @@ def from_mat_struct(
new_group = Group(
id=g_name, name=g_name, members=group_members, kind="partonomy"
)
- new_group.annotation["sbo"] = "SBO:0000633"
+ new_group.annotation["sbo"] = ["SBO:0000633"]
new_groups.append(new_group)
model.add_groups(new_groups)
diff --git a/src/cobra/io/sbml.py b/src/cobra/io/sbml.py
index 2447816e8..cc7bacaae 100644
--- a/src/cobra/io/sbml.py
+++ b/src/cobra/io/sbml.py
@@ -9,6 +9,8 @@
Parsing of fbc models was implemented as efficient as possible, whereas
(discouraged) fallback solutions are not optimized for efficiency.
+#TODO - fix the following paragraph, which is incorrect.
+ Load up keyvalue pairs from notes??
Notes are only supported in a minimal way relevant for constraint-based
models. I.e., structured information from notes in the form
key: value
@@ -19,10 +21,8 @@
Annotations are read in the Object.annotation fields.
Some SBML related issues are still open, please refer to the respective issue:
-- update annotation format and support qualifiers (depends on decision
- for new annotation format; https://github.com/opencobra/cobrapy/issues/684)
- write compartment annotations and notes (depends on updated first-class
- compartments; see https://github.com/opencobra/cobrapy/issues/760)
+ compartments; see https://github.com/opencobra/cobrapy/issues/760interface
- support compression on file handles (depends on solution for
https://github.com/opencobra/cobrapy/issues/812)
"""
@@ -32,17 +32,30 @@
import re
from ast import And, BoolOp, Module, Name, Or
from collections import defaultdict, namedtuple
-from copy import deepcopy
from io import StringIO
from pathlib import Path
from sys import platform
-from typing import IO, Match, Optional, Pattern, Tuple, Type, Union
+from typing import IO, List, Match, Optional, Pattern, Tuple, Type, Union
import libsbml
import cobra
-
-from ..core import GPR, Gene, Group, Metabolite, Model, Reaction
+from cobra.core.metadata.custom import CustomAnnotation, CustomAnnotationStore
+
+from ..core import (
+ GPR,
+ Creator,
+ Gene,
+ Group,
+ Metabolite,
+ Metadata,
+ Model,
+ Reaction,
+ Resource,
+ StandardizedAnnotation,
+)
+from ..core.metadata.history import STRTIME_FORMAT
+from ..core.metadata.standardized import StandardizedAnnotationStore
from ..manipulation.validate import check_metabolite_compartment_formula
from ..util.solver import linear_reaction_coefficients, set_objective
@@ -584,6 +597,7 @@ def _sbml_to_model(
result = doc.convert(conversion_properties)
if result != libsbml.LIBSBML_OPERATION_SUCCESS:
raise Exception("Conversion of SBML fbc v1 to fbc v2 failed")
+ # TODO: Convert v2 to v3 if necessary
# Model
model_id = model.getIdAttribute()
@@ -597,7 +611,6 @@ def _sbml_to_model(
"model.id": model_id,
"level": model.getLevel(),
"version": model.getVersion(),
- "packages": [],
}
# History
creators = []
@@ -610,21 +623,25 @@ def _sbml_to_model(
c: "libsbml.ModelCreator"
for c in history.getListCreators():
- creators.append(
- {
- "familyName": c.getFamilyName() if c.isSetFamilyName() else None,
- "givenName": c.getGivenName() if c.isSetGivenName() else None,
- "organisation": (
- c.getOrganisation() if c.isSetOrganisation() else None
- ),
- "email": c.getEmail() if c.isSetEmail() else None,
- }
- )
+ creator_data = {
+ "organisation": (
+ c.getOrganisation() if c.isSetOrganisation() else None
+ ),
+ "email": c.getEmail() if c.isSetEmail() else None,
+ }
+ if c.isSetName():
+ creator_data["name"] = c.getName()
+ else:
+ name = c.getGivenName() if c.isSetGivenName() else ""
+ if c.isSetFamilyName():
+ name = f"{name} {c.getFamilyName()}"
+ creator_data["name"] = name.strip()
+ creators.append(creator_data)
meta["creators"] = creators
meta["created"] = created
meta["notes"] = _parse_notes_dict(doc)
- meta["annotation"] = _parse_annotations(doc)
+ meta["metadata"] = _parse_annotations(doc)
info = f"<{model_id}> SBML L{model.getLevel()}V{model.getVersion()}"
packages = {}
@@ -638,20 +655,21 @@ def _sbml_to_model(
f"SBML package '{key}' not supported by cobrapy, "
f"information is not parsed"
)
- meta["info"] = info
+
meta["packages"] = packages
+ meta["info"] = info
+
cobra_model._sbml = meta
# notes and annotations
cobra_model.notes = _parse_notes_dict(model)
- cobra_model.annotation = _parse_annotations(model)
+ cobra_model.metadata = _parse_annotations(model)
# Compartments
# FIXME: update with new compartments
compartments = {}
- for (
- compartment
- ) in model.getListOfCompartments(): # noqa: E501 type: libsbml.Compartment
+ compartment: libsbml.Compartment
+ for compartment in model.getListOfCompartments():
cid = _check_required(compartment, compartment.getIdAttribute(), "id")
compartments[cid] = compartment.getName()
cobra_model.compartments = compartments
@@ -671,12 +689,22 @@ def _sbml_to_model(
met = Metabolite(sid)
met.name = specie.getName()
met.notes = _parse_notes_dict(specie)
- met.annotation = _parse_annotations(specie)
+ met.metadata = _parse_annotations(specie)
met.compartment = specie.getCompartment()
specie_fbc: "libsbml.FbcSpeciesPlugin" = specie.getPlugin("fbc")
if specie_fbc:
- met.charge = specie_fbc.getCharge()
+ if specie_fbc.isSetCharge():
+ if specie_fbc.getPackageVersion() >= 3:
+ met.charge = specie_fbc.getChargeAsDouble()
+ else:
+ met.charge = specie_fbc.getCharge()
+ else:
+ LOGGER.warning(
+ "The fbc:charge attribute was not set, setting "
+ f"charge to 0: {specie_fbc}"
+ )
+ met.charge = 0.0
met.formula = specie_fbc.getChemicalFormula() or None
else:
if specie.isSetCharge():
@@ -685,17 +713,16 @@ def _sbml_to_model(
f"discouraged, use fbc:charge instead: {specie}"
)
met.charge = specie.getCharge()
- else:
- if "CHARGE" in met.notes:
- LOGGER.warning(
- f"Use of CHARGE in the notes element is "
- f"discouraged, use fbc:charge instead: {specie}"
- )
- try:
- met.charge = int(met.notes["CHARGE"])
- except ValueError:
- # handle nan, na, NA, ...
- pass
+ elif "CHARGE" in met.notes:
+ LOGGER.warning(
+ f"Use of CHARGE in the notes element is "
+ f"discouraged, use fbc:charge instead: {specie}"
+ )
+ try:
+ met.charge = int(met.notes["CHARGE"])
+ except ValueError:
+ # handle nan, na, NA, ...
+ pass
if "FORMULA" in met.notes:
LOGGER.warning(
@@ -718,7 +745,7 @@ def _sbml_to_model(
ex_rid = f"EX_{met.id}"
ex_reaction = Reaction(ex_rid)
ex_reaction.name = ex_rid
- ex_reaction.annotation = {"sbo": SBO_EXCHANGE_REACTION}
+ ex_reaction.metadata.sbo = [SBO_EXCHANGE_REACTION]
ex_reaction.lower_bound = config.lower_bound
ex_reaction.upper_bound = config.upper_bound
LOGGER.warning(
@@ -732,9 +759,8 @@ def _sbml_to_model(
# Genes
if model_fbc:
- for (
- gp
- ) in model_fbc.getListOfGeneProducts(): # noqa: E501 type: libsbml.GeneProduct
+ gp: "libsbml.GeneProduct"
+ for gp in model_fbc.getListOfGeneProducts():
gid = _check_required(gp, gp.getIdAttribute(), "id")
if f_replace and F_GENE in f_replace:
gid = f_replace[F_GENE](gid)
@@ -742,23 +768,16 @@ def _sbml_to_model(
cobra_gene.name = gp.getName()
if cobra_gene.name is None:
cobra_gene.name = gid
- cobra_gene.annotation = _parse_annotations(gp)
+ cobra_gene.metadata = _parse_annotations(gp)
cobra_gene.notes = _parse_notes_dict(gp)
cobra_model.genes.append(cobra_gene)
else:
- for (
- cobra_reaction
- ) in model.getListOfReactions(): # noqa: E501 type: libsbml.Reaction
+ cobra_reaction: "libsbml.Reaction"
+ for cobra_reaction in model.getListOfReactions():
# fallback to notes information
notes = _parse_notes_dict(cobra_reaction)
- if "GENE ASSOCIATION" in notes:
- gpr = notes["GENE ASSOCIATION"]
- elif "GENE_ASSOCIATION" in notes:
- gpr = notes["GENE_ASSOCIATION"]
- else:
- gpr = ""
-
+ gpr = notes.get("GENE ASSOCIATION", "") or notes.get("GENE_ASSOCIATION", "")
if len(gpr) > 0:
gpr = gpr.replace("(", ";")
gpr = gpr.replace(")", ";")
@@ -822,7 +841,7 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
rid = f_replace[F_REACTION](rid)
cobra_reaction = Reaction(rid)
cobra_reaction.name = reaction.getName().strip()
- cobra_reaction.annotation = _parse_annotations(reaction)
+ cobra_reaction.metadata = _parse_annotations(reaction)
cobra_reaction.notes = _parse_notes_dict(reaction)
# set bounds
@@ -853,14 +872,10 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
elif reaction.isSetKineticLaw():
# some legacy models encode bounds in kinetic laws
klaw: "libsbml.KineticLaw" = reaction.getKineticLaw()
- p_lb = klaw.getParameter(
- "LOWER_BOUND"
- ) # noqa: E501 type: libsbml.LocalParameter
+ p_lb: "libsbml.LocalParameter" = klaw.getParameter("LOWER_BOUND")
if p_lb:
cobra_reaction.lower_bound = p_lb.getValue()
- p_ub = klaw.getParameter(
- "UPPER_BOUND"
- ) # noqa: E501 type: libsbml.LocalParameter
+ p_ub: "libsbml.LocalParameter" = klaw.getParameter("UPPER_BOUND")
if p_ub:
cobra_reaction.upper_bound = p_ub.getValue()
@@ -894,9 +909,8 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
# parse equation
stoichiometry = defaultdict(lambda: 0)
- for (
- sref
- ) in reaction.getListOfReactants(): # noqa: E501 type: libsbml.SpeciesReference
+ sref: "libsbml.SpeciesReference"
+ for sref in reaction.getListOfReactants():
sid = _check_required(sref, sref.getSpecies(), "species")
if f_replace and F_SPECIE in f_replace:
@@ -905,9 +919,7 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
_check_required(sref, sref.getStoichiometry(), "stoichiometry")
)
- for (
- sref
- ) in reaction.getListOfProducts(): # noqa: E501 type: libsbml.SpeciesReference
+ for sref in reaction.getListOfProducts():
sid = _check_required(sref, sref.getSpecies(), "species")
if f_replace and F_SPECIE in f_replace:
@@ -926,24 +938,15 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
# GPR
if r_fbc:
gpr = None
- gpa = (
- r_fbc.getGeneProductAssociation()
- ) # noqa: E501 type: libsbml.GeneProductAssociation
+ gpa: libsbml.GeneProductAssociation = r_fbc.getGeneProductAssociation()
if gpa is not None:
- association = (
- gpa.getAssociation()
- ) # noqa: E501 type: libsbml.FbcAssociation
+ association: libsbml.FbcAssociation = gpa.getAssociation()
gpr = Module(process_association(association))
cobra_reaction.gpr = GPR(gpr_from=gpr)
else:
# fallback to notes information
notes = cobra_reaction.notes
- if "GENE ASSOCIATION" in notes:
- gpr = notes["GENE ASSOCIATION"]
- elif "GENE_ASSOCIATION" in notes:
- gpr = notes["GENE_ASSOCIATION"]
- else:
- gpr = ""
+ gpr = notes.get("GENE ASSOCIATION", "") or notes.get("GENE_ASSOCIATION", "")
if len(gpr) > 0:
LOGGER.warning(
@@ -961,9 +964,7 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
obj_direction = "max"
coefficients = {}
if model_fbc:
- obj_list = (
- model_fbc.getListOfObjectives()
- ) # noqa: E501 type: libsbml.ListOfObjectives
+ obj_list: "libsbml.ListOfObjectives" = model_fbc.getListOfObjectives()
if obj_list is None:
LOGGER.warning("listOfObjectives element not found")
elif obj_list.size() == 0:
@@ -975,11 +976,8 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
obj: "libsbml.Objective" = model_fbc.getObjective(obj_id)
obj_direction = LONG_SHORT_DIRECTION[obj.getType()]
- for (
- flux_obj
- ) in (
- obj.getListOfFluxObjectives()
- ): # noqa: E501 type: libsbml.FluxObjective
+ flux_obj: "libsbml.FluxObjective"
+ for flux_obj in obj.getListOfFluxObjectives():
rid = flux_obj.getReaction()
if f_replace and F_REACTION in f_replace:
rid = f_replace[F_REACTION](rid)
@@ -1055,7 +1053,7 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
cobra_group.name = group.getName()
if group.isSetKind():
cobra_group.kind = group.getKindAsString()
- cobra_group.annotation = _parse_annotations(group)
+ cobra_group.metadata = _parse_annotations(group)
cobra_group.notes = _parse_notes_dict(group)
cobra_members = []
@@ -1112,7 +1110,7 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
if f_replace and F_GROUP in f_replace:
gid = f_replace[F_GROUP](gid)
cobra_group = Group(gid, name=gid, kind="partonomy")
- cobra_group.annotation["sbo"] = "SBO:0000633"
+ cobra_group.metadata.sbo = ["SBO:0000633"]
cobra_group.add_members(cobra_members)
groups.append(cobra_group)
@@ -1141,7 +1139,7 @@ def write_sbml_model(
) -> None:
"""Write cobra model to filename.
- The created model is SBML level 3 version 1 (L1V3) with
+ The created model is SBML level 3 version 2 (L2V3) with
fbc package v2 (fbc-v2).
If the given filename ends with the suffix ".gz" (for example,
@@ -1202,8 +1200,8 @@ def _model_to_sbml(
if f_replace is None:
f_replace = {}
- sbml_ns = libsbml.SBMLNamespaces(3, 1) # SBML L3V1
- sbml_ns.addPackageNamespace("fbc", 2) # fbc-v2
+ sbml_ns = libsbml.SBMLNamespaces(3, 2) # SBML L3V1
+ sbml_ns.addPackageNamespace("fbc", 3) # fbc-v2
doc: "libsbml.SBMLDocument" = libsbml.SBMLDocument(sbml_ns)
doc.setPackageRequired("fbc", False)
@@ -1221,16 +1219,17 @@ def _model_to_sbml(
if cobra_model.name is not None:
model.setName(cobra_model.name)
- # for parsing annotation corresponding to the model
- _sbase_annotations(model, cobra_model.annotation)
+ # for parsing annotation corresponding to the model, including model history
+ _sbase_annotations(model, cobra_model.metadata)
# for parsing notes corresponding to the model
_sbase_notes_dict(model, cobra_model.notes)
# Meta information (ModelHistory) related to SBMLDocument
- if hasattr(cobra_model, "_sbml"):
- meta = cobra_model._sbml
- if "annotation" in meta:
- _sbase_annotations(doc, meta["annotation"])
+ meta = getattr(cobra_model, "_sbml", None)
+ if meta:
+ if "metadata" in meta:
+ _sbase_annotations(doc, meta["metadata"])
+
if "notes" in meta:
_sbase_notes_dict(doc, meta["notes"])
@@ -1249,10 +1248,8 @@ def _model_to_sbml(
"creators"
]: # noqa: E501 type: libsbml.ModelCreator
creator = libsbml.ModelCreator()
- if cobra_creator.get("familyName", None):
- creator.setFamilyName(cobra_creator["familyName"])
- if cobra_creator.get("givenName", None):
- creator.setGivenName(cobra_creator["givenName"])
+ if cobra_creator.get("name", None):
+ creator.setName(cobra_creator["name"])
if cobra_creator.get("organisation", None):
creator.setOrganisation(cobra_creator["organisation"])
if cobra_creator.get("email", None):
@@ -1320,11 +1317,11 @@ def _model_to_sbml(
specie.setCompartment(metabolite.compartment)
s_fbc: "libsbml.FbcSpeciesPlugin" = specie.getPlugin("fbc")
if metabolite.charge is not None:
- s_fbc.setCharge(metabolite.charge)
+ s_fbc.setCharge(float(metabolite.charge))
if metabolite.formula is not None:
s_fbc.setChemicalFormula(metabolite.formula)
- _sbase_annotations(specie, metabolite.annotation)
+ _sbase_annotations(specie, metabolite.metadata)
_sbase_notes_dict(specie, metabolite.notes)
# Genes
@@ -1340,7 +1337,7 @@ def _model_to_sbml(
gp.setName(gname)
gp.setLabel(gid)
- _sbase_annotations(gp, cobra_gene.annotation)
+ _sbase_annotations(gp, cobra_gene.metadata)
_sbase_notes_dict(gp, cobra_gene.notes)
# Objective
@@ -1360,7 +1357,7 @@ def _model_to_sbml(
reaction.setName(cobra_reaction.name)
reaction.setFast(False)
reaction.setReversible((cobra_reaction.lower_bound < 0))
- _sbase_annotations(reaction, cobra_reaction.annotation)
+ _sbase_annotations(reaction, cobra_reaction.metadata)
_sbase_notes_dict(reaction, cobra_reaction.notes)
# stoichiometry
@@ -1369,16 +1366,12 @@ def _model_to_sbml(
if f_replace and F_SPECIE_REV in f_replace:
sid = f_replace[F_SPECIE_REV](sid)
if stoichiometry < 0:
- sref = (
- reaction.createReactant()
- ) # noqa: E501 type: libsbml.SpeciesReference
+ sref: libsbml.SpeciesReference = reaction.createReactant()
sref.setSpecies(sid)
sref.setStoichiometry(-stoichiometry)
sref.setConstant(True)
else:
- sref = (
- reaction.createProduct()
- ) # noqa: E501 type: libsbml.SpeciesReference
+ sref: libsbml.SpeciesReference = reaction.createProduct()
sref.setSpecies(sid)
sref.setStoichiometry(stoichiometry)
sref.setConstant(True)
@@ -1416,18 +1409,14 @@ def _model_to_sbml(
else:
gpr_new = gpr.to_string()
- gpa = (
- r_fbc.createGeneProductAssociation()
- ) # noqa: E501 type: libsbml.GeneProductAssociation
+ gpa: libsbml.GeneProductAssociation = r_fbc.createGeneProductAssociation()
# uses ids to identify GeneProducts (True),
# does not create GeneProducts (False)
_check(gpa.setAssociation(gpr_new, True, False), "set gpr: " + gpr_new)
# objective coefficients
if reaction_coefficients.get(cobra_reaction, 0) != 0:
- flux_obj = (
- objective.createFluxObjective()
- ) # noqa: E501 type: libsbml.FluxObjective
+ flux_obj: libsbml.FluxObjective = objective.createFluxObjective()
flux_obj.setReaction(rid)
flux_obj.setCoefficient(cobra_reaction.objective_coefficient)
@@ -1437,9 +1426,7 @@ def _model_to_sbml(
"http://www.sbml.org/sbml/level3/version1/groups/version1", "groups", True
)
doc.setPackageRequired("groups", False)
- model_group = model.getPlugin(
- "groups"
- ) # noqa: E501 type: libsbml.GroupsModelPlugin
+ model_group: libsbml.GroupsModelPlugin = model.getPlugin("groups")
for cobra_group in cobra_model.groups:
group: "libsbml.Group" = model_group.createGroup()
if f_replace and F_GROUP_REV in f_replace:
@@ -1451,7 +1438,7 @@ def _model_to_sbml(
group.setKind(cobra_group.kind)
_sbase_notes_dict(group, cobra_group.notes)
- _sbase_annotations(group, cobra_group.annotation)
+ _sbase_annotations(group, cobra_group.metadata)
for cobra_member in cobra_group.members:
member: "libsbml.Member" = group.createMember()
@@ -1459,15 +1446,12 @@ def _model_to_sbml(
m_type = str(type(cobra_member))
# id replacements
- if "Reaction" in m_type:
- if f_replace and F_REACTION_REV in f_replace:
- mid = f_replace[F_REACTION_REV](mid)
- if "Metabolite" in m_type:
- if f_replace and F_SPECIE_REV in f_replace:
- mid = f_replace[F_SPECIE_REV](mid)
- if "Gene" in m_type:
- if f_replace and F_GENE_REV in f_replace:
- mid = f_replace[F_GENE_REV](mid)
+ if "Reaction" in m_type and f_replace and F_REACTION_REV in f_replace:
+ mid = f_replace[F_REACTION_REV](mid)
+ if "Metabolite" in m_type and f_replace and F_SPECIE_REV in f_replace:
+ mid = f_replace[F_SPECIE_REV](mid)
+ if "Gene" in m_type and f_replace and F_GENE_REV in f_replace:
+ mid = f_replace[F_GENE_REV](mid)
member.setIdRef(mid)
if cobra_member.name and len(cobra_member.name) > 0:
@@ -1702,6 +1686,7 @@ def _sbase_notes_dict(sbase: libsbml.SBase, notes: dict) -> None:
# -----------------------------------------------------------------------------
# Annotations
# -----------------------------------------------------------------------------
+# TODO: FIX
"""
cobra annotations will be dictionaries of the form:
object.annotation = {
@@ -1720,24 +1705,21 @@ def _sbase_notes_dict(sbase: libsbml.SBase, notes: dict) -> None:
In the current stage the new annotation format is not completely supported yet.
"""
-URL_IDENTIFIERS_PATTERN = re.compile(r"^https?://identifiers.org/(.+?)[:/](.+)")
-
-URL_IDENTIFIERS_PREFIX = "https://identifiers.org"
-QUALIFIER_TYPES = {
- "is": libsbml.BQB_IS,
- "hasPart": libsbml.BQB_HAS_PART,
- "isPartOf": libsbml.BQB_IS_PART_OF,
- "isVersionOf": libsbml.BQB_IS_VERSION_OF,
- "hasVersion": libsbml.BQB_HAS_VERSION,
- "isHomologTo": libsbml.BQB_IS_HOMOLOG_TO,
- "isDescribedBy": libsbml.BQB_IS_DESCRIBED_BY,
- "isEncodedBy": libsbml.BQB_IS_ENCODED_BY,
- "encodes": libsbml.BQB_ENCODES,
- "occursIn": libsbml.BQB_OCCURS_IN,
- "hasProperty": libsbml.BQB_HAS_PROPERTY,
- "isPropertyOf": libsbml.BQB_IS_PROPERTY_OF,
- "hasTaxon": libsbml.BQB_HAS_TAXON,
- "unknown": libsbml.BQB_UNKNOWN,
+QUALIFIER_TYPES_COBRA_SBML_DICT = {
+ "bqb_is": libsbml.BQB_IS,
+ "bqb_hasPart": libsbml.BQB_HAS_PART,
+ "bqb_isPartOf": libsbml.BQB_IS_PART_OF,
+ "bqb_isVersionOf": libsbml.BQB_IS_VERSION_OF,
+ "bqb_hasVersion": libsbml.BQB_HAS_VERSION,
+ "bqb_isHomologTo": libsbml.BQB_IS_HOMOLOG_TO,
+ "bqb_isDescribedBy": libsbml.BQB_IS_DESCRIBED_BY,
+ "bqb_isEncodedBy": libsbml.BQB_IS_ENCODED_BY,
+ "bqb_encodes": libsbml.BQB_ENCODES,
+ "bqb_occursIn": libsbml.BQB_OCCURS_IN,
+ "bqb_hasProperty": libsbml.BQB_HAS_PROPERTY,
+ "bqb_isPropertyOf": libsbml.BQB_IS_PROPERTY_OF,
+ "bqb_hasTaxon": libsbml.BQB_HAS_TAXON,
+ "bqb_unknown": libsbml.BQB_UNKNOWN,
"bqm_is": libsbml.BQM_IS,
"bqm_isDescribedBy": libsbml.BQM_IS_DESCRIBED_BY,
"bqm_isDerivedFrom": libsbml.BQM_IS_DERIVED_FROM,
@@ -1745,12 +1727,33 @@ def _sbase_notes_dict(sbase: libsbml.SBase, notes: dict) -> None:
"bqm_hasInstance": libsbml.BQM_HAS_INSTANCE,
"bqm_unknown": libsbml.BQM_UNKNOWN,
}
+BIOLOGY_QUALIFIER_TYPES_TO_COBRA_DICT = {
+ value: key
+ for key, value in QUALIFIER_TYPES_COBRA_SBML_DICT.items()
+ if re.match("bqb", key)
+}
+MODEL_QUALIFIER_TYPES_TO_COBRA_DICT = {
+ value: key
+ for key, value in QUALIFIER_TYPES_COBRA_SBML_DICT.items()
+ if re.match("bqm", key)
+}
-def _parse_annotations(sbase: libsbml.SBase) -> dict:
+def _parse_annotations(sbase: libsbml.SBase) -> Metadata:
"""Parse cobra annotations from a given SBase object.
- Annotations are dictionaries with the providers as keys.
+ The annotation format has been changed. We no longer have
+ simple dictionaries for storing annotation data. Dedicated
+ classes for storing CVTerm data, History data and key-value
+ pair data corresponding to an SBase object have been made.
+ The metadata classes inside cobra.core directory contains
+ of them. All the existing issues in old annotation format have
+ been solved. The new format annotation is completely backward
+ compatible. It can read models with old annotation format,
+ can convert old format annotation to new format annotation,
+ and writes annotation in new format only (for JSON and other
+ formats). The JSON schema v2 specifies the new format annotation
+ whereas JSON schema v1 have annotation data defined in old format.
Parameters
----------
@@ -1759,155 +1762,308 @@ def _parse_annotations(sbase: libsbml.SBase) -> dict:
Returns
-------
- dict (annotation dictionary)
+ Metadata
+ a metadata object storing COBRA annotation
"""
- # FIXME: annotation format must be updated (this is a big collection of
- # fixes) - see: https://github.com/opencobra/cobrapy/issues/684)
- annotation = {}
+ annotations = Metadata()
# SBO term
if sbase.isSetSBOTerm():
- # FIXME: correct handling of annotations
- annotation["sbo"] = sbase.getSBOTermID()
+ annotations.sbo = sbase.getSBOTermID()
+
+ def _kvpair_to_cobra(_kvpair: "libsbml.KeyValuePair") -> Optional[CustomAnnotation]:
+ """Parse the libsbml.KeyValuePair object to a cobra CustomAnnotation.
+
+ Parameters
+ ----------
+ _kvpair : libsbml.KeyValuePair
+ The libsbml.KeyValuePair object from which data is to be parsed.
+
+ Returns
+ -------
+ CustomAnnotation or None
+ The parsed data of the given libsbml.KeyValuePair object as
+ CustomAnnotation. If no key is set in the key-value pair, this function will
+ return None.
+ """
+ if not _kvpair.isSetKey():
+ return None
+ ca = CustomAnnotation(
+ key=_kvpair.getKey(),
+ value=(_kvpair.getValue() if _kvpair.isSetValue() else None),
+ uri=(_kvpair.getUri() if _kvpair.isSetUri() else None),
+ )
+ if _kvpair.isSetName():
+ ca.name = _kvpair.getName()
+ if _kvpair.isSetId():
+ ca.id = _kvpair.getId()
+
+ ca.metadata = _parse_annotations(_kvpair)
+ return ca
+
+ # Custom key-value pair annotations.
+ if not isinstance(sbase, libsbml.SBMLDocument):
+ sbase_fbc: "libsbml.FbcSBasePlugin" = sbase.getPlugin("fbc")
+ if sbase_fbc:
+ # We should probably do a FBC version check. But right now the version seems
+ # stuck at 2, even though it is defined as 3 in a SBML file.
+ if sbase_fbc.getNumKeyValuePairs() > 0:
+ for kvp in sbase_fbc.getListOfKeyValuePairs():
+ if (ca := _kvpair_to_cobra(kvp)) is not None:
+ annotations.custom.add(ca)
+
+ def _cvterm_to_cobra(_cvterm: "libsbml.CVTerm") -> Optional[StandardizedAnnotation]:
+ """Parse the libsbml.CVTerm object to cobra StandardizedAnnotation.
+
+ Parameters
+ ----------
+ _cvterm : libsbml.CVTerm
+ The libsbml.CVTerm object from which data is to be parsed.
+
+ Returns
+ -------
+ StandardizedAnnotation or None
+ The parsed data of the given libsbml.CVTerm object as
+ StandardizedAnnotation. If the qualifier is unknown, this function will
+ return None.
+ """
+ qualifier_type = _cvterm.getQualifierType()
+ if qualifier_type == libsbml.BIOLOGICAL_QUALIFIER:
+ qualifier = BIOLOGY_QUALIFIER_TYPES_TO_COBRA_DICT[
+ _cvterm.getBiologicalQualifierType()
+ ]
+ elif qualifier_type == libsbml.MODEL_QUALIFIER:
+ qualifier = MODEL_QUALIFIER_TYPES_TO_COBRA_DICT[
+ _cvterm.getModelQualifierType()
+ ]
+ else:
+ LOGGER.warning(f"The cvterm {_cvterm} has an unkown qualifier. Ignoring it")
+ return None
+ resources = [
+ # Prefer loading models over having strictly correct annotations
+ Resource(_cvterm.getResourceURI(k), strict=False)
+ for k in range(_cvterm.getNumResources())
+ ]
+
+ nested_cv_terms = [
+ _cvterm.getNestedCVTerm(index)
+ for index in range(_cvterm.getNumNestedCVTerms())
+ ]
+ # This kludge is necessary since _cvterm.getListNestedCVTerms() doesn't give a
+ # python list, but a Swig List_t * and then SwigPyObject is not iterable
+ nested_data = [
+ cobra_cvterm
+ for _nested_cvterm in nested_cv_terms
+ if _nested_cvterm is not None
+ and (cobra_cvterm := _cvterm_to_cobra(_nested_cvterm)) is not None
+ ]
+ return StandardizedAnnotation(
+ resources=resources, qualifier=qualifier, annotations=nested_data
+ )
# RDF annotation
cvterms = sbase.getCVTerms()
- if cvterms is None:
- return annotation
+ if cvterms is not None:
+ annotations.add_standardized(
+ [
+ cobra_cvterm
+ for cvterm in cvterms
+ if cvterm is not None
+ and (cobra_cvterm := _cvterm_to_cobra(cvterm)) is not None
+ ]
+ )
- cvterm: "libsbml.CVTerm"
- for cvterm in cvterms:
- for k in range(cvterm.getNumResources()):
- # FIXME: read and store the qualifier
+ # history of the component
+ # TODO: Should we maybe keep track of the creators and reference the same object
+ # when there is a match? This would reduce the number of objects created and
+ # facilitate fixing a mistake.
+ if sbase.isSetModelHistory():
+ model_history: "libsbml.ModelHistory" = sbase.getModelHistory()
+ annotations.history.creators = [
+ (
+ Creator(
+ name=creator.getName() or None,
+ email=creator.getEmail() or None,
+ organisation=creator.getOrganisation() or None,
+ )
+ if creator.isSetName()
+ else Creator(
+ given_name=creator.getGivenName() or None,
+ family_name=creator.getFamilyName() or None,
+ email=creator.getEmail() or None,
+ organisation=creator.getOrganisation() or None,
+ )
+ )
+ for creator in model_history.getListCreators()
+ ]
- uri = cvterm.getResourceURI(k)
- data = _parse_annotation_info(uri)
- if data is None:
- continue
- else:
- provider, identifier = data
-
- if provider in annotation:
- if isinstance(annotation[provider], str):
- annotation[provider] = [annotation[provider]]
- # FIXME: use a list
- if identifier not in annotation[provider]:
- annotation[provider].append(identifier)
- else:
- # FIXME: always in list
- annotation[provider] = identifier
+ if model_history.isSetCreatedDate():
+ date: libsbml.Date = model_history.getCreatedDate()
+ annotations.history.created_date = date.getDateAsString()
- return annotation
+ annotations.history.modified_dates = [
+ _date.getDateAsString() for _date in model_history.getListModifiedDates()
+ ]
+ return annotations
-def _parse_annotation_info(uri: str) -> Union[None, Tuple[str, str]]:
- """Parse provider and term from given identifiers annotation uri.
+
+def _add_custom_annotations_to_sbase_fbc(
+ sbase_fbc: "libsbml.FbcSBasePlugin",
+ custom_ann: CustomAnnotationStore,
+) -> None:
+ """Convert cobra CustomAnnotations to libsbml.KeyValuePair and add to SBase object.
Parameters
----------
- uri : str
- uri (identifiers.org url)
+ sbase_fbc: libsbml.FbcSBasePlugin
+ custom_ann: CustomAnnotationStore
+ cobra CustomAnnotationStore object
+ """
+ for ca in custom_ann.values():
+ kvp: "libsbml.KeyValuePair" = sbase_fbc.createKeyValuePair()
+ kvp.setKey(ca.key)
+ if ca.value is not None:
+ kvp.setValue(ca.value)
+ if ca.uri is not None:
+ kvp.setUri(ca.uri)
+ if ca.id is not None:
+ kvp.setId(ca.id)
+ if ca.name is not None:
+ kvp.setName(ca.name)
+ _sbase_annotations(kvp, ca.metadata)
+ # FIX: This is currently not written to the file, since libsbml has not
+ # implemented that yet.
+
+
+def _cvterms_to_sbml(cvterms: StandardizedAnnotationStore) -> List["libsbml.CVTerm"]:
+ """Convert cobra StandardizedAnnotationStore to libsbml.CVTerm list.
+
+ Parameters
+ ----------
+ cvterms: StandardizedAnnotationStore
+ cobra StandardizedAnnotationStore object
Returns
-------
- (provider, identifier) if resolvable, None otherwise
+ list
+ List of libsbml.CVTerm
"""
- match = URL_IDENTIFIERS_PATTERN.match(uri)
- if match:
- provider, identifier = match.group(1), match.group(2)
- if provider.isupper():
- identifier = f"{provider}:{identifier}"
- provider = provider.lower()
- else:
- LOGGER.warning(
- f"{uri} does not conform to "
- f"'http(s)://identifiers.org/collection/id' or"
- f"'http(s)://identifiers.org/COLLECTION:id"
- )
- return None
+ cv_list = []
+ for cvterm in cvterms:
+ qualifier = cvterm.qualifier
+ if qualifier.value.startswith("bqb"):
+ qualifier_type = libsbml.BIOLOGICAL_QUALIFIER
+ elif qualifier.value.startswith("bqm"):
+ qualifier_type = libsbml.MODEL_QUALIFIER
+ else:
+ raise CobraSBMLError(f"Unsupported qualifier: {qualifier}")
+
+ cv: "libsbml.CVTerm" = libsbml.CVTerm()
+ cv.setQualifierType(qualifier_type)
+ if qualifier_type == libsbml.BIOLOGICAL_QUALIFIER:
+ cv.setBiologicalQualifierType(
+ QUALIFIER_TYPES_COBRA_SBML_DICT[qualifier.value]
+ )
+ elif qualifier_type == libsbml.MODEL_QUALIFIER:
+ cv.setModelQualifierType(QUALIFIER_TYPES_COBRA_SBML_DICT[qualifier.value])
+ else:
+ raise CobraSBMLError(f"Unsupported qualifier: {qualifier}")
+ for uri in sorted(x.uri for x in cvterm.resources):
+ cv.addResource(uri)
+
+ for _cv in _cvterms_to_sbml(cvterm.annotations):
+ _check(cv.addNestedCVTerm(_cv), f"Adding nested cvterm: {_cv}")
+
+ cv_list.append(cv)
- return provider, identifier
+ return cv_list
-def _sbase_annotations(sbase: libsbml.SBase, annotation: dict) -> None:
+def _sbase_annotations(sbase: libsbml.SBase, annotations: Metadata) -> None:
"""Set SBase annotations based on cobra annotations.
Parameters
----------
sbase : libsbml.SBase
SBML object to annotate
- annotation : dict, cobra annotation structure
+ annotations : dict, cobra annotation structure
cobra object with annotation information
Raises
------
CobraSBMLError for unsupported qualifier
"""
- # FIXME: annotation format must be updated
- # (https://github.com/opencobra/cobrapy/issues/684)
- if not annotation or len(annotation) == 0:
- return
-
- # standardize annotations
- annotation_data = deepcopy(annotation)
- for key, value in annotation_data.items():
- # handling of non-string annotations (e.g. integers)
- if isinstance(value, (float, int)):
- value = str(value)
- if isinstance(value, str):
- annotation_data[key] = [("is", value)]
+ if not isinstance(annotations, Metadata):
+ raise TypeError(
+ f"The annotations object must be of type 'Metadata': {annotations}"
+ )
- for _key, value in annotation_data.items():
- for idx, item in enumerate(value):
- if isinstance(item, str):
- value[idx] = ("is", item)
+ if (sbo_term := getattr(annotations, "sbo", None)) is not None and sbo_term != "":
+ if isinstance(sbo_term, list):
+ sbo_term = sbo_term[0]
+ _check(sbase.setSBOTerm(sbo_term), f"Setting SBOTerm: {sbo_term}")
# set metaId
+ # TODO: Set Id + MetaID when none was set (KeyValuePair)
meta_id = f"meta_{sbase.getId()}"
sbase.setMetaId(meta_id)
- # rdf_items = []
- for provider, data in annotation_data.items():
- # set SBOTerm
- if provider in ["SBO", "sbo"]:
- if provider == "SBO":
- LOGGER.warning(
- "'SBO' provider is deprecated, use 'sbo' provider instead"
- )
- sbo_term = data[0][1]
- _check(sbase.setSBOTerm(sbo_term), f"Setting SBOTerm: {sbo_term}")
-
- # FIXME: sbo should also be written as CVTerm
- continue
-
- for item in data:
- qualifier_str, entity = item[0], item[1]
- qualifier = QUALIFIER_TYPES.get(qualifier_str, None)
- if qualifier is None:
- qualifier = libsbml.BQB_IS
- LOGGER.error(
- f"Qualifier type is not supported on annotation: '{qualifier_str}'"
- )
+ # Custom key-value pair annotations.
+ if annotations.custom:
+ if not isinstance(sbase, libsbml.SBMLDocument):
+ sbase_fbc: "libsbml.FbcSBasePlugin" = sbase.getPlugin("fbc")
+ if sbase_fbc:
+ _add_custom_annotations_to_sbase_fbc(sbase_fbc, annotations.custom)
+
+ # set standardized
+ # Question for @matthiaskoenig - should I be using createCVTerms?
+ for cv in _cvterms_to_sbml(annotations.standardized):
+ _check(sbase.addCVTerm(cv, newBag=True), f"Setting cvterm: {cv}")
+
+ # set history
+ if not annotations.history.is_empty():
+ comp_history = libsbml.ModelHistory()
+
+ for creator in annotations.history.creators:
+ comp_creator = libsbml.ModelCreator()
+ if creator.name:
+ comp_creator.setName(creator.name)
+ if creator.email:
+ comp_creator.setEmail(creator.email)
+ if creator.organisation:
+ comp_creator.setOrganisation(creator.organisation)
+ _check(
+ comp_history.addCreator(comp_creator),
+ f"adding creator to {sbase.getId}.",
+ )
- qualifier_type = libsbml.BIOLOGICAL_QUALIFIER
- if qualifier_str.startswith("bqm_"):
- qualifier_type = libsbml.MODEL_QUALIFIER
-
- cv: "libsbml.CVTerm" = libsbml.CVTerm()
- cv.setQualifierType(qualifier_type)
- if qualifier_type == libsbml.BIOLOGICAL_QUALIFIER:
- cv.setBiologicalQualifierType(qualifier)
- elif qualifier_type == libsbml.MODEL_QUALIFIER:
- cv.setModelQualifierType(qualifier)
- else:
- raise CobraSBMLError(f"Unsupported qualifier: {qualifier}")
- resource = f"{URL_IDENTIFIERS_PREFIX}/{provider}/{entity}"
- cv.addResource(resource)
+ if annotations.history.created_date:
+ date = libsbml.Date(
+ annotations.history.created_date.strftime(STRTIME_FORMAT)
+ )
_check(
- sbase.addCVTerm(cv),
- f"Setting cvterm: {cv}, resource: {resource}",
+ comp_history.setCreatedDate(date), f"set creation date for {sbase.id}"
)
+ elif isinstance(sbase, libsbml.SBMLDocument):
+ time = datetime.datetime.now()
+ timestr = time.strftime(STRTIME_FORMAT)
+ date = libsbml.Date(timestr)
+ _check(comp_history.setCreatedDate(date), "set creation date for document")
+
+ for modified_date in annotations.history.modified_dates:
+ date = libsbml.Date(modified_date.strftime(STRTIME_FORMAT))
+ _check(
+ comp_history.addModifiedDate(date),
+ f"add modification date for {sbase.id}",
+ )
+
+ # finally add the compo_history
+ _check(
+ sbase.setModelHistory(comp_history),
+ f"Setting ModelHistory: {comp_history}",
+ )
# -----------------------------------------------------------------------------
@@ -1954,17 +2110,30 @@ def validate_sbml_model(
from the libsbml validator. COBRA_* types are from the cobrapy SBML
parser.
"""
- keys = (
- "SBML_FATAL",
- "SBML_ERROR",
- "SBML_SCHEMA_ERROR",
- "SBML_WARNING",
- "COBRA_FATAL",
- "COBRA_ERROR",
- "COBRA_WARNING",
- "COBRA_CHECK",
- )
- errors = {key: [] for key in keys}
+ cobra_sbml_error_dict = {
+ "SBML_FATAL": libsbml.LIBSBML_SEV_FATAL,
+ "SBML_ERROR": libsbml.LIBSBML_SEV_ERROR,
+ "SBML_SCHEMA_ERROR": libsbml.LIBSBML_SEV_SCHEMA_ERROR,
+ "SBML_WARNING": libsbml.LIBSBML_SEV_WARNING,
+ "COBRA_FATAL": None,
+ "COBRA_ERROR": None,
+ "COBRA_WARNING": None,
+ "COBRA_CHECK": None,
+ }
+ sbml_severity_dict = {
+ value: key for key, value in cobra_sbml_error_dict.items() if value
+ }
+ errors = {key: [] for key in cobra_sbml_error_dict.keys()}
+ sbml_log_dict = {
+ "SBML_FATAL": "SBML errors",
+ "SBML_ERROR": "SBML errors",
+ "SBML_SCHEMA_ERROR": "SBML errors",
+ "SBML_WARNING": "SBML warnings",
+ "COBRA_FATAL": "COBRA errors",
+ "COBRA_ERROR": "COBRA errors",
+ "COBRA_WARNING": "COBRA warnings",
+ "COBRA_CHECK": "COBRA warnings",
+ }
# [1] libsbml validation
doc: "libsbml.SBMLDocument" = _get_doc_from_filename(filename)
@@ -1986,14 +2155,7 @@ def validate_sbml_model(
e: "libsbml.SBMLError" = doc.getError(k)
msg = _error_string(e, k=k)
sev = e.getSeverity()
- if sev == libsbml.LIBSBML_SEV_FATAL:
- errors["SBML_FATAL"].append(msg)
- elif sev == libsbml.LIBSBML_SEV_ERROR:
- errors["SBML_ERROR"].append(msg)
- elif sev == libsbml.LIBSBML_SEV_SCHEMA_ERROR:
- errors["SBML_SCHEMA_ERROR"].append(msg)
- elif sev == libsbml.LIBSBML_SEV_WARNING:
- errors["SBML_WARNING"].append(msg)
+ errors[sbml_severity_dict[sev]].append(msg)
# [2] cobrapy validation (check that SBML can be read into model)
# all warnings generated while loading will be logged as errors
@@ -2010,10 +2172,10 @@ def validate_sbml_model(
model = _sbml_to_model(doc, **kwargs)
except CobraSBMLError as e:
errors["COBRA_ERROR"].append(str(e))
- return None, errors
+ model = None # If we return, we won't get to the errors["COBRA_ERROR"]
except Exception as e:
errors["COBRA_FATAL"].append(str(e))
- return None, errors
+ model = None
cobra_errors = log_stream.getvalue().split("\n")
for cobra_error in cobra_errors:
@@ -2034,21 +2196,11 @@ def validate_sbml_model(
if check_model:
errors["COBRA_CHECK"].extend(check_metabolite_compartment_formula(model))
- for key in ["SBML_FATAL", "SBML_ERROR", "SBML_SCHEMA_ERROR"]:
- if len(errors[key]) > 0:
- LOGGER.error("SBML errors in validation, check error log for details.")
- break
- for key in ["SBML_WARNING"]:
+ for key in sbml_log_dict.keys():
if len(errors[key]) > 0:
- LOGGER.error("SBML warnings in validation, check error log for details.")
- break
- for key in ["COBRA_FATAL", "COBRA_ERROR"]:
- if len(errors[key]) > 0:
- LOGGER.error("COBRA errors in validation, check error log for details.")
- break
- for key in ["COBRA_WARNING", "COBRA_CHECK"]:
- if len(errors[key]) > 0:
- LOGGER.error("COBRA warnings in validation, check error log for details.")
+ LOGGER.error(
+ f"{sbml_log_dict[key]} in validation, check error log for details."
+ )
break
return model, errors
diff --git a/src/cobra/io/schema_v1.json b/src/cobra/io/schema_v1.json
index edc9756fb..8fd7cb0a4 100644
--- a/src/cobra/io/schema_v1.json
+++ b/src/cobra/io/schema_v1.json
@@ -153,5 +153,5 @@
"metabolites",
"genes"
],
- "additionalProperties": false
+ "additionalProperties": true
}
diff --git a/src/cobra/io/schema_v2.json b/src/cobra/io/schema_v2.json
new file mode 100644
index 000000000..96779f464
--- /dev/null
+++ b/src/cobra/io/schema_v2.json
@@ -0,0 +1,349 @@
+{
+ "$schema": "http://json-schema.org/draft-04/schema#",
+ "title": "COBRA",
+ "description": "JSON representation of COBRA model",
+ "definitions": {
+ "metadata": {
+ "type": "object",
+ "properties": {
+ "sbo": {
+ "type": "string"
+ },
+ "standardized": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "qualifiers": {
+ "type": "string"
+ },
+ "resources": {
+ "type": "array",
+ "items": {
+ "type": "string"
+ }
+ },
+ "annotations": {
+ "$ref": "#/definitions/metadata/standardized"
+ }
+ }
+ }
+ },
+ "history": {
+ "type": "object",
+ "properties": {
+ "creators": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "email": {
+ "type": "string"
+ },
+ "name": {
+ "type": "string"
+ },
+ "organisation": {
+ "type": "string"
+ }
+ },
+ "required": ["name"],
+ "additionalProperties": false
+ }
+ },
+ "created_date": {
+ "type": "string",
+ "format": "date-time"
+ },
+ "modified_dates": {
+ "type": "array",
+ "items": {
+ "type": "string",
+ "format": "date-time"
+ }
+ }
+ },
+ "required": ["creators", "created_date", "modified_dates"],
+ "additionalProperties": false
+ },
+ "custom": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "key": {
+ "type": "string"
+ },
+ "value": {
+ "type": "string"
+ },
+ "uri": {
+ "type": "string"
+ },
+ "metadata": {
+ "$ref": "#/definitions/metadata"
+ }
+ },
+ "required": ["key"],
+ "additionalProperties": false
+ }
+ }
+ }
+ }
+ },
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "version": {
+ "type": "string",
+ "default": "1"
+ },
+ "reactions": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "metabolites": {
+ "type": "object",
+ "patternProperties": {
+ ".*": {
+ "type": "number"
+ }
+ }
+ },
+ "gene_reaction_rule": {
+ "type": "string"
+ },
+ "lower_bound": {
+ "type": "number"
+ },
+ "upper_bound": {
+ "type": "number"
+ },
+ "objective_coefficient": {
+ "type": "number",
+ "default": 0
+ },
+ "subsystem": {
+ "type": "string"
+ },
+ "notes": {
+ "type": "string"
+ },
+ "metadata": {
+ "$ref": "#/definitions/metadata"
+ }
+ },
+ "required": [
+ "id",
+ "name",
+ "metabolites",
+ "lower_bound",
+ "upper_bound",
+ "gene_reaction_rule"
+ ],
+ "additionalProperties": false
+ }
+ },
+ "metabolites": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "compartment": {
+ "type": "string",
+ "pattern": "[a-z]{1,2}"
+ },
+ "charge": {
+ "type": "number"
+ },
+ "formula": {
+ "type": "string"
+ },
+ "_bound": {
+ "type": "number",
+ "default": 0
+ },
+ "notes": {
+ "type": "string"
+ },
+ "metadata": {
+ "$ref": "#/definitions/metadata"
+ }
+ },
+ "required": ["id", "name", "compartment"],
+ "additionalProperties": false
+ }
+ },
+ "genes": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "notes": {
+ "type": "string"
+ },
+ "metadata": {
+ "$ref": "#/definitions/metadata"
+ }
+ },
+ "required": ["id", "name"],
+ "additionalProperties": false
+ }
+ },
+ "compartments": {
+ "type": "object",
+ "patternProperties": {
+ "[a-z]{1,2}": {
+ "type": "string"
+ }
+ }
+ },
+ "groups": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "notes": {
+ "type": "string"
+ },
+ "metadata": {
+ "$ref": "#/definitions/metadata"
+ },
+ "kind": {
+ "type": "string",
+ "enum": ["collection", "classification", "partonomy"]
+ },
+ "members": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "idRef": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "type": {
+ "type": "string"
+ }
+ },
+ "required": ["idRef", "type"]
+ }
+ }
+ },
+ "required": ["kind", "members"]
+ }
+ },
+ "user_defined_constraints": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "lower_bound": {
+ "type": "number"
+ },
+ "upper_bound": {
+ "type": "number"
+ },
+ "constraint_comps": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "coefficient": {
+ "type": "number"
+ },
+ "variable": {
+ "type": "string"
+ },
+ "variable_type": {
+ "type": "string",
+ "enum": ["linear", "quadratic"]
+ },
+ "notes": {
+ "type": "string"
+ },
+ "metadata": {
+ "$ref": "#/definitions/metadata"
+ }
+ },
+ "required": ["variable"],
+ "additionalProperties": false
+ }
+ },
+ "notes": {
+ "type": "string"
+ },
+ "metadata": {
+ "$ref": "#/definitions/metadata"
+ }
+ },
+ "required": ["lower_bound", "upper_bound", "constraint_comps"],
+ "additionalProperties": false
+ }
+ },
+ "notes": {
+ "type": "string"
+ },
+ "metadata": {
+ "$ref": "#/definitions/metadata"
+ }
+ },
+ "required": ["id", "reactions", "metabolites", "genes"],
+ "additionalProperties": true
+}
diff --git a/src/cobra/manipulation/annotate.py b/src/cobra/manipulation/annotate.py
index 6f989dd2a..9bad70d41 100644
--- a/src/cobra/manipulation/annotate.py
+++ b/src/cobra/manipulation/annotate.py
@@ -22,15 +22,18 @@ def add_SBO(model: "Model") -> None:
The model whose demand and exchange reactions need to be annotated.
"""
+ # ??? Should this be done with boundary?
for r in model.reactions:
# don't annotate already annotated reactions
- if r.annotation.get("sbo"):
+ if len(r.annotation.get("sbo")) != 0 and r.annotation.sbo:
continue
# only doing exchanges
if len(r.metabolites) != 1:
continue
met_id = list(r._metabolites)[0].id
if r.id.startswith("EX_") and r.id == "EX_" + met_id:
- r.annotation["sbo"] = "SBO:0000627"
+ r.annotation["sbo"] = ["SBO:0000627"]
elif r.id.startswith("DM_") and r.id == "DM_" + met_id:
- r.annotation["sbo"] = "SBO:0000628"
+ r.annotation["sbo"] = ["SBO:0000628"]
+ elif r.id.startswith("SK_") and r.id == "SK_" + met_id:
+ r.annotation["sbo"] = ["SBO:0000632"]
diff --git a/src/cobra/manipulation/validate.py b/src/cobra/manipulation/validate.py
index 344a05437..34c821690 100644
--- a/src/cobra/manipulation/validate.py
+++ b/src/cobra/manipulation/validate.py
@@ -33,7 +33,7 @@ def check_mass_balance(model: "Model") -> Dict["Reaction", Dict["Metabolite", fl
"""
unbalanced = {}
for reaction in model.reactions:
- if reaction.annotation.get("sbo") not in _NOT_MASS_BALANCED_TERMS:
+ if set(reaction.annotation.get("sbo", [])).isdisjoint(_NOT_MASS_BALANCED_TERMS):
balance = reaction.check_mass_balance()
if balance:
unbalanced[reaction] = balance
diff --git a/src/cobra/medium/boundary_types.py b/src/cobra/medium/boundary_types.py
index 971480f57..6a6811224 100644
--- a/src/cobra/medium/boundary_types.py
+++ b/src/cobra/medium/boundary_types.py
@@ -128,9 +128,9 @@ def is_boundary_type(
"""
# Check if the reaction has an annotation. Annotations dominate everything.
sbo_term = reaction.annotation.get("sbo", "")
- if isinstance(sbo_term, list):
+ if isinstance(sbo_term, list) and len(sbo_term) != 0:
sbo_term = sbo_term[0]
- sbo_term = sbo_term.upper()
+ sbo_term = sbo_term.upper()
if sbo_term == sbo_terms[boundary_type]:
return True
diff --git a/tests/conftest.py b/tests/conftest.py
index 6c63f84f5..31a062e8e 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -23,7 +23,7 @@ def create_test_model(model_name: str = "salmonella") -> Model:
Parameters
----------
model_name: str
- One of 'ecoli', 'textbook', or 'salmonella', or the
+ One of 'ecoli', 'textbook', or 'salmonella', 'ecoli_annotation' or the
path to a pickled cobra.Model .
Returns
@@ -46,6 +46,14 @@ def create_test_model(model_name: str = "salmonella") -> Model:
elif model_name == "mini":
mini_sbml = str((data_dir / "mini_fbc2.xml").resolve())
return read_sbml_model(mini_sbml)
+ elif model_name == "ecoli_annotation":
+ ecoli_annotation_sbml = str(
+ (data_dir / "e_coli_core_for_annotation.xml").resolve()
+ )
+ return read_sbml_model(ecoli_annotation_sbml)
+ elif model_name == "complex_annotation":
+ complex_annotation_sbml = str((data_dir / "annotation_complex.xml").resolve())
+ return read_sbml_model(complex_annotation_sbml)
elif model_name == "salmonella":
salmonella_pickle = str((data_dir / "salmonella.pickle").resolve())
model_name = salmonella_pickle
@@ -113,6 +121,30 @@ def salmonella(medium_model: Model) -> Model:
return medium_model.copy()
+@pytest.fixture(scope="session")
+def ecoli_annotation_model() -> Model:
+ """Provide session-level fixture for ecoli_annotation model."""
+ return create_test_model("ecoli_annotation")
+
+
+@pytest.fixture(scope="function")
+def annotation_model(ecoli_annotation_model: Model) -> Model:
+ """Provide function-level fixture for ecoli_annotation model."""
+ return ecoli_annotation_model.copy()
+
+
+@pytest.fixture(scope="session")
+def complex_annotation_model() -> Model:
+ """Provide session-level fixture for complex_annotation model."""
+ return create_test_model("complex_annotation")
+
+
+@pytest.fixture(scope="function")
+def complex_model(complex_annotation_model: Model) -> Model:
+ """Provide function-level fixture for complex_annotation model."""
+ return complex_annotation_model.copy()
+
+
@pytest.fixture(scope="function")
def solved_model(data_directory: Path) -> Tuple[Solution, Model]:
"""Provide function-level fixture for solved textbook model."""
diff --git a/tests/data/annotation_complex.xml b/tests/data/annotation_complex.xml
new file mode 100644
index 000000000..fb1a2f54a
--- /dev/null
+++ b/tests/data/annotation_complex.xml
@@ -0,0 +1,1477 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/tests/data/cvterms_nested.json b/tests/data/cvterms_nested.json
new file mode 100644
index 000000000..87c2c9315
--- /dev/null
+++ b/tests/data/cvterms_nested.json
@@ -0,0 +1,27 @@
+[
+ {
+ "resources": [
+ "https://identifiers.org/uniprot/P69905",
+ "https://identifiers.org/uniprot/P68871",
+ "https://identifiers.org/kegg.compound/C00032"
+ ],
+ "qualifier": "bqb_hasPart"
+ },
+ {
+ "qualifier": "bqb_hasPart",
+ "resources": [
+ "https://identifiers.org/uniprot/P69905",
+ "https://www.uniprot.org/uniprot/P68871",
+ "https://identifiers.org/chebi/CHEBI:17627"
+ ],
+ "annotations": [
+ {
+ "qualifier": "bqb_isDescribedBy",
+ "resources": [
+ "https://identifiers.org/pubmed/1111111",
+ "https://identifiers.org/eco/000000"
+ ]
+ }
+ ]
+ }
+]
diff --git a/tests/data/e_coli_core.json b/tests/data/e_coli_core.json
new file mode 100644
index 000000000..39db77321
--- /dev/null
+++ b/tests/data/e_coli_core.json
@@ -0,0 +1,14786 @@
+{
+"metabolites":[
+{
+"id":"glc__D_e",
+"name":"D-Glucose",
+"compartment":"e",
+"charge":0,
+"formula":"C6H12O6",
+"notes":{
+"original_bigg_ids":[
+"glc_D_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"glc__D"
+],
+"biocyc":[
+"META:Glucopyranose"
+],
+"chebi":[
+"CHEBI:12965",
+"CHEBI:20999",
+"CHEBI:4167",
+"CHEBI:17634"
+],
+"hmdb":[
+"HMDB00122",
+"HMDB06564"
+],
+"inchi_key":[
+"WQZGKKKJIJFFOK-GASJEMHNSA-N"
+],
+"kegg.compound":[
+"C00031"
+],
+"kegg.drug":[
+"D00009"
+],
+"metanetx.chemical":[
+"MNXM41"
+],
+"sabiork":[
+"1406",
+"1407"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd26821",
+"cpd00027"
+]
+}
+},
+{
+"id":"gln__L_c",
+"name":"L-Glutamine",
+"compartment":"c",
+"charge":0,
+"formula":"C5H10N2O3",
+"notes":{
+"original_bigg_ids":[
+"gln_L_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"gln__L"
+],
+"biocyc":[
+"META:GLN"
+],
+"chebi":[
+"CHEBI:42943",
+"CHEBI:42899",
+"CHEBI:32679",
+"CHEBI:32678",
+"CHEBI:58359",
+"CHEBI:28300",
+"CHEBI:42812",
+"CHEBI:13110",
+"CHEBI:18050",
+"CHEBI:32666",
+"CHEBI:6227",
+"CHEBI:32665",
+"CHEBI:21308",
+"CHEBI:42814",
+"CHEBI:5432",
+"CHEBI:24316"
+],
+"hmdb":[
+"HMDB00641"
+],
+"inchi_key":[
+"ZDXPYRJPNDTMRX-VKHMYHEASA-N"
+],
+"kegg.compound":[
+"C00064",
+"C00303"
+],
+"kegg.drug":[
+"D00015"
+],
+"metanetx.chemical":[
+"MNXM37"
+],
+"reactome.compound":[
+"113522",
+"212615",
+"29472"
+],
+"sabiork":[
+"2011",
+"74"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00253",
+"cpd00053"
+]
+}
+},
+{
+"id":"gln__L_e",
+"name":"L-Glutamine",
+"compartment":"e",
+"charge":0,
+"formula":"C5H10N2O3",
+"notes":{
+"original_bigg_ids":[
+"gln_L_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"gln__L"
+],
+"biocyc":[
+"META:GLN"
+],
+"chebi":[
+"CHEBI:42943",
+"CHEBI:42899",
+"CHEBI:32679",
+"CHEBI:32678",
+"CHEBI:58359",
+"CHEBI:28300",
+"CHEBI:42812",
+"CHEBI:13110",
+"CHEBI:18050",
+"CHEBI:32666",
+"CHEBI:6227",
+"CHEBI:32665",
+"CHEBI:21308",
+"CHEBI:42814",
+"CHEBI:5432",
+"CHEBI:24316"
+],
+"hmdb":[
+"HMDB00641"
+],
+"inchi_key":[
+"ZDXPYRJPNDTMRX-VKHMYHEASA-N"
+],
+"kegg.compound":[
+"C00064",
+"C00303"
+],
+"kegg.drug":[
+"D00015"
+],
+"metanetx.chemical":[
+"MNXM37"
+],
+"reactome.compound":[
+"113522",
+"212615",
+"29472"
+],
+"sabiork":[
+"2011",
+"74"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00253",
+"cpd00053"
+]
+}
+},
+{
+"id":"glu__L_c",
+"name":"L-Glutamate",
+"compartment":"c",
+"charge":-1,
+"formula":"C5H8NO4",
+"notes":{
+"original_bigg_ids":[
+"glu_L_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"glu__L"
+],
+"biocyc":[
+"META:Glutamates",
+"META:GLT"
+],
+"chebi":[
+"CHEBI:76051",
+"CHEBI:21301",
+"CHEBI:29985",
+"CHEBI:42825",
+"CHEBI:29987",
+"CHEBI:18237",
+"CHEBI:24314",
+"CHEBI:16015",
+"CHEBI:13107",
+"CHEBI:5431",
+"CHEBI:21304",
+"CHEBI:6224",
+"CHEBI:14321",
+"CHEBI:29988"
+],
+"hmdb":[
+"HMDB00148",
+"HMDB60475"
+],
+"inchi_key":[
+"WHUUTDBJXJRKMK-VKHMYHEASA-M"
+],
+"kegg.compound":[
+"C00025",
+"C00302"
+],
+"kegg.drug":[
+"D00007",
+"D04341"
+],
+"metanetx.chemical":[
+"MNXM89557"
+],
+"reactome.compound":[
+"428614",
+"29404",
+"113552",
+"210382"
+],
+"sabiork":[
+"73",
+"2010"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd27177",
+"cpd00023",
+"cpd19002"
+]
+}
+},
+{
+"id":"glu__L_e",
+"name":"L-Glutamate",
+"compartment":"e",
+"charge":-1,
+"formula":"C5H8NO4",
+"notes":{
+"original_bigg_ids":[
+"glu_L_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"glu__L"
+],
+"biocyc":[
+"META:Glutamates",
+"META:GLT"
+],
+"chebi":[
+"CHEBI:76051",
+"CHEBI:21301",
+"CHEBI:29985",
+"CHEBI:42825",
+"CHEBI:29987",
+"CHEBI:18237",
+"CHEBI:24314",
+"CHEBI:16015",
+"CHEBI:13107",
+"CHEBI:5431",
+"CHEBI:21304",
+"CHEBI:6224",
+"CHEBI:14321",
+"CHEBI:29988"
+],
+"hmdb":[
+"HMDB00148",
+"HMDB60475"
+],
+"inchi_key":[
+"WHUUTDBJXJRKMK-VKHMYHEASA-M"
+],
+"kegg.compound":[
+"C00025",
+"C00302"
+],
+"kegg.drug":[
+"D00007",
+"D04341"
+],
+"metanetx.chemical":[
+"MNXM89557"
+],
+"reactome.compound":[
+"428614",
+"29404",
+"113552",
+"210382"
+],
+"sabiork":[
+"73",
+"2010"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd27177",
+"cpd00023",
+"cpd19002"
+]
+}
+},
+{
+"id":"glx_c",
+"name":"Glyoxylate",
+"compartment":"c",
+"charge":-1,
+"formula":"C2H1O3",
+"notes":{
+"original_bigg_ids":[
+"glx_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"glx"
+],
+"biocyc":[
+"META:GLYOX"
+],
+"chebi":[
+"CHEBI:24420",
+"CHEBI:36655",
+"CHEBI:14368",
+"CHEBI:24421",
+"CHEBI:42767",
+"CHEBI:16891",
+"CHEBI:35977",
+"CHEBI:5509"
+],
+"envipath":[
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/cdffdb1a-3322-4cc1-9171-d857bfaa198a",
+"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/aecbda66-6e98-4c11-aeaf-6a072f4f963c",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/9dc0aa3b-447a-4b5d-8157-501b036f9626",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/43b74f4f-bc8a-4b8b-b587-c97d8e9eed48"
+],
+"hmdb":[
+"HMDB00119"
+],
+"inchi_key":[
+"HHLFWLYXYJOTON-UHFFFAOYSA-M"
+],
+"kegg.compound":[
+"C00048"
+],
+"metanetx.chemical":[
+"MNXM69"
+],
+"reactome.compound":[
+"904849",
+"389678"
+],
+"sabiork":[
+"1838"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00040"
+]
+}
+},
+{
+"id":"h2o_c",
+"name":"H2O H2O",
+"compartment":"c",
+"charge":0,
+"formula":"H2O",
+"notes":{
+"original_bigg_ids":[
+"h2o_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"h2o"
+],
+"biocyc":[
+"META:CPD-15815",
+"META:OXONIUM",
+"META:HYDROXYL-GROUP",
+"META:WATER",
+"META:OH"
+],
+"chebi":[
+"CHEBI:13352",
+"CHEBI:30490",
+"CHEBI:43228",
+"CHEBI:33813",
+"CHEBI:44292",
+"CHEBI:44641",
+"CHEBI:27313",
+"CHEBI:42043",
+"CHEBI:44819",
+"CHEBI:29356",
+"CHEBI:5594",
+"CHEBI:10743",
+"CHEBI:15377",
+"CHEBI:42857",
+"CHEBI:13365",
+"CHEBI:29412",
+"CHEBI:16234",
+"CHEBI:13419",
+"CHEBI:5585",
+"CHEBI:44701"
+],
+"envipath":[
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/799908db-b8c9-4982-86cb-1f225e2ad08c",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/e7f34a8e-cded-4793-b6d5-792335b38636",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/969d0227-3069-4e44-9525-7ae7bad84170"
+],
+"hmdb":[
+"HMDB02111",
+"HMDB01039"
+],
+"inchi_key":[
+"XLYOFNOQVPJJNP-UHFFFAOYSA-N"
+],
+"kegg.compound":[
+"C00001",
+"C01328"
+],
+"kegg.drug":[
+"D00001",
+"D06322"
+],
+"metanetx.chemical":[
+"MNXM2"
+],
+"reactome.compound":[
+"113521",
+"141343",
+"2022884",
+"5278291",
+"29356",
+"189422",
+"5668574",
+"5693747",
+"109276",
+"113519",
+"1605715",
+"8851517",
+"113518",
+"351603"
+],
+"sabiork":[
+"40"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd27222",
+"cpd00001",
+"cpd15275"
+]
+}
+},
+{
+"id":"h2o_e",
+"name":"H2O H2O",
+"compartment":"e",
+"charge":0,
+"formula":"H2O",
+"notes":{
+"original_bigg_ids":[
+"h2o_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"h2o"
+],
+"biocyc":[
+"META:CPD-15815",
+"META:OXONIUM",
+"META:HYDROXYL-GROUP",
+"META:WATER",
+"META:OH"
+],
+"chebi":[
+"CHEBI:13352",
+"CHEBI:30490",
+"CHEBI:43228",
+"CHEBI:33813",
+"CHEBI:44292",
+"CHEBI:44641",
+"CHEBI:27313",
+"CHEBI:42043",
+"CHEBI:44819",
+"CHEBI:29356",
+"CHEBI:5594",
+"CHEBI:10743",
+"CHEBI:15377",
+"CHEBI:42857",
+"CHEBI:13365",
+"CHEBI:29412",
+"CHEBI:16234",
+"CHEBI:13419",
+"CHEBI:5585",
+"CHEBI:44701"
+],
+"envipath":[
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/799908db-b8c9-4982-86cb-1f225e2ad08c",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/e7f34a8e-cded-4793-b6d5-792335b38636",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/969d0227-3069-4e44-9525-7ae7bad84170"
+],
+"hmdb":[
+"HMDB02111",
+"HMDB01039"
+],
+"inchi_key":[
+"XLYOFNOQVPJJNP-UHFFFAOYSA-N"
+],
+"kegg.compound":[
+"C00001",
+"C01328"
+],
+"kegg.drug":[
+"D00001",
+"D06322"
+],
+"metanetx.chemical":[
+"MNXM2"
+],
+"reactome.compound":[
+"113521",
+"141343",
+"2022884",
+"5278291",
+"29356",
+"189422",
+"5668574",
+"5693747",
+"109276",
+"113519",
+"1605715",
+"8851517",
+"113518",
+"351603"
+],
+"sabiork":[
+"40"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd27222",
+"cpd00001",
+"cpd15275"
+]
+}
+},
+{
+"id":"h_c",
+"name":"H+",
+"compartment":"c",
+"charge":1,
+"formula":"H",
+"notes":{
+"original_bigg_ids":[
+"h_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"h"
+],
+"biocyc":[
+"META:PROTON"
+],
+"chebi":[
+"CHEBI:5584",
+"CHEBI:13357",
+"CHEBI:15378",
+"CHEBI:10744"
+],
+"hmdb":[
+"HMDB59597"
+],
+"inchi_key":[
+"GPRLSGONYQIRFK-UHFFFAOYSA-N"
+],
+"kegg.compound":[
+"C00080"
+],
+"metanetx.chemical":[
+"MNXM1"
+],
+"reactome.compound":[
+"2000349",
+"425978",
+"74722",
+"428040",
+"427899",
+"428548",
+"156540",
+"70106",
+"425969",
+"1132304",
+"5668577",
+"1470067",
+"163953",
+"193465",
+"113529",
+"351626",
+"425999",
+"194688",
+"374900",
+"2872447",
+"372511"
+],
+"sabiork":[
+"39"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00067"
+]
+}
+},
+{
+"id":"h_e",
+"name":"H+",
+"compartment":"e",
+"charge":1,
+"formula":"H",
+"notes":{
+"original_bigg_ids":[
+"h_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"h"
+],
+"biocyc":[
+"META:PROTON"
+],
+"chebi":[
+"CHEBI:5584",
+"CHEBI:13357",
+"CHEBI:15378",
+"CHEBI:10744"
+],
+"hmdb":[
+"HMDB59597"
+],
+"inchi_key":[
+"GPRLSGONYQIRFK-UHFFFAOYSA-N"
+],
+"kegg.compound":[
+"C00080"
+],
+"metanetx.chemical":[
+"MNXM1"
+],
+"reactome.compound":[
+"2000349",
+"425978",
+"74722",
+"428040",
+"427899",
+"428548",
+"156540",
+"70106",
+"425969",
+"1132304",
+"5668577",
+"1470067",
+"163953",
+"193465",
+"113529",
+"351626",
+"425999",
+"194688",
+"374900",
+"2872447",
+"372511"
+],
+"sabiork":[
+"39"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00067"
+]
+}
+},
+{
+"id":"icit_c",
+"name":"Isocitrate",
+"compartment":"c",
+"charge":-3,
+"formula":"C6H5O7",
+"notes":{
+"original_bigg_ids":[
+"icit_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"icit"
+],
+"chebi":[
+"CHEBI:16087",
+"CHEBI:36454",
+"CHEBI:5998",
+"CHEBI:24886",
+"CHEBI:36453",
+"CHEBI:14465",
+"CHEBI:30887",
+"CHEBI:24884"
+],
+"hmdb":[
+"HMDB00193"
+],
+"inchi_key":[
+"ODBLHEXUDAPZAU-UHFFFAOYSA-K"
+],
+"kegg.compound":[
+"C00311"
+],
+"metanetx.chemical":[
+"MNXM89661"
+],
+"sabiork":[
+"2013"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00260"
+]
+}
+},
+{
+"id":"lac__D_c",
+"name":"D-Lactate",
+"compartment":"c",
+"charge":-1,
+"formula":"C3H5O3",
+"notes":{
+"original_bigg_ids":[
+"lac_D_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"lac__D"
+],
+"biocyc":[
+"META:D-LACTATE"
+],
+"chebi":[
+"CHEBI:16004",
+"CHEBI:341",
+"CHEBI:18684",
+"CHEBI:43701",
+"CHEBI:11001",
+"CHEBI:42111",
+"CHEBI:42105"
+],
+"hmdb":[
+"HMDB01311",
+"HMDB00171"
+],
+"inchi_key":[
+"JVTAAEKCZFNVCJ-UWTATZPHSA-M"
+],
+"kegg.compound":[
+"C00256"
+],
+"metanetx.chemical":[
+"MNXM285"
+],
+"sabiork":[
+"1997",
+"2284"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00221"
+]
+}
+},
+{
+"id":"lac__D_e",
+"name":"D-Lactate",
+"compartment":"e",
+"charge":-1,
+"formula":"C3H5O3",
+"notes":{
+"original_bigg_ids":[
+"lac_D_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"lac__D"
+],
+"biocyc":[
+"META:D-LACTATE"
+],
+"chebi":[
+"CHEBI:16004",
+"CHEBI:341",
+"CHEBI:18684",
+"CHEBI:43701",
+"CHEBI:11001",
+"CHEBI:42111",
+"CHEBI:42105"
+],
+"hmdb":[
+"HMDB01311",
+"HMDB00171"
+],
+"inchi_key":[
+"JVTAAEKCZFNVCJ-UWTATZPHSA-M"
+],
+"kegg.compound":[
+"C00256"
+],
+"metanetx.chemical":[
+"MNXM285"
+],
+"sabiork":[
+"1997",
+"2284"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00221"
+]
+}
+},
+{
+"id":"mal__L_c",
+"name":"L-Malate",
+"compartment":"c",
+"charge":-2,
+"formula":"C4H4O5",
+"notes":{
+"original_bigg_ids":[
+"mal_L_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"mal__L"
+],
+"biocyc":[
+"META:MAL"
+],
+"chebi":[
+"CHEBI:15589",
+"CHEBI:30797",
+"CHEBI:423",
+"CHEBI:18784",
+"CHEBI:18785",
+"CHEBI:13140",
+"CHEBI:11066"
+],
+"hmdb":[
+"HMDB00156"
+],
+"inchi_key":[
+"BJEPYKJPYRNKOW-REOHCLBHSA-L"
+],
+"kegg.compound":[
+"C00149"
+],
+"metanetx.chemical":[
+"MNXM98"
+],
+"reactome.compound":[
+"198498",
+"113544"
+],
+"sabiork":[
+"1918"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00130"
+]
+}
+},
+{
+"id":"mal__L_e",
+"name":"L-Malate",
+"compartment":"e",
+"charge":-2,
+"formula":"C4H4O5",
+"notes":{
+"original_bigg_ids":[
+"mal_L_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"mal__L"
+],
+"biocyc":[
+"META:MAL"
+],
+"chebi":[
+"CHEBI:15589",
+"CHEBI:30797",
+"CHEBI:423",
+"CHEBI:18784",
+"CHEBI:18785",
+"CHEBI:13140",
+"CHEBI:11066"
+],
+"hmdb":[
+"HMDB00156"
+],
+"inchi_key":[
+"BJEPYKJPYRNKOW-REOHCLBHSA-L"
+],
+"kegg.compound":[
+"C00149"
+],
+"metanetx.chemical":[
+"MNXM98"
+],
+"reactome.compound":[
+"198498",
+"113544"
+],
+"sabiork":[
+"1918"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00130"
+]
+}
+},
+{
+"id":"nad_c",
+"name":"Nicotinamide adenine dinucleotide",
+"compartment":"c",
+"charge":-1,
+"formula":"C21H26N7O14P2",
+"notes":{
+"original_bigg_ids":[
+"nad_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"nad"
+],
+"biocyc":[
+"META:NAD"
+],
+"chebi":[
+"CHEBI:7422",
+"CHEBI:44215",
+"CHEBI:13394",
+"CHEBI:21901",
+"CHEBI:57540",
+"CHEBI:15846",
+"CHEBI:44281",
+"CHEBI:44214",
+"CHEBI:13393",
+"CHEBI:29867"
+],
+"hmdb":[
+"HMDB00902"
+],
+"inchi_key":[
+"BAWFJGJZGIEFAR-NNYOXOHSSA-M"
+],
+"kegg.compound":[
+"C00003"
+],
+"kegg.drug":[
+"D00002"
+],
+"metanetx.chemical":[
+"MNXM8"
+],
+"reactome.compound":[
+"352330",
+"192307",
+"194653",
+"113526",
+"29360"
+],
+"sabiork":[
+"37"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00003"
+]
+}
+},
+{
+"id":"nadh_c",
+"name":"Nicotinamide adenine dinucleotide - reduced",
+"compartment":"c",
+"charge":-2,
+"formula":"C21H27N7O14P2",
+"notes":{
+"original_bigg_ids":[
+"nadh_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"nadh"
+],
+"biocyc":[
+"META:NADH"
+],
+"chebi":[
+"CHEBI:13395",
+"CHEBI:21902",
+"CHEBI:7423",
+"CHEBI:44216",
+"CHEBI:57945",
+"CHEBI:16908",
+"CHEBI:13396"
+],
+"hmdb":[
+"HMDB01487"
+],
+"inchi_key":[
+"BOPGDPNILDQYTO-NNYOXOHSSA-L"
+],
+"kegg.compound":[
+"C00004"
+],
+"metanetx.chemical":[
+"MNXM10"
+],
+"reactome.compound":[
+"192305",
+"73473",
+"29362",
+"194697"
+],
+"sabiork":[
+"38"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00004"
+]
+}
+},
+{
+"id":"nadp_c",
+"name":"Nicotinamide adenine dinucleotide phosphate",
+"compartment":"c",
+"charge":-3,
+"formula":"C21H25N7O17P3",
+"notes":{
+"original_bigg_ids":[
+"nadp_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"nadp"
+],
+"biocyc":[
+"META:NADP"
+],
+"chebi":[
+"CHEBI:29868",
+"CHEBI:44405",
+"CHEBI:25523",
+"CHEBI:13397",
+"CHEBI:18009",
+"CHEBI:7424",
+"CHEBI:13398",
+"CHEBI:21903",
+"CHEBI:58349",
+"CHEBI:44409"
+],
+"hmdb":[
+"HMDB00217"
+],
+"inchi_key":[
+"XJLXINKUBYWONI-NNYOXOHSSA-K"
+],
+"kegg.compound":[
+"C00006"
+],
+"metanetx.chemical":[
+"MNXM5"
+],
+"reactome.compound":[
+"194668",
+"113563",
+"6790191",
+"5623650",
+"2000348",
+"389556",
+"29366",
+"351628",
+"113564"
+],
+"sabiork":[
+"1263"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00006"
+]
+}
+},
+{
+"id":"nadph_c",
+"name":"Nicotinamide adenine dinucleotide phosphate - reduced",
+"compartment":"c",
+"charge":-4,
+"formula":"C21H26N7O17P3",
+"notes":{
+"original_bigg_ids":[
+"nadph_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"nadph"
+],
+"biocyc":[
+"META:NADPH"
+],
+"chebi":[
+"CHEBI:16474",
+"CHEBI:7425",
+"CHEBI:57783",
+"CHEBI:21904",
+"CHEBI:13399",
+"CHEBI:13400",
+"CHEBI:44286"
+],
+"hmdb":[
+"HMDB06341",
+"HMDB00221",
+"HMDB00799"
+],
+"inchi_key":[
+"ACFIXJIJDZMPPO-NNYOXOHSSA-J"
+],
+"kegg.compound":[
+"C00005"
+],
+"metanetx.chemical":[
+"MNXM6"
+],
+"reactome.compound":[
+"113600",
+"6790135",
+"113602",
+"113601",
+"2000347",
+"351627",
+"29364",
+"5623644",
+"194725"
+],
+"sabiork":[
+"1262"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00005"
+]
+}
+},
+{
+"id":"nh4_c",
+"name":"Ammonium",
+"compartment":"c",
+"charge":1,
+"formula":"H4N",
+"notes":{
+"original_bigg_ids":[
+"nh4_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"nh4"
+],
+"biocyc":[
+"META:AMMONIUM",
+"META:AMMONIA"
+],
+"chebi":[
+"CHEBI:44284",
+"CHEBI:135980",
+"CHEBI:22533",
+"CHEBI:13406",
+"CHEBI:29337",
+"CHEBI:29340",
+"CHEBI:13771",
+"CHEBI:16134",
+"CHEBI:28938",
+"CHEBI:22534",
+"CHEBI:13405",
+"CHEBI:49783",
+"CHEBI:7434",
+"CHEBI:7435",
+"CHEBI:44269",
+"CHEBI:44404",
+"CHEBI:13407"
+],
+"envipath":[
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/96667bd9-aeae-4e8f-89d3-100d0396af05",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/41e4c903-407f-49f7-bf6b-0a94d39fa3a7",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/27a89bdf-42f7-478f-91d8-e39881581096"
+],
+"hmdb":[
+"HMDB00051",
+"HMDB41827"
+],
+"inchi_key":[
+"QGZKDVFQNNGYKY-UHFFFAOYSA-O"
+],
+"kegg.compound":[
+"C00014",
+"C01342"
+],
+"kegg.drug":[
+"D02916",
+"D02915"
+],
+"metanetx.chemical":[
+"MNXM15"
+],
+"reactome.compound":[
+"5693978",
+"1132163",
+"29382",
+"76230",
+"140912",
+"389843",
+"2022135",
+"31633",
+"113561"
+],
+"sabiork":[
+"1268",
+"43"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd19013",
+"cpd00013"
+]
+}
+},
+{
+"id":"13dpg_c",
+"name":"3-Phospho-D-glyceroyl phosphate",
+"compartment":"c",
+"charge":-4,
+"formula":"C3H4O10P2",
+"notes":{
+"original_bigg_ids":[
+"13dpg_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"13dpg"
+],
+"biocyc":[
+"META:DPG"
+],
+"chebi":[
+"CHEBI:57604",
+"CHEBI:20189",
+"CHEBI:11881",
+"CHEBI:16001",
+"CHEBI:1658"
+],
+"hmdb":[
+"HMDB62758"
+],
+"inchi_key":[
+"LJQLQCAXBUHEAZ-UWTATZPHSA-J"
+],
+"kegg.compound":[
+"C00236"
+],
+"metanetx.chemical":[
+"MNXM261"
+],
+"reactome.compound":[
+"29800"
+],
+"sabiork":[
+"21215"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00203"
+]
+}
+},
+{
+"id":"nh4_e",
+"name":"Ammonium",
+"compartment":"e",
+"charge":1,
+"formula":"H4N",
+"notes":{
+"original_bigg_ids":[
+"nh4_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"nh4"
+],
+"biocyc":[
+"META:AMMONIUM",
+"META:AMMONIA"
+],
+"chebi":[
+"CHEBI:44284",
+"CHEBI:135980",
+"CHEBI:22533",
+"CHEBI:13406",
+"CHEBI:29337",
+"CHEBI:29340",
+"CHEBI:13771",
+"CHEBI:16134",
+"CHEBI:28938",
+"CHEBI:22534",
+"CHEBI:13405",
+"CHEBI:49783",
+"CHEBI:7434",
+"CHEBI:7435",
+"CHEBI:44269",
+"CHEBI:44404",
+"CHEBI:13407"
+],
+"envipath":[
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/96667bd9-aeae-4e8f-89d3-100d0396af05",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/41e4c903-407f-49f7-bf6b-0a94d39fa3a7",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/27a89bdf-42f7-478f-91d8-e39881581096"
+],
+"hmdb":[
+"HMDB00051",
+"HMDB41827"
+],
+"inchi_key":[
+"QGZKDVFQNNGYKY-UHFFFAOYSA-O"
+],
+"kegg.compound":[
+"C00014",
+"C01342"
+],
+"kegg.drug":[
+"D02916",
+"D02915"
+],
+"metanetx.chemical":[
+"MNXM15"
+],
+"reactome.compound":[
+"5693978",
+"1132163",
+"29382",
+"76230",
+"140912",
+"389843",
+"2022135",
+"31633",
+"113561"
+],
+"sabiork":[
+"1268",
+"43"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd19013",
+"cpd00013"
+]
+}
+},
+{
+"id":"o2_c",
+"name":"O2 O2",
+"compartment":"c",
+"charge":0,
+"formula":"O2",
+"notes":{
+"original_bigg_ids":[
+"o2_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"o2"
+],
+"biocyc":[
+"META:OXYGEN-MOLECULE"
+],
+"chebi":[
+"CHEBI:7860",
+"CHEBI:26689",
+"CHEBI:29097",
+"CHEBI:15379",
+"CHEBI:13416",
+"CHEBI:27140",
+"CHEBI:29793",
+"CHEBI:30491",
+"CHEBI:44742",
+"CHEBI:23833",
+"CHEBI:25366",
+"CHEBI:10745"
+],
+"envipath":[
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/d5d12248-82d3-4cf3-b7d0-2e3d096768b4"
+],
+"hmdb":[
+"HMDB01377"
+],
+"inchi_key":[
+"MYMOFIZGZYHOMD-UHFFFAOYSA-N"
+],
+"kegg.compound":[
+"C00007"
+],
+"kegg.drug":[
+"D00003"
+],
+"metanetx.chemical":[
+"MNXM4"
+],
+"reactome.compound":[
+"113534",
+"113535",
+"113685",
+"5668566",
+"189461",
+"113533",
+"1131511",
+"352327",
+"351593",
+"29368",
+"1236709"
+],
+"sabiork":[
+"1264"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00007"
+]
+}
+},
+{
+"id":"2pg_c",
+"name":"D-Glycerate 2-phosphate",
+"compartment":"c",
+"charge":-3,
+"formula":"C3H4O7P",
+"notes":{
+"original_bigg_ids":[
+"2pg_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"2pg"
+],
+"biocyc":[
+"META:2-PG"
+],
+"chebi":[
+"CHEBI:39868",
+"CHEBI:21028",
+"CHEBI:58289",
+"CHEBI:24344",
+"CHEBI:12986",
+"CHEBI:17835",
+"CHEBI:11651",
+"CHEBI:1267",
+"CHEBI:88350"
+],
+"hmdb":[
+"HMDB00362",
+"HMDB62707",
+"HMDB03391"
+],
+"inchi_key":[
+"GXIURPTVHJPJLF-UWTATZPHSA-K"
+],
+"kegg.compound":[
+"C00631"
+],
+"metanetx.chemical":[
+"MNXM275"
+],
+"reactome.compound":[
+"30485"
+],
+"sabiork":[
+"31"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00482"
+]
+}
+},
+{
+"id":"o2_e",
+"name":"O2 O2",
+"compartment":"e",
+"charge":0,
+"formula":"O2",
+"notes":{
+"original_bigg_ids":[
+"o2_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"o2"
+],
+"biocyc":[
+"META:OXYGEN-MOLECULE"
+],
+"chebi":[
+"CHEBI:7860",
+"CHEBI:26689",
+"CHEBI:29097",
+"CHEBI:15379",
+"CHEBI:13416",
+"CHEBI:27140",
+"CHEBI:29793",
+"CHEBI:30491",
+"CHEBI:44742",
+"CHEBI:23833",
+"CHEBI:25366",
+"CHEBI:10745"
+],
+"envipath":[
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/d5d12248-82d3-4cf3-b7d0-2e3d096768b4"
+],
+"hmdb":[
+"HMDB01377"
+],
+"inchi_key":[
+"MYMOFIZGZYHOMD-UHFFFAOYSA-N"
+],
+"kegg.compound":[
+"C00007"
+],
+"kegg.drug":[
+"D00003"
+],
+"metanetx.chemical":[
+"MNXM4"
+],
+"reactome.compound":[
+"113534",
+"113535",
+"113685",
+"5668566",
+"189461",
+"113533",
+"1131511",
+"352327",
+"351593",
+"29368",
+"1236709"
+],
+"sabiork":[
+"1264"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00007"
+]
+}
+},
+{
+"id":"3pg_c",
+"name":"3-Phospho-D-glycerate",
+"compartment":"c",
+"charge":-3,
+"formula":"C3H4O7P",
+"notes":{
+"original_bigg_ids":[
+"3pg_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"3pg"
+],
+"biocyc":[
+"META:G3P"
+],
+"chebi":[
+"CHEBI:11879",
+"CHEBI:11880",
+"CHEBI:17794",
+"CHEBI:21029",
+"CHEBI:1657",
+"CHEBI:58272",
+"CHEBI:12987"
+],
+"hmdb":[
+"HMDB60180"
+],
+"inchi_key":[
+"OSJPPGNTCRNQQC-UWTATZPHSA-K"
+],
+"kegg.compound":[
+"C00197"
+],
+"metanetx.chemical":[
+"MNXM126"
+],
+"reactome.compound":[
+"6799493",
+"29728"
+],
+"sabiork":[
+"21216"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00169"
+]
+}
+},
+{
+"id":"oaa_c",
+"name":"Oxaloacetate",
+"compartment":"c",
+"charge":-2,
+"formula":"C4H2O5",
+"notes":{
+"original_bigg_ids":[
+"oaa_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"oaa"
+],
+"biocyc":[
+"META:OXALACETIC_ACID"
+],
+"chebi":[
+"CHEBI:25731",
+"CHEBI:24959",
+"CHEBI:12820",
+"CHEBI:16452",
+"CHEBI:30744",
+"CHEBI:14703",
+"CHEBI:24958",
+"CHEBI:7812",
+"CHEBI:25734",
+"CHEBI:29049"
+],
+"envipath":[
+"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/133a11f3-81b0-4384-837e-1ccdd0a2a645",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/40afaad4-431a-4e3c-b4c7-020dbe4bdd2a",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/be7c543c-40bd-4698-9821-22f2e65c38f3"
+],
+"hmdb":[
+"HMDB00223"
+],
+"inchi_key":[
+"KHPXUQMNIQBQEV-UHFFFAOYSA-L"
+],
+"kegg.compound":[
+"C00036"
+],
+"lipidmaps":[
+"LMFA01170120"
+],
+"metanetx.chemical":[
+"MNXM46"
+],
+"reactome.compound":[
+"6810070",
+"113587",
+"76213"
+],
+"sabiork":[
+"1915"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00032"
+]
+}
+},
+{
+"id":"pep_c",
+"name":"Phosphoenolpyruvate",
+"compartment":"c",
+"charge":-3,
+"formula":"C3H2O6P",
+"notes":{
+"original_bigg_ids":[
+"pep_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"pep"
+],
+"biocyc":[
+"META:PHOSPHO-ENOL-PYRUVATE"
+],
+"chebi":[
+"CHEBI:18021",
+"CHEBI:44894",
+"CHEBI:26054",
+"CHEBI:14812",
+"CHEBI:26055",
+"CHEBI:8147",
+"CHEBI:58702",
+"CHEBI:44897"
+],
+"hmdb":[
+"HMDB00263"
+],
+"inchi_key":[
+"DTBNBXWJWCWCIK-UHFFFAOYSA-K"
+],
+"kegg.compound":[
+"C00074"
+],
+"metanetx.chemical":[
+"MNXM73"
+],
+"reactome.compound":[
+"372364",
+"29492"
+],
+"sabiork":[
+"32"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00061"
+]
+}
+},
+{
+"id":"6pgc_c",
+"name":"6-Phospho-D-gluconate",
+"compartment":"c",
+"charge":-3,
+"formula":"C6H10O10P",
+"notes":{
+"original_bigg_ids":[
+"6pgc_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"6pgc"
+],
+"biocyc":[
+"META:CPD-2961"
+],
+"chebi":[
+"CHEBI:33851",
+"CHEBI:2231",
+"CHEBI:16863",
+"CHEBI:40282",
+"CHEBI:12232",
+"CHEBI:48928",
+"CHEBI:58759"
+],
+"hmdb":[
+"HMDB01316",
+"HMDB62800"
+],
+"inchi_key":[
+"BIRSGZKFKXLSJQ-SQOUGZDYSA-K"
+],
+"kegg.compound":[
+"C00345"
+],
+"metanetx.chemical":[
+"MNXM325"
+],
+"reactome.compound":[
+"29996"
+],
+"sabiork":[
+"22801",
+"2024"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00284"
+]
+}
+},
+{
+"id":"pi_c",
+"name":"Phosphate",
+"compartment":"c",
+"charge":-2,
+"formula":"HO4P",
+"notes":{
+"original_bigg_ids":[
+"pi_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"pi"
+],
+"biocyc":[
+"META:Pi",
+"META:CPD-16459",
+"META:PHOSPHATE-GROUP"
+],
+"chebi":[
+"CHEBI:26078",
+"CHEBI:18367",
+"CHEBI:29139",
+"CHEBI:39739",
+"CHEBI:43470",
+"CHEBI:35780",
+"CHEBI:43474",
+"CHEBI:26020",
+"CHEBI:45024",
+"CHEBI:39745",
+"CHEBI:29137",
+"CHEBI:14791",
+"CHEBI:7793"
+],
+"envipath":[
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/db5219ee-60cb-4370-b066-340c9faf069c",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/84684967-eade-48d4-b25d-c4aede0a0836",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/ad82c39b-2edb-4953-b971-79a2d2ea6e26",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/aac01fea-4223-49c1-8b12-cd50f11ebfc8",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c581b2ce-6238-45de-abc0-60ca8d47ed04"
+],
+"hmdb":[
+"HMDB02105",
+"HMDB00973",
+"HMDB01429",
+"HMDB02142",
+"HMDB05947"
+],
+"inchi_key":[
+"NBIIXXVUZAFLBC-UHFFFAOYSA-L"
+],
+"kegg.compound":[
+"C00009"
+],
+"kegg.drug":[
+"D05467"
+],
+"metanetx.chemical":[
+"MNXM9"
+],
+"reactome.compound":[
+"5228339",
+"113550",
+"8851513",
+"113551",
+"109277",
+"29372",
+"8851226",
+"113548"
+],
+"sabiork":[
+"36"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd27787",
+"cpd00009"
+]
+}
+},
+{
+"id":"6pgl_c",
+"name":"6-phospho-D-glucono-1,5-lactone",
+"compartment":"c",
+"charge":-2,
+"formula":"C6H9O9P",
+"notes":{
+"original_bigg_ids":[
+"6pgl_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"6pgl"
+],
+"biocyc":[
+"META:D-6-P-GLUCONO-DELTA-LACTONE"
+],
+"chebi":[
+"CHEBI:12233",
+"CHEBI:4160",
+"CHEBI:57955",
+"CHEBI:16938",
+"CHEBI:20989",
+"CHEBI:12958"
+],
+"hmdb":[
+"HMDB62628",
+"HMDB01127"
+],
+"inchi_key":[
+"IJOJIVNDFQSGAB-SQOUGZDYSA-L"
+],
+"kegg.compound":[
+"C01236"
+],
+"metanetx.chemical":[
+"MNXM429"
+],
+"reactome.compound":[
+"31467"
+],
+"sabiork":[
+"1366"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00911"
+]
+}
+},
+{
+"id":"pi_e",
+"name":"Phosphate",
+"compartment":"e",
+"charge":-2,
+"formula":"HO4P",
+"notes":{
+"original_bigg_ids":[
+"pi_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"pi"
+],
+"biocyc":[
+"META:Pi",
+"META:CPD-16459",
+"META:PHOSPHATE-GROUP"
+],
+"chebi":[
+"CHEBI:26078",
+"CHEBI:18367",
+"CHEBI:29139",
+"CHEBI:39739",
+"CHEBI:43470",
+"CHEBI:35780",
+"CHEBI:43474",
+"CHEBI:26020",
+"CHEBI:45024",
+"CHEBI:39745",
+"CHEBI:29137",
+"CHEBI:14791",
+"CHEBI:7793"
+],
+"envipath":[
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/db5219ee-60cb-4370-b066-340c9faf069c",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/84684967-eade-48d4-b25d-c4aede0a0836",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/ad82c39b-2edb-4953-b971-79a2d2ea6e26",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/aac01fea-4223-49c1-8b12-cd50f11ebfc8",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c581b2ce-6238-45de-abc0-60ca8d47ed04"
+],
+"hmdb":[
+"HMDB02105",
+"HMDB00973",
+"HMDB01429",
+"HMDB02142",
+"HMDB05947"
+],
+"inchi_key":[
+"NBIIXXVUZAFLBC-UHFFFAOYSA-L"
+],
+"kegg.compound":[
+"C00009"
+],
+"kegg.drug":[
+"D05467"
+],
+"metanetx.chemical":[
+"MNXM9"
+],
+"reactome.compound":[
+"5228339",
+"113550",
+"8851513",
+"113551",
+"109277",
+"29372",
+"8851226",
+"113548"
+],
+"sabiork":[
+"36"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd27787",
+"cpd00009"
+]
+}
+},
+{
+"id":"ac_c",
+"name":"Acetate",
+"compartment":"c",
+"charge":-1,
+"formula":"C2H3O2",
+"notes":{
+"original_bigg_ids":[
+"ac_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"ac"
+],
+"biocyc":[
+"META:ACET"
+],
+"chebi":[
+"CHEBI:13704",
+"CHEBI:22165",
+"CHEBI:22169",
+"CHEBI:40480",
+"CHEBI:15366",
+"CHEBI:2387",
+"CHEBI:30089",
+"CHEBI:40486"
+],
+"envipath":[
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/9e26dcbe-4db9-46a0-8614-9f03545032d2",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/5e4989fc-13d3-45d4-ad57-3be380a9d3c0",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/a8f0be58-24e8-441b-8d81-a516a0ead4b3",
+"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/d45256fe-61fa-4f5b-bb16-91a3d615e3d8",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/3e2d750f-df31-4445-9255-163c627e9b4a"
+],
+"hmdb":[
+"HMDB00042"
+],
+"inchi_key":[
+"QTBSBXVTEAMEQO-UHFFFAOYSA-M"
+],
+"kegg.compound":[
+"C00033"
+],
+"kegg.drug":[
+"D00010"
+],
+"lipidmaps":[
+"LMFA01010002"
+],
+"metanetx.chemical":[
+"MNXM26"
+],
+"reactome.compound":[
+"1524044",
+"390305",
+"113539",
+"2022890",
+"29416"
+],
+"sabiork":[
+"1278"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00029"
+],
+"slm":[
+"000000449"
+]
+}
+},
+{
+"id":"pyr_c",
+"name":"Pyruvate",
+"compartment":"c",
+"charge":-1,
+"formula":"C3H3O3",
+"notes":{
+"original_bigg_ids":[
+"pyr_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"pyr"
+],
+"biocyc":[
+"META:PYRUVATE"
+],
+"chebi":[
+"CHEBI:26462",
+"CHEBI:26466",
+"CHEBI:8685",
+"CHEBI:32816",
+"CHEBI:45253",
+"CHEBI:14987",
+"CHEBI:15361"
+],
+"envipath":[
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/ccc99777-54dc-42d4-a97e-009b780d3905",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc01020e-8c7e-4087-9f56-cf8c962b7437"
+],
+"hmdb":[
+"HMDB00243"
+],
+"inchi_key":[
+"LCTONWCANYUPML-UHFFFAOYSA-M"
+],
+"kegg.compound":[
+"C00022"
+],
+"lipidmaps":[
+"LMFA01060077"
+],
+"metanetx.chemical":[
+"MNXM23"
+],
+"reactome.compound":[
+"1130930",
+"5357717",
+"113557",
+"29398",
+"389680"
+],
+"sabiork":[
+"33"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00020"
+]
+}
+},
+{
+"id":"pyr_e",
+"name":"Pyruvate",
+"compartment":"e",
+"charge":-1,
+"formula":"C3H3O3",
+"notes":{
+"original_bigg_ids":[
+"pyr_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"pyr"
+],
+"biocyc":[
+"META:PYRUVATE"
+],
+"chebi":[
+"CHEBI:26462",
+"CHEBI:26466",
+"CHEBI:8685",
+"CHEBI:32816",
+"CHEBI:45253",
+"CHEBI:14987",
+"CHEBI:15361"
+],
+"envipath":[
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/ccc99777-54dc-42d4-a97e-009b780d3905",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc01020e-8c7e-4087-9f56-cf8c962b7437"
+],
+"hmdb":[
+"HMDB00243"
+],
+"inchi_key":[
+"LCTONWCANYUPML-UHFFFAOYSA-M"
+],
+"kegg.compound":[
+"C00022"
+],
+"lipidmaps":[
+"LMFA01060077"
+],
+"metanetx.chemical":[
+"MNXM23"
+],
+"reactome.compound":[
+"1130930",
+"5357717",
+"113557",
+"29398",
+"389680"
+],
+"sabiork":[
+"33"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00020"
+]
+}
+},
+{
+"id":"q8_c",
+"name":"Ubiquinone-8",
+"compartment":"c",
+"charge":0,
+"formula":"C49H74O4",
+"notes":{
+"original_bigg_ids":[
+"q8_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"q8"
+],
+"biocyc":[
+"META:UBIQUINONE-8"
+],
+"chebi":[
+"CHEBI:61683"
+],
+"inchi_key":[
+"ICFIZJQGJAJRSU-SGHXUWJISA-N"
+],
+"kegg.compound":[
+"C17569"
+],
+"lipidmaps":[
+"LMPR02010005"
+],
+"metanetx.chemical":[
+"MNXM232"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd15560"
+]
+}
+},
+{
+"id":"q8h2_c",
+"name":"Ubiquinol-8",
+"compartment":"c",
+"charge":0,
+"formula":"C49H76O4",
+"notes":{
+"original_bigg_ids":[
+"q8h2_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"q8h2"
+],
+"biocyc":[
+"META:CPD-9956"
+],
+"chebi":[
+"CHEBI:61682"
+],
+"hmdb":[
+"HMDB01060"
+],
+"inchi_key":[
+"LOJUQFSPYHMHEO-SGHXUWJISA-N"
+],
+"metanetx.chemical":[
+"MNXM191"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd29608",
+"cpd15561"
+]
+}
+},
+{
+"id":"r5p_c",
+"name":"Alpha-D-Ribose 5-phosphate",
+"compartment":"c",
+"charge":-2,
+"formula":"C5H9O8P",
+"notes":{
+"original_bigg_ids":[
+"r5p_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"r5p"
+],
+"biocyc":[
+"META:CPD-15318"
+],
+"chebi":[
+"CHEBI:18189",
+"CHEBI:22413",
+"CHEBI:12331",
+"CHEBI:10270"
+],
+"inchi_key":[
+"KTVPXOYAKDPRHY-AIHAYLRMSA-L"
+],
+"kegg.compound":[
+"C03736"
+],
+"metanetx.chemical":[
+"MNXM15900"
+],
+"sabiork":[
+"1473"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd19028"
+]
+}
+},
+{
+"id":"ru5p__D_c",
+"name":"D-Ribulose 5-phosphate",
+"compartment":"c",
+"charge":-2,
+"formula":"C5H9O8P",
+"notes":{
+"original_bigg_ids":[
+"ru5p_D_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"ru5p__D"
+],
+"biocyc":[
+"META:RIBULOSE-5P"
+],
+"chebi":[
+"CHEBI:40192",
+"CHEBI:21088",
+"CHEBI:17363",
+"CHEBI:26572",
+"CHEBI:13040",
+"CHEBI:37455",
+"CHEBI:58121",
+"CHEBI:13018",
+"CHEBI:4243"
+],
+"hmdb":[
+"HMDB02033",
+"HMDB02694",
+"HMDB00618"
+],
+"inchi_key":[
+"FNZLKVNUWIIPSJ-UHNVWZDZSA-L"
+],
+"kegg.compound":[
+"C00199"
+],
+"metanetx.chemical":[
+"MNXM145"
+],
+"reactome.compound":[
+"29732"
+],
+"sabiork":[
+"22814",
+"1313"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00171"
+]
+}
+},
+{
+"id":"ac_e",
+"name":"Acetate",
+"compartment":"e",
+"charge":-1,
+"formula":"C2H3O2",
+"notes":{
+"original_bigg_ids":[
+"ac_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"ac"
+],
+"biocyc":[
+"META:ACET"
+],
+"chebi":[
+"CHEBI:13704",
+"CHEBI:22165",
+"CHEBI:22169",
+"CHEBI:40480",
+"CHEBI:15366",
+"CHEBI:2387",
+"CHEBI:30089",
+"CHEBI:40486"
+],
+"envipath":[
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/9e26dcbe-4db9-46a0-8614-9f03545032d2",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/5e4989fc-13d3-45d4-ad57-3be380a9d3c0",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/a8f0be58-24e8-441b-8d81-a516a0ead4b3",
+"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/d45256fe-61fa-4f5b-bb16-91a3d615e3d8",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/3e2d750f-df31-4445-9255-163c627e9b4a"
+],
+"hmdb":[
+"HMDB00042"
+],
+"inchi_key":[
+"QTBSBXVTEAMEQO-UHFFFAOYSA-M"
+],
+"kegg.compound":[
+"C00033"
+],
+"kegg.drug":[
+"D00010"
+],
+"lipidmaps":[
+"LMFA01010002"
+],
+"metanetx.chemical":[
+"MNXM26"
+],
+"reactome.compound":[
+"1524044",
+"390305",
+"113539",
+"2022890",
+"29416"
+],
+"sabiork":[
+"1278"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00029"
+],
+"slm":[
+"000000449"
+]
+}
+},
+{
+"id":"acald_c",
+"name":"Acetaldehyde",
+"compartment":"c",
+"charge":0,
+"formula":"C2H4O",
+"notes":{
+"original_bigg_ids":[
+"acald_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"acald"
+],
+"biocyc":[
+"META:ACETALD"
+],
+"chebi":[
+"CHEBI:40533",
+"CHEBI:13703",
+"CHEBI:2383",
+"CHEBI:22158",
+"CHEBI:15343"
+],
+"envipath":[
+"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/9c8865b2-a99d-42e4-a042-c88504f04b51",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/47aa8e53-36ae-4be3-987c-c1cfab66af78",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/ee2c714d-ff9d-4df8-b343-48c1ec76ef0e",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/78f3645f-408e-4001-9dda-a52ea62a15d4"
+],
+"hmdb":[
+"HMDB00990"
+],
+"inchi_key":[
+"IKHGUXGNUITLKF-UHFFFAOYSA-N"
+],
+"kegg.compound":[
+"C00084"
+],
+"metanetx.chemical":[
+"MNXM75"
+],
+"reactome.compound":[
+"113532",
+"29510",
+"113681",
+"113745"
+],
+"sabiork":[
+"1292"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00071"
+]
+}
+},
+{
+"id":"s7p_c",
+"name":"Sedoheptulose 7-phosphate",
+"compartment":"c",
+"charge":-2,
+"formula":"C7H13O10P",
+"notes":{
+"original_bigg_ids":[
+"s7p_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"s7p"
+],
+"biocyc":[
+"META:D-SEDOHEPTULOSE-7-P"
+],
+"chebi":[
+"CHEBI:4244",
+"CHEBI:15073",
+"CHEBI:15721",
+"CHEBI:26621",
+"CHEBI:9083",
+"CHEBI:15074",
+"CHEBI:57483"
+],
+"hmdb":[
+"HMDB01068",
+"HMDB62754"
+],
+"inchi_key":[
+"JDTUMPKOJBQPKX-GBNDHIKLSA-L"
+],
+"kegg.compound":[
+"C05382"
+],
+"metanetx.chemical":[
+"MNXM271"
+],
+"reactome.compound":[
+"29882"
+],
+"sabiork":[
+"1618",
+"1325"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00238"
+]
+}
+},
+{
+"id":"acald_e",
+"name":"Acetaldehyde",
+"compartment":"e",
+"charge":0,
+"formula":"C2H4O",
+"notes":{
+"original_bigg_ids":[
+"acald_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"acald"
+],
+"biocyc":[
+"META:ACETALD"
+],
+"chebi":[
+"CHEBI:40533",
+"CHEBI:13703",
+"CHEBI:2383",
+"CHEBI:22158",
+"CHEBI:15343"
+],
+"envipath":[
+"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/9c8865b2-a99d-42e4-a042-c88504f04b51",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/47aa8e53-36ae-4be3-987c-c1cfab66af78",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/ee2c714d-ff9d-4df8-b343-48c1ec76ef0e",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/78f3645f-408e-4001-9dda-a52ea62a15d4"
+],
+"hmdb":[
+"HMDB00990"
+],
+"inchi_key":[
+"IKHGUXGNUITLKF-UHFFFAOYSA-N"
+],
+"kegg.compound":[
+"C00084"
+],
+"metanetx.chemical":[
+"MNXM75"
+],
+"reactome.compound":[
+"113532",
+"29510",
+"113681",
+"113745"
+],
+"sabiork":[
+"1292"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00071"
+]
+}
+},
+{
+"id":"accoa_c",
+"name":"Acetyl-CoA",
+"compartment":"c",
+"charge":-4,
+"formula":"C23H34N7O17P3S",
+"notes":{
+"original_bigg_ids":[
+"accoa_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"accoa"
+],
+"biocyc":[
+"META:ACETYL-COA"
+],
+"chebi":[
+"CHEBI:57288",
+"CHEBI:22192",
+"CHEBI:15351",
+"CHEBI:13712",
+"CHEBI:2408",
+"CHEBI:40470"
+],
+"envipath":[
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/57bd5e24-9d14-4b91-bc60-64c8ea6c2d11"
+],
+"hmdb":[
+"HMDB01206"
+],
+"inchi_key":[
+"ZSLZBFCDCINBPY-ZSJPKINUSA-J"
+],
+"kegg.compound":[
+"C00024"
+],
+"lipidmaps":[
+"LMFA07050029",
+"LMFA07050281"
+],
+"metanetx.chemical":[
+"MNXM21"
+],
+"reactome.compound":[
+"727753",
+"76183",
+"113560",
+"353123",
+"113559"
+],
+"sabiork":[
+"1276"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00022"
+],
+"slm":[
+"000000297"
+]
+}
+},
+{
+"id":"succ_c",
+"name":"Succinate",
+"compartment":"c",
+"charge":-2,
+"formula":"C4H4O4",
+"notes":{
+"original_bigg_ids":[
+"succ_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"succ"
+],
+"biocyc":[
+"META:SUC"
+],
+"chebi":[
+"CHEBI:22941",
+"CHEBI:26803",
+"CHEBI:15741",
+"CHEBI:132287",
+"CHEBI:45639",
+"CHEBI:30779",
+"CHEBI:15125",
+"CHEBI:22943",
+"CHEBI:26807",
+"CHEBI:9304",
+"CHEBI:90372",
+"CHEBI:30031"
+],
+"envipath":[
+"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/cc98aff0-7f64-4db4-9d59-de961c228496",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/6377658b-03f6-4fed-a5bf-ff0f2389b693",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/600b74d3-8fe5-426d-bedf-291175bd23e4",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/8fdfd425-4343-4bf2-8427-b2ffa57fdbd7"
+],
+"hmdb":[
+"HMDB00254"
+],
+"inchi_key":[
+"KDYFGRWQOYBRFD-UHFFFAOYSA-L"
+],
+"kegg.compound":[
+"C00042"
+],
+"lipidmaps":[
+"LMFA01170043"
+],
+"metanetx.chemical":[
+"MNXM25"
+],
+"reactome.compound":[
+"389583",
+"5278787",
+"159939",
+"433123",
+"29434",
+"113536"
+],
+"sabiork":[
+"1924"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00036"
+]
+}
+},
+{
+"id":"succ_e",
+"name":"Succinate",
+"compartment":"e",
+"charge":-2,
+"formula":"C4H4O4",
+"notes":{
+"original_bigg_ids":[
+"succ_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"succ"
+],
+"biocyc":[
+"META:SUC"
+],
+"chebi":[
+"CHEBI:22941",
+"CHEBI:26803",
+"CHEBI:15741",
+"CHEBI:132287",
+"CHEBI:45639",
+"CHEBI:30779",
+"CHEBI:15125",
+"CHEBI:22943",
+"CHEBI:26807",
+"CHEBI:9304",
+"CHEBI:90372",
+"CHEBI:30031"
+],
+"envipath":[
+"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/cc98aff0-7f64-4db4-9d59-de961c228496",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/6377658b-03f6-4fed-a5bf-ff0f2389b693",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/600b74d3-8fe5-426d-bedf-291175bd23e4",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/8fdfd425-4343-4bf2-8427-b2ffa57fdbd7"
+],
+"hmdb":[
+"HMDB00254"
+],
+"inchi_key":[
+"KDYFGRWQOYBRFD-UHFFFAOYSA-L"
+],
+"kegg.compound":[
+"C00042"
+],
+"lipidmaps":[
+"LMFA01170043"
+],
+"metanetx.chemical":[
+"MNXM25"
+],
+"reactome.compound":[
+"389583",
+"5278787",
+"159939",
+"433123",
+"29434",
+"113536"
+],
+"sabiork":[
+"1924"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00036"
+]
+}
+},
+{
+"id":"succoa_c",
+"name":"Succinyl-CoA",
+"compartment":"c",
+"charge":-5,
+"formula":"C25H35N7O19P3S",
+"notes":{
+"original_bigg_ids":[
+"succoa_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"succoa"
+],
+"biocyc":[
+"META:SUC-COA"
+],
+"chebi":[
+"CHEBI:57292",
+"CHEBI:10746",
+"CHEBI:15127",
+"CHEBI:15380",
+"CHEBI:9310",
+"CHEBI:45541",
+"CHEBI:26811"
+],
+"envipath":[
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/359075fb-98d9-458d-ba82-db4020e753f3"
+],
+"hmdb":[
+"HMDB01022"
+],
+"inchi_key":[
+"VNOYUJKHFWYWIR-ITIYDSSPSA-I"
+],
+"kegg.compound":[
+"C00091"
+],
+"lipidmaps":[
+"LMFA07050370"
+],
+"metanetx.chemical":[
+"MNXM92"
+],
+"reactome.compound":[
+"70958"
+],
+"sabiork":[
+"1931"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00078"
+]
+}
+},
+{
+"id":"acon_C_c",
+"name":"Cis-Aconitate",
+"compartment":"c",
+"charge":-3,
+"formula":"C6H3O6",
+"notes":{
+"original_bigg_ids":[
+"acon_C_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"acon_C"
+],
+"biocyc":[
+"META:CIS-ACONITATE"
+],
+"chebi":[
+"CHEBI:23306",
+"CHEBI:16383",
+"CHEBI:12798",
+"CHEBI:32805",
+"CHEBI:23308",
+"CHEBI:10482"
+],
+"envipath":[
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/643481e5-a35b-477e-8665-70f4dca66baa"
+],
+"hmdb":[
+"HMDB00461",
+"HMDB00072"
+],
+"inchi_key":[
+"GTZCVFVGUGFEME-IWQZZHSRSA-K"
+],
+"kegg.compound":[
+"C00417"
+],
+"metanetx.chemical":[
+"MNXM813"
+],
+"sabiork":[
+"2043"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00331"
+]
+}
+},
+{
+"id":"xu5p__D_c",
+"name":"D-Xylulose 5-phosphate",
+"compartment":"c",
+"charge":-2,
+"formula":"C5H9O8P",
+"notes":{
+"original_bigg_ids":[
+"xu5p_D_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"xu5p__D"
+],
+"biocyc":[
+"META:XYLULOSE-5-PHOSPHATE"
+],
+"chebi":[
+"CHEBI:13036",
+"CHEBI:27354",
+"CHEBI:4269",
+"CHEBI:16332",
+"CHEBI:57737",
+"CHEBI:21121"
+],
+"hmdb":[
+"HMDB06212",
+"HMDB00868"
+],
+"inchi_key":[
+"FNZLKVNUWIIPSJ-RFZPGFLSSA-L"
+],
+"kegg.compound":[
+"C00231"
+],
+"metanetx.chemical":[
+"MNXM186"
+],
+"reactome.compound":[
+"29790"
+],
+"sabiork":[
+"1317"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00198"
+]
+}
+},
+{
+"id":"actp_c",
+"name":"Acetyl phosphate",
+"compartment":"c",
+"charge":-2,
+"formula":"C2H3O5P",
+"notes":{
+"original_bigg_ids":[
+"actp_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"actp"
+],
+"biocyc":[
+"META:ACETYL-P"
+],
+"chebi":[
+"CHEBI:13711",
+"CHEBI:46262",
+"CHEBI:15350",
+"CHEBI:22191",
+"CHEBI:2407"
+],
+"hmdb":[
+"HMDB01494"
+],
+"inchi_key":[
+"LIPOUNRJVLNBCD-UHFFFAOYSA-L"
+],
+"kegg.compound":[
+"C00227"
+],
+"metanetx.chemical":[
+"MNXM280"
+],
+"sabiork":[
+"1316"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00196"
+]
+}
+},
+{
+"id":"adp_c",
+"name":"ADP C10H12N5O10P2",
+"compartment":"c",
+"charge":-3,
+"formula":"C10H12N5O10P2",
+"notes":{
+"original_bigg_ids":[
+"adp_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"adp"
+],
+"biocyc":[
+"META:ADP"
+],
+"chebi":[
+"CHEBI:2342",
+"CHEBI:16761",
+"CHEBI:456216",
+"CHEBI:40553",
+"CHEBI:22244",
+"CHEBI:87518",
+"CHEBI:13222"
+],
+"hmdb":[
+"HMDB01341"
+],
+"inchi_key":[
+"XTWYTFMLZFPYCI-KQYNXXCUSA-K"
+],
+"kegg.compound":[
+"C00008"
+],
+"kegg.glycan":[
+"G11113"
+],
+"metanetx.chemical":[
+"MNXM7"
+],
+"reactome.compound":[
+"114565",
+"211606",
+"114564",
+"6798177",
+"5632457",
+"5696026",
+"8869360",
+"29370",
+"113581",
+"113582"
+],
+"sabiork":[
+"35"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00008"
+]
+}
+},
+{
+"id":"akg_c",
+"name":"2-Oxoglutarate",
+"compartment":"c",
+"charge":-2,
+"formula":"C5H4O5",
+"notes":{
+"original_bigg_ids":[
+"akg_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"akg"
+],
+"biocyc":[
+"META:2-KETOGLUTARATE"
+],
+"chebi":[
+"CHEBI:40661",
+"CHEBI:16810",
+"CHEBI:11638",
+"CHEBI:30916",
+"CHEBI:19749",
+"CHEBI:1253",
+"CHEBI:30915",
+"CHEBI:19748"
+],
+"envipath":[
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/5b0a94f6-d411-44fd-bcc1-fb79b4e697f5",
+"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/6557f3f2-0ab8-494b-a865-8ce0eae788a9"
+],
+"hmdb":[
+"HMDB00208",
+"HMDB02812",
+"HMDB62781"
+],
+"inchi_key":[
+"KPGXRSRHYNQIFN-UHFFFAOYSA-L"
+],
+"kegg.compound":[
+"C00026"
+],
+"metanetx.chemical":[
+"MNXM20"
+],
+"reactome.compound":[
+"113594",
+"561075",
+"5278317",
+"113671",
+"29406",
+"389537"
+],
+"sabiork":[
+"1922"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00024"
+]
+}
+},
+{
+"id":"akg_e",
+"name":"2-Oxoglutarate",
+"compartment":"e",
+"charge":-2,
+"formula":"C5H4O5",
+"notes":{
+"original_bigg_ids":[
+"akg_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"akg"
+],
+"biocyc":[
+"META:2-KETOGLUTARATE"
+],
+"chebi":[
+"CHEBI:40661",
+"CHEBI:16810",
+"CHEBI:11638",
+"CHEBI:30916",
+"CHEBI:19749",
+"CHEBI:1253",
+"CHEBI:30915",
+"CHEBI:19748"
+],
+"envipath":[
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/5b0a94f6-d411-44fd-bcc1-fb79b4e697f5",
+"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/6557f3f2-0ab8-494b-a865-8ce0eae788a9"
+],
+"hmdb":[
+"HMDB00208",
+"HMDB02812",
+"HMDB62781"
+],
+"inchi_key":[
+"KPGXRSRHYNQIFN-UHFFFAOYSA-L"
+],
+"kegg.compound":[
+"C00026"
+],
+"metanetx.chemical":[
+"MNXM20"
+],
+"reactome.compound":[
+"113594",
+"561075",
+"5278317",
+"113671",
+"29406",
+"389537"
+],
+"sabiork":[
+"1922"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00024"
+]
+}
+},
+{
+"id":"amp_c",
+"name":"AMP C10H12N5O7P",
+"compartment":"c",
+"charge":-2,
+"formula":"C10H12N5O7P",
+"notes":{
+"original_bigg_ids":[
+"amp_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"amp"
+],
+"biocyc":[
+"META:AMP-GROUP",
+"META:AMP"
+],
+"chebi":[
+"CHEBI:13736",
+"CHEBI:2356",
+"CHEBI:13234",
+"CHEBI:22242",
+"CHEBI:40786",
+"CHEBI:16027",
+"CHEBI:40721",
+"CHEBI:40510",
+"CHEBI:456215",
+"CHEBI:13235",
+"CHEBI:22245",
+"CHEBI:40726",
+"CHEBI:47222",
+"CHEBI:13740",
+"CHEBI:40826",
+"CHEBI:12056"
+],
+"hmdb":[
+"HMDB00045"
+],
+"inchi_key":[
+"UDMBCSSLTHHNCD-KQYNXXCUSA-L"
+],
+"kegg.compound":[
+"C00020"
+],
+"kegg.drug":[
+"D02769"
+],
+"metanetx.chemical":[
+"MNXM14"
+],
+"reactome.compound":[
+"389620",
+"159448",
+"76577",
+"109275",
+"164121"
+],
+"sabiork":[
+"1273"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd22272",
+"cpd00018"
+]
+}
+},
+{
+"id":"atp_c",
+"name":"ATP C10H12N5O13P3",
+"compartment":"c",
+"charge":-4,
+"formula":"C10H12N5O13P3",
+"notes":{
+"original_bigg_ids":[
+"atp_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"atp"
+],
+"biocyc":[
+"META:ATP"
+],
+"chebi":[
+"CHEBI:15422",
+"CHEBI:10789",
+"CHEBI:10841",
+"CHEBI:2359",
+"CHEBI:22249",
+"CHEBI:13236",
+"CHEBI:237958",
+"CHEBI:30616",
+"CHEBI:57299",
+"CHEBI:40938"
+],
+"hmdb":[
+"HMDB00538"
+],
+"inchi_key":[
+"ZKHQWZAMYRWXGA-KQYNXXCUSA-J"
+],
+"kegg.compound":[
+"C00002"
+],
+"kegg.drug":[
+"D08646"
+],
+"metanetx.chemical":[
+"MNXM3"
+],
+"reactome.compound":[
+"8878982",
+"389573",
+"8938081",
+"211579",
+"113593",
+"113592",
+"5632460",
+"5696069",
+"29358",
+"8869363",
+"6798184"
+],
+"sabiork":[
+"34"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00002"
+]
+}
+},
+{
+"id":"cit_c",
+"name":"Citrate",
+"compartment":"c",
+"charge":-3,
+"formula":"C6H5O7",
+"notes":{
+"original_bigg_ids":[
+"cit_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"cit"
+],
+"biocyc":[
+"META:CIT"
+],
+"chebi":[
+"CHEBI:35802",
+"CHEBI:133748",
+"CHEBI:35809",
+"CHEBI:76049",
+"CHEBI:41523",
+"CHEBI:35810",
+"CHEBI:30769",
+"CHEBI:13999",
+"CHEBI:23322",
+"CHEBI:35808",
+"CHEBI:42563",
+"CHEBI:16947",
+"CHEBI:132362",
+"CHEBI:35804",
+"CHEBI:23321",
+"CHEBI:3727",
+"CHEBI:35806"
+],
+"hmdb":[
+"HMDB00094"
+],
+"inchi_key":[
+"KRKNYBCHXYNGOX-UHFFFAOYSA-K"
+],
+"kegg.compound":[
+"C00158"
+],
+"kegg.drug":[
+"D00037"
+],
+"metanetx.chemical":[
+"MNXM131"
+],
+"reactome.compound":[
+"29654",
+"433138",
+"76190"
+],
+"sabiork":[
+"1952"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00137"
+]
+}
+},
+{
+"id":"co2_c",
+"name":"CO2 CO2",
+"compartment":"c",
+"charge":0,
+"formula":"CO2",
+"notes":{
+"original_bigg_ids":[
+"co2_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"co2"
+],
+"biocyc":[
+"META:CARBON-DIOXIDE"
+],
+"chebi":[
+"CHEBI:23011",
+"CHEBI:3283",
+"CHEBI:48829",
+"CHEBI:16526",
+"CHEBI:13283",
+"CHEBI:13285",
+"CHEBI:13284",
+"CHEBI:13282"
+],
+"envipath":[
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/2ec3da94-5f50-4525-81b1-5607c5c7a3d3",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/05f60af4-0a3f-4ead-9a29-33bb0f123379"
+],
+"hmdb":[
+"HMDB01967"
+],
+"inchi_key":[
+"CURLTUGMZLYLDI-UHFFFAOYSA-N"
+],
+"kegg.compound":[
+"C00011"
+],
+"kegg.drug":[
+"D00004"
+],
+"metanetx.chemical":[
+"MNXM13"
+],
+"reactome.compound":[
+"29376",
+"5668565",
+"189480",
+"1132345",
+"113528",
+"1237009",
+"159751",
+"389536",
+"159942"
+],
+"sabiork":[
+"1266"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00011"
+]
+}
+},
+{
+"id":"co2_e",
+"name":"CO2 CO2",
+"compartment":"e",
+"charge":0,
+"formula":"CO2",
+"notes":{
+"original_bigg_ids":[
+"co2_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"co2"
+],
+"biocyc":[
+"META:CARBON-DIOXIDE"
+],
+"chebi":[
+"CHEBI:23011",
+"CHEBI:3283",
+"CHEBI:48829",
+"CHEBI:16526",
+"CHEBI:13283",
+"CHEBI:13285",
+"CHEBI:13284",
+"CHEBI:13282"
+],
+"envipath":[
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/2ec3da94-5f50-4525-81b1-5607c5c7a3d3",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/05f60af4-0a3f-4ead-9a29-33bb0f123379"
+],
+"hmdb":[
+"HMDB01967"
+],
+"inchi_key":[
+"CURLTUGMZLYLDI-UHFFFAOYSA-N"
+],
+"kegg.compound":[
+"C00011"
+],
+"kegg.drug":[
+"D00004"
+],
+"metanetx.chemical":[
+"MNXM13"
+],
+"reactome.compound":[
+"29376",
+"5668565",
+"189480",
+"1132345",
+"113528",
+"1237009",
+"159751",
+"389536",
+"159942"
+],
+"sabiork":[
+"1266"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00011"
+]
+}
+},
+{
+"id":"coa_c",
+"name":"Coenzyme A",
+"compartment":"c",
+"charge":-4,
+"formula":"C21H32N7O16P3S",
+"notes":{
+"original_bigg_ids":[
+"coa_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"coa"
+],
+"biocyc":[
+"META:COA-GROUP",
+"META:CO-A"
+],
+"chebi":[
+"CHEBI:41631",
+"CHEBI:41597",
+"CHEBI:741566",
+"CHEBI:23355",
+"CHEBI:13295",
+"CHEBI:13298",
+"CHEBI:57287",
+"CHEBI:15346",
+"CHEBI:3771",
+"CHEBI:13294"
+],
+"envipath":[
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/19310484-6aa5-4dcf-b1da-855a8c21ecfd"
+],
+"hmdb":[
+"HMDB01423",
+"HMDB62184"
+],
+"inchi_key":[
+"RGJOEKWQDUBAIZ-IBOSZNHHSA-J"
+],
+"kegg.compound":[
+"C00010"
+],
+"metanetx.chemical":[
+"MNXM12"
+],
+"reactome.compound":[
+"193514",
+"162743",
+"2485002",
+"1678675",
+"29374",
+"76194",
+"8939024"
+],
+"sabiork":[
+"1265"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd22528",
+"cpd00010"
+]
+}
+},
+{
+"id":"dhap_c",
+"name":"Dihydroxyacetone phosphate",
+"compartment":"c",
+"charge":-2,
+"formula":"C3H5O6P",
+"notes":{
+"original_bigg_ids":[
+"dhap_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"dhap"
+],
+"biocyc":[
+"META:DIHYDROXY-ACETONE-PHOSPHATE"
+],
+"chebi":[
+"CHEBI:14341",
+"CHEBI:5454",
+"CHEBI:16108",
+"CHEBI:14342",
+"CHEBI:24355",
+"CHEBI:39571",
+"CHEBI:57642"
+],
+"hmdb":[
+"HMDB11735",
+"HMDB01473"
+],
+"inchi_key":[
+"GNGACRATGGDKBX-UHFFFAOYSA-L"
+],
+"kegg.compound":[
+"C00111"
+],
+"metanetx.chemical":[
+"MNXM77"
+],
+"reactome.compound":[
+"390404",
+"75970",
+"188451"
+],
+"sabiork":[
+"28"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00095"
+]
+}
+},
+{
+"id":"e4p_c",
+"name":"D-Erythrose 4-phosphate",
+"compartment":"c",
+"charge":-2,
+"formula":"C4H7O7P",
+"notes":{
+"original_bigg_ids":[
+"e4p_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"e4p"
+],
+"biocyc":[
+"META:ERYTHROSE-4P"
+],
+"chebi":[
+"CHEBI:4114",
+"CHEBI:20927",
+"CHEBI:12921",
+"CHEBI:48153",
+"CHEBI:16897",
+"CHEBI:42349"
+],
+"hmdb":[
+"HMDB01321"
+],
+"inchi_key":[
+"NGHMDNPXVRFFGS-IUYQGCFVSA-L"
+],
+"kegg.compound":[
+"C00279"
+],
+"metanetx.chemical":[
+"MNXM258"
+],
+"reactome.compound":[
+"29878"
+],
+"sabiork":[
+"1324"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00236"
+]
+}
+},
+{
+"id":"etoh_c",
+"name":"Ethanol",
+"compartment":"c",
+"charge":0,
+"formula":"C2H6O",
+"notes":{
+"original_bigg_ids":[
+"etoh_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"etoh"
+],
+"biocyc":[
+"META:ETOH"
+],
+"chebi":[
+"CHEBI:42377",
+"CHEBI:23978",
+"CHEBI:30880",
+"CHEBI:16236",
+"CHEBI:52092",
+"CHEBI:30878",
+"CHEBI:4879",
+"CHEBI:44594",
+"CHEBI:14222"
+],
+"envipath":[
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/a4a354fd-5003-4b7b-b11b-f54204aea384",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/f89efe7c-1a6a-4d21-b99c-e3e1070a8062",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/56e18a05-c059-433a-94f6-0e26c01b010f",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/9fb1fbdf-101b-4b82-a596-d2f52c870e4f"
+],
+"hmdb":[
+"HMDB00108"
+],
+"inchi_key":[
+"LFQSCWFLJHTTHZ-UHFFFAOYSA-N"
+],
+"kegg.compound":[
+"C00469"
+],
+"kegg.drug":[
+"D06542",
+"D02798",
+"D00068",
+"D04855"
+],
+"metanetx.chemical":[
+"MNXM303"
+],
+"reactome.compound":[
+"113748",
+"30203"
+],
+"sabiork":[
+"56"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00363"
+]
+}
+},
+{
+"id":"etoh_e",
+"name":"Ethanol",
+"compartment":"e",
+"charge":0,
+"formula":"C2H6O",
+"notes":{
+"original_bigg_ids":[
+"etoh_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"etoh"
+],
+"biocyc":[
+"META:ETOH"
+],
+"chebi":[
+"CHEBI:42377",
+"CHEBI:23978",
+"CHEBI:30880",
+"CHEBI:16236",
+"CHEBI:52092",
+"CHEBI:30878",
+"CHEBI:4879",
+"CHEBI:44594",
+"CHEBI:14222"
+],
+"envipath":[
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/a4a354fd-5003-4b7b-b11b-f54204aea384",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/f89efe7c-1a6a-4d21-b99c-e3e1070a8062",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/56e18a05-c059-433a-94f6-0e26c01b010f",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/9fb1fbdf-101b-4b82-a596-d2f52c870e4f"
+],
+"hmdb":[
+"HMDB00108"
+],
+"inchi_key":[
+"LFQSCWFLJHTTHZ-UHFFFAOYSA-N"
+],
+"kegg.compound":[
+"C00469"
+],
+"kegg.drug":[
+"D06542",
+"D02798",
+"D00068",
+"D04855"
+],
+"metanetx.chemical":[
+"MNXM303"
+],
+"reactome.compound":[
+"113748",
+"30203"
+],
+"sabiork":[
+"56"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00363"
+]
+}
+},
+{
+"id":"f6p_c",
+"name":"D-Fructose 6-phosphate",
+"compartment":"c",
+"charge":-2,
+"formula":"C6H11O9P",
+"notes":{
+"original_bigg_ids":[
+"f6p_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"f6p"
+],
+"biocyc":[
+"META:FRUCTOSE-6P"
+],
+"chebi":[
+"CHEBI:16084",
+"CHEBI:12352",
+"CHEBI:57634",
+"CHEBI:22768",
+"CHEBI:10375",
+"CHEBI:42378"
+],
+"hmdb":[
+"HMDB03971"
+],
+"inchi_key":[
+"BGWGXPAPYGQALX-ARQDHWQXSA-L"
+],
+"kegg.compound":[
+"C05345"
+],
+"metanetx.chemical":[
+"MNXM89621"
+],
+"sabiork":[
+"25"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd19035"
+]
+}
+},
+{
+"id":"fdp_c",
+"name":"D-Fructose 1,6-bisphosphate",
+"compartment":"c",
+"charge":-4,
+"formula":"C6H10O12P2",
+"notes":{
+"original_bigg_ids":[
+"fdp_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"fdp"
+],
+"chebi":[
+"CHEBI:37736",
+"CHEBI:49299"
+],
+"inchi_key":[
+"RNBGYGVWRKECFJ-VRPWFDPXSA-J"
+],
+"kegg.compound":[
+"C00354"
+],
+"metanetx.chemical":[
+"MNXM417"
+],
+"sabiork":[
+"1465"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00290"
+]
+}
+},
+{
+"id":"for_c",
+"name":"Formate",
+"compartment":"c",
+"charge":-1,
+"formula":"CH1O2",
+"notes":{
+"original_bigg_ids":[
+"for_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"for"
+],
+"biocyc":[
+"META:CPD1G-1532",
+"META:CPD1G-1535",
+"META:FORMATE",
+"META:CPD-9845",
+"META:CPD1G-1534",
+"META:CARBOXYL-GROUP",
+"META:CPD1G-1533"
+],
+"chebi":[
+"CHEBI:24081",
+"CHEBI:30751",
+"CHEBI:15740",
+"CHEBI:5145",
+"CHEBI:42460",
+"CHEBI:14276",
+"CHEBI:24082"
+],
+"envipath":[
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/9a9d20ae-b6ec-40a9-93ca-1de20597b1ed",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/09c1ad08-016e-4477-8840-b97a031eae23",
+"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/bf16ab32-cb3c-4427-a65a-089ab754823e",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/34fe3cd9-9b0b-46b0-a1c5-8a66509f1919",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/1d077cf2-3f9f-4163-aa49-0fca1b2b3ab3"
+],
+"hmdb":[
+"HMDB00142"
+],
+"inchi_key":[
+"BDAGIHXWWSANSR-UHFFFAOYSA-M"
+],
+"kegg.compound":[
+"C00058"
+],
+"metanetx.chemical":[
+"MNXM39"
+],
+"reactome.compound":[
+"29460",
+"194712",
+"389585",
+"6801451"
+],
+"sabiork":[
+"1285"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00047",
+"cpd22511"
+]
+}
+},
+{
+"id":"for_e",
+"name":"Formate",
+"compartment":"e",
+"charge":-1,
+"formula":"CH1O2",
+"notes":{
+"original_bigg_ids":[
+"for_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"for"
+],
+"biocyc":[
+"META:CPD1G-1532",
+"META:CPD1G-1535",
+"META:FORMATE",
+"META:CPD-9845",
+"META:CPD1G-1534",
+"META:CARBOXYL-GROUP",
+"META:CPD1G-1533"
+],
+"chebi":[
+"CHEBI:24081",
+"CHEBI:30751",
+"CHEBI:15740",
+"CHEBI:5145",
+"CHEBI:42460",
+"CHEBI:14276",
+"CHEBI:24082"
+],
+"envipath":[
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/9a9d20ae-b6ec-40a9-93ca-1de20597b1ed",
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/09c1ad08-016e-4477-8840-b97a031eae23",
+"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/bf16ab32-cb3c-4427-a65a-089ab754823e",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/34fe3cd9-9b0b-46b0-a1c5-8a66509f1919",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/1d077cf2-3f9f-4163-aa49-0fca1b2b3ab3"
+],
+"hmdb":[
+"HMDB00142"
+],
+"inchi_key":[
+"BDAGIHXWWSANSR-UHFFFAOYSA-M"
+],
+"kegg.compound":[
+"C00058"
+],
+"metanetx.chemical":[
+"MNXM39"
+],
+"reactome.compound":[
+"29460",
+"194712",
+"389585",
+"6801451"
+],
+"sabiork":[
+"1285"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00047",
+"cpd22511"
+]
+}
+},
+{
+"id":"fru_e",
+"name":"D-Fructose",
+"compartment":"e",
+"charge":0,
+"formula":"C6H12O6",
+"notes":{
+"original_bigg_ids":[
+"fru_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"fru"
+],
+"biocyc":[
+"META:D-Fructopyranose",
+"META:Fructofuranose",
+"META:CPD-15382",
+"META:FRU"
+],
+"chebi":[
+"CHEBI:47424",
+"CHEBI:28757",
+"CHEBI:24110",
+"CHEBI:20929",
+"CHEBI:4119",
+"CHEBI:15824",
+"CHEBI:5172",
+"CHEBI:24104",
+"CHEBI:12923",
+"CHEBI:4118",
+"CHEBI:37714",
+"CHEBI:37721",
+"CHEBI:48095"
+],
+"hmdb":[
+"HMDB62538"
+],
+"inchi_key":[
+"RFSUNEUAIZKAJO-VRPWFDPXSA-N"
+],
+"kegg.compound":[
+"C01496",
+"C05003",
+"C00095",
+"C10906"
+],
+"kegg.drug":[
+"D00114"
+],
+"metanetx.chemical":[
+"MNXM175"
+],
+"reactome.compound":[
+"189049",
+"29532"
+],
+"sabiork":[
+"25055",
+"1463",
+"1464"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00082",
+"cpd19015",
+"cpd27040"
+]
+}
+},
+{
+"id":"fum_c",
+"name":"Fumarate",
+"compartment":"c",
+"charge":-2,
+"formula":"C4H2O4",
+"notes":{
+"original_bigg_ids":[
+"fum_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"fum"
+],
+"biocyc":[
+"META:FUM"
+],
+"chebi":[
+"CHEBI:36180",
+"CHEBI:37155",
+"CHEBI:42511",
+"CHEBI:5190",
+"CHEBI:18012",
+"CHEBI:42743",
+"CHEBI:22956",
+"CHEBI:22957",
+"CHEBI:24124",
+"CHEBI:14284",
+"CHEBI:37154",
+"CHEBI:29806",
+"CHEBI:22958",
+"CHEBI:24122"
+],
+"envipath":[
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/709035ec-4868-4de8-9095-06428f6be14b"
+],
+"hmdb":[
+"HMDB00134"
+],
+"inchi_key":[
+"VZCYOOQTPOCHFL-OWOJBTEDSA-L"
+],
+"kegg.compound":[
+"C00122"
+],
+"kegg.drug":[
+"D02308"
+],
+"metanetx.chemical":[
+"MNXM93"
+],
+"reactome.compound":[
+"113588",
+"29586"
+],
+"sabiork":[
+"1910"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00106"
+]
+}
+},
+{
+"id":"fum_e",
+"name":"Fumarate",
+"compartment":"e",
+"charge":-2,
+"formula":"C4H2O4",
+"notes":{
+"original_bigg_ids":[
+"fum_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"fum"
+],
+"biocyc":[
+"META:FUM"
+],
+"chebi":[
+"CHEBI:36180",
+"CHEBI:37155",
+"CHEBI:42511",
+"CHEBI:5190",
+"CHEBI:18012",
+"CHEBI:42743",
+"CHEBI:22956",
+"CHEBI:22957",
+"CHEBI:24124",
+"CHEBI:14284",
+"CHEBI:37154",
+"CHEBI:29806",
+"CHEBI:22958",
+"CHEBI:24122"
+],
+"envipath":[
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/709035ec-4868-4de8-9095-06428f6be14b"
+],
+"hmdb":[
+"HMDB00134"
+],
+"inchi_key":[
+"VZCYOOQTPOCHFL-OWOJBTEDSA-L"
+],
+"kegg.compound":[
+"C00122"
+],
+"kegg.drug":[
+"D02308"
+],
+"metanetx.chemical":[
+"MNXM93"
+],
+"reactome.compound":[
+"113588",
+"29586"
+],
+"sabiork":[
+"1910"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00106"
+]
+}
+},
+{
+"id":"g3p_c",
+"name":"Glyceraldehyde 3-phosphate",
+"compartment":"c",
+"charge":-2,
+"formula":"C3H5O6P",
+"notes":{
+"original_bigg_ids":[
+"g3p_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"g3p"
+],
+"biocyc":[
+"META:GAP"
+],
+"chebi":[
+"CHEBI:5446",
+"CHEBI:14333",
+"CHEBI:12984",
+"CHEBI:181",
+"CHEBI:17138",
+"CHEBI:21026",
+"CHEBI:12983",
+"CHEBI:18324",
+"CHEBI:58027",
+"CHEBI:59776",
+"CHEBI:29052"
+],
+"hmdb":[
+"HMDB01112"
+],
+"inchi_key":[
+"LXJXRIRHZLFYRP-VKHMYHEASA-L"
+],
+"kegg.compound":[
+"C00661",
+"C00118"
+],
+"metanetx.chemical":[
+"MNXM74"
+],
+"reactome.compound":[
+"29578"
+],
+"sabiork":[
+"27",
+"1687"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00102",
+"cpd19005"
+]
+}
+},
+{
+"id":"g6p_c",
+"name":"D-Glucose 6-phosphate",
+"compartment":"c",
+"charge":-2,
+"formula":"C6H11O9P",
+"notes":{
+"original_bigg_ids":[
+"g6p_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"g6p"
+],
+"biocyc":[
+"META:D-glucopyranose-6-phosphate"
+],
+"chebi":[
+"CHEBI:61548",
+"CHEBI:14314",
+"CHEBI:4170"
+],
+"hmdb":[
+"HMDB01549",
+"HMDB01401",
+"HMDB06793"
+],
+"inchi_key":[
+"NBSCHQHZLSJFNQ-GASJEMHNSA-L"
+],
+"kegg.compound":[
+"C00092"
+],
+"metanetx.chemical":[
+"MNXM160"
+],
+"reactome.compound":[
+"1629756"
+],
+"sabiork":[
+"1404",
+"1405"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00079",
+"cpd26836"
+]
+}
+}
+],
+"reactions":[
+{
+"id":"PFK",
+"name":"Phosphofructokinase",
+"metabolites":{
+"adp_c":1.0,
+"atp_c":-1.0,
+"f6p_c":-1.0,
+"fdp_c":1.0,
+"h_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3916 or b1723",
+"subsystem":"Glycolysis/Gluconeogenesis",
+"notes":{
+"original_bigg_ids":[
+"PFK"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PFK"
+],
+"ec-code":[
+"2.7.1.11"
+],
+"metanetx.reaction":[
+"MNXR102507"
+],
+"rhea":[
+"16111",
+"16109",
+"16110",
+"16112"
+],
+"sbo":"SBO:0000176"
+}
+},
+{
+"id":"PFL",
+"name":"Pyruvate formate lyase",
+"metabolites":{
+"accoa_c":1.0,
+"coa_c":-1.0,
+"for_c":1.0,
+"pyr_c":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"((b0902 and b0903) and b2579) or (b0902 and b0903) or (b0902 and b3114) or (b3951 and b3952)",
+"subsystem":"Pyruvate Metabolism",
+"notes":{
+"original_bigg_ids":[
+"PFL"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PFL"
+],
+"biocyc":[
+"META:PYRUVFORMLY-RXN"
+],
+"ec-code":[
+"2.3.1.54"
+],
+"kegg.reaction":[
+"R00212"
+],
+"metanetx.reaction":[
+"MNXR102514"
+],
+"rhea":[
+"11847",
+"11845",
+"11844",
+"11846"
+],
+"sabiork":[
+"146"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00157"
+]
+}
+},
+{
+"id":"PGI",
+"name":"Glucose-6-phosphate isomerase",
+"metabolites":{
+"f6p_c":1.0,
+"g6p_c":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b4025",
+"subsystem":"Glycolysis/Gluconeogenesis",
+"notes":{
+"original_bigg_ids":[
+"PGI"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PGI"
+],
+"biocyc":[
+"META:PGLUCISOM-RXN"
+],
+"ec-code":[
+"5.3.1.9"
+],
+"metanetx.reaction":[
+"MNXR102535"
+],
+"sbo":"SBO:0000176"
+}
+},
+{
+"id":"PGK",
+"name":"Phosphoglycerate kinase",
+"metabolites":{
+"13dpg_c":1.0,
+"3pg_c":-1.0,
+"adp_c":1.0,
+"atp_c":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2926",
+"subsystem":"Glycolysis/Gluconeogenesis",
+"notes":{
+"original_bigg_ids":[
+"PGK"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PGK"
+],
+"biocyc":[
+"META:PHOSGLYPHOS-RXN"
+],
+"ec-code":[
+"2.7.2.3"
+],
+"kegg.reaction":[
+"R01512"
+],
+"metanetx.reaction":[
+"MNXR102538"
+],
+"reactome.reaction":[
+"R-ATH-71850",
+"R-DME-71850",
+"R-GGA-71850",
+"R-SPO-71850",
+"R-OSA-71850",
+"R-GGA-353039",
+"R-GGA-353023",
+"R-BTA-71850",
+"R-CFA-70486",
+"R-MMU-71850",
+"R-DME-70486",
+"R-PFA-71850",
+"R-SPO-70486",
+"R-SCE-70486",
+"R-PFA-70486",
+"R-SSC-70486",
+"R-ATH-70486",
+"R-DRE-70486",
+"R-HSA-70486",
+"R-OSA-70486",
+"R-XTR-71850",
+"R-MMU-70486",
+"R-RNO-70486",
+"R-TGU-70486",
+"R-DRE-71850",
+"R-SSC-71850",
+"R-SCE-71850",
+"R-CFA-71850",
+"R-XTR-70486",
+"R-DDI-70486",
+"R-DDI-71850",
+"R-RNO-71850",
+"R-BTA-70486",
+"R-CEL-70486",
+"R-HSA-71850",
+"R-CEL-71850",
+"R-GGA-70486",
+"R-TGU-71850"
+],
+"rhea":[
+"14801",
+"14804",
+"14802",
+"14803"
+],
+"sabiork":[
+"7644"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn01100"
+]
+}
+},
+{
+"id":"PGL",
+"name":"6-phosphogluconolactonase",
+"metabolites":{
+"6pgc_c":1.0,
+"6pgl_c":-1.0,
+"h2o_c":-1.0,
+"h_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0767",
+"subsystem":"Pentose Phosphate Pathway",
+"notes":{
+"original_bigg_ids":[
+"PGL"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PGL"
+],
+"biocyc":[
+"META:6PGLUCONOLACT-RXN"
+],
+"ec-code":[
+"3.1.1.31"
+],
+"kegg.reaction":[
+"R02035"
+],
+"metanetx.reaction":[
+"MNXR102539"
+],
+"reactome.reaction":[
+"R-OSA-71296",
+"R-CFA-71296",
+"R-CEL-71296",
+"R-GGA-71296",
+"R-MMU-71296",
+"R-SSC-71296",
+"R-BTA-71296",
+"R-ATH-71296",
+"R-DME-71296",
+"R-DRE-71296",
+"R-SCE-71296",
+"R-HSA-71296",
+"R-XTR-71296",
+"R-RNO-71296",
+"R-DDI-71296",
+"R-SPO-71296"
+],
+"rhea":[
+"12559",
+"12556",
+"12557",
+"12558"
+],
+"sabiork":[
+"109"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn01476"
+]
+}
+},
+{
+"id":"ACALD",
+"name":"Acetaldehyde dehydrogenase (acetylating)",
+"metabolites":{
+"acald_c":-1.0,
+"accoa_c":1.0,
+"coa_c":-1.0,
+"h_c":1.0,
+"nad_c":-1.0,
+"nadh_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0351 or b1241",
+"subsystem":"Pyruvate Metabolism",
+"notes":{
+"original_bigg_ids":[
+"ACALD"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ACALD"
+],
+"biocyc":[
+"META:ACETALD-DEHYDROG-RXN"
+],
+"ec-code":[
+"1.2.1.10"
+],
+"kegg.reaction":[
+"R00228"
+],
+"metanetx.reaction":[
+"MNXR95210"
+],
+"rhea":[
+"23290",
+"23291",
+"23289",
+"23288"
+],
+"sabiork":[
+"163"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00171"
+]
+}
+},
+{
+"id":"AKGt2r",
+"name":"2 oxoglutarate reversible transport via symport",
+"metabolites":{
+"akg_c":1.0,
+"akg_e":-1.0,
+"h_c":1.0,
+"h_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2587",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"AKGt2r"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"AKGt2r"
+],
+"biocyc":[
+"META:TRANS-RXN-23"
+],
+"metanetx.reaction":[
+"MNXR95661"
+],
+"rhea":[
+"29011",
+"29013",
+"29012",
+"29014"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn05493",
+"rxn08095",
+"rxn09827"
+]
+}
+},
+{
+"id":"PGM",
+"name":"Phosphoglycerate mutase",
+"metabolites":{
+"2pg_c":-1.0,
+"3pg_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3612 or b4395 or b0755",
+"subsystem":"Glycolysis/Gluconeogenesis",
+"notes":{
+"original_bigg_ids":[
+"PGM"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PGM"
+],
+"biocyc":[
+"META:3PGAREARR-RXN",
+"META:RXN-15513"
+],
+"ec-code":[
+"5.4.2.1",
+"5.4.2.11",
+"5.4.2.12"
+],
+"kegg.reaction":[
+"R01518"
+],
+"metanetx.reaction":[
+"MNXR102547"
+],
+"reactome.reaction":[
+"R-XTR-71654",
+"R-SSC-71654",
+"R-DME-71445",
+"R-XTR-71445",
+"R-RNO-71445",
+"R-GGA-71654",
+"R-SSC-71445",
+"R-GGA-71445",
+"R-DDI-71654",
+"R-SPO-71654",
+"R-MMU-71445",
+"R-BTA-71445",
+"R-CFA-71445",
+"R-PFA-71445",
+"R-GGA-352994",
+"R-TGU-71654",
+"R-SPO-71445",
+"R-HSA-71445",
+"R-ATH-71654",
+"R-MMU-71654",
+"R-BTA-71654",
+"R-GGA-353014",
+"R-DRE-71654",
+"R-HSA-71654",
+"R-CFA-71654",
+"R-OSA-71654",
+"R-DDI-71445",
+"R-RNO-71654",
+"R-DRE-71445",
+"R-OSA-71445",
+"R-PFA-71654",
+"R-DME-71654",
+"R-TGU-71445",
+"R-SCE-71445",
+"R-ATH-71445",
+"R-SCE-71654"
+],
+"rhea":[
+"15902",
+"15903",
+"15901",
+"15904"
+],
+"sabiork":[
+"7641"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn01106"
+]
+}
+},
+{
+"id":"PIt2r",
+"name":"Phosphate reversible transport via symport",
+"metabolites":{
+"h_c":1.0,
+"h_e":-1.0,
+"pi_c":1.0,
+"pi_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2987 or b3493",
+"subsystem":"Inorganic Ion Transport and Metabolism",
+"notes":{
+"original_bigg_ids":[
+"PIt2r"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PIt2r"
+],
+"biocyc":[
+"META:TRANS-RXN-114"
+],
+"metanetx.reaction":[
+"MNXR102872"
+],
+"rhea":[
+"29939",
+"29941",
+"29940",
+"29942"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn05312",
+"rxn09833",
+"rxn09811",
+"rxn09872",
+"rxn09723",
+"rxn09120"
+]
+}
+},
+{
+"id":"ALCD2x",
+"name":"Alcohol dehydrogenase (ethanol)",
+"metabolites":{
+"acald_c":1.0,
+"etoh_c":-1.0,
+"h_c":1.0,
+"nad_c":-1.0,
+"nadh_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0356 or b1478 or b1241",
+"subsystem":"Pyruvate Metabolism",
+"notes":{
+"original_bigg_ids":[
+"ALCD2x"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ALCD2x"
+],
+"biocyc":[
+"META:ALCOHOL-DEHYDROG-RXN"
+],
+"ec-code":[
+"1.1.1.71",
+"1.1.1.1"
+],
+"kegg.reaction":[
+"R00754"
+],
+"metanetx.reaction":[
+"MNXR95725"
+],
+"reactome.reaction":[
+"R-MMU-71707",
+"R-XTR-71707",
+"R-CFA-71707",
+"R-OSA-71707",
+"R-RNO-71707",
+"R-HSA-71707",
+"R-SSC-71707",
+"R-GGA-71707",
+"R-SPO-71707",
+"R-DME-71707",
+"R-DRE-71707",
+"R-BTA-71707",
+"R-ATH-71707",
+"R-SCE-71707",
+"R-TGU-71707",
+"R-CEL-71707",
+"R-DDI-71707"
+],
+"rhea":[
+"25292",
+"25290",
+"25291",
+"25293"
+],
+"sabiork":[
+"597"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00543"
+]
+}
+},
+{
+"id":"ACALDt",
+"name":"Acetaldehyde reversible transport",
+"metabolites":{
+"acald_c":1.0,
+"acald_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"s0001",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"ACALDt"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ACALDt"
+],
+"metanetx.reaction":[
+"MNXR95212"
+],
+"reactome.reaction":[
+"R-HSA-449872"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn09700",
+"rxn08033",
+"rxn13212",
+"rxn08032"
+]
+}
+},
+{
+"id":"ACKr",
+"name":"Acetate kinase",
+"metabolites":{
+"ac_c":-1.0,
+"actp_c":1.0,
+"adp_c":1.0,
+"atp_c":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3115 or b2296 or b1849",
+"subsystem":"Pyruvate Metabolism",
+"notes":{
+"original_bigg_ids":[
+"ACKr"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ACKr"
+],
+"biocyc":[
+"META:ACETATEKIN-RXN"
+],
+"ec-code":[
+"2.7.2.15",
+"2.7.2.1"
+],
+"kegg.reaction":[
+"R00315"
+],
+"metanetx.reaction":[
+"MNXR95269"
+],
+"rhea":[
+"11354",
+"11355",
+"11353",
+"11352"
+],
+"sabiork":[
+"71"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00225"
+]
+}
+},
+{
+"id":"PPC",
+"name":"Phosphoenolpyruvate carboxylase",
+"metabolites":{
+"co2_c":-1.0,
+"h2o_c":-1.0,
+"h_c":1.0,
+"oaa_c":1.0,
+"pep_c":-1.0,
+"pi_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3956",
+"subsystem":"Anaplerotic reactions",
+"notes":{
+"original_bigg_ids":[
+"PPC"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PPC"
+],
+"ec-code":[
+"4.1.1.31"
+],
+"kegg.reaction":[
+"R00345"
+],
+"metanetx.reaction":[
+"MNXR103096"
+],
+"rhea":[
+"23073",
+"23072",
+"23075",
+"23074"
+],
+"sabiork":[
+"150"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00251"
+]
+}
+},
+{
+"id":"ACONTa",
+"name":"Aconitase (half-reaction A, Citrate hydro-lyase)",
+"metabolites":{
+"acon_C_c":1.0,
+"cit_c":-1.0,
+"h2o_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0118 or b1276",
+"subsystem":"Citric Acid Cycle",
+"notes":{
+"original_bigg_ids":[
+"ACONTa"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ACONTa"
+],
+"biocyc":[
+"META:ACONITATEDEHYDR-RXN"
+],
+"ec-code":[
+"4.2.1.3"
+],
+"kegg.reaction":[
+"R01325"
+],
+"metanetx.reaction":[
+"MNXR95386"
+],
+"rhea":[
+"10230",
+"10229",
+"10231",
+"10228"
+],
+"sabiork":[
+"268"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00974"
+]
+}
+},
+{
+"id":"ACONTb",
+"name":"Aconitase (half-reaction B, Isocitrate hydro-lyase)",
+"metabolites":{
+"acon_C_c":-1.0,
+"h2o_c":-1.0,
+"icit_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0118 or b1276",
+"subsystem":"Citric Acid Cycle",
+"notes":{
+"original_bigg_ids":[
+"ACONTb"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ACONTb"
+],
+"ec-code":[
+"4.2.1.3"
+],
+"kegg.reaction":[
+"R01900"
+],
+"metanetx.reaction":[
+"MNXR95387"
+],
+"rhea":[
+"22145",
+"22144",
+"22146",
+"22147"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn01388"
+]
+}
+},
+{
+"id":"ATPM",
+"name":"ATP maintenance requirement",
+"metabolites":{
+"adp_c":1.0,
+"atp_c":-1.0,
+"h2o_c":-1.0,
+"h_c":1.0,
+"pi_c":1.0
+},
+"lower_bound":8.39,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Biomass and maintenance functions",
+"notes":{
+"original_bigg_ids":[
+"ATPM"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ATPM"
+],
+"biocyc":[
+"META:ATPASE-RXN"
+],
+"ec-code":[
+"3.6.1.5",
+"3.6.3.34",
+"3.6.3.20",
+"3.6.3.53",
+"3.6.3.8",
+"3.6.3.32",
+"3.6.4.12",
+"3.6.3.48",
+"3.6.3.40",
+"3.6.3.9",
+"3.6.3.23",
+"3.6.3.22",
+"3.6.3.54",
+"3.6.3.1",
+"3.6.1.8",
+"3.6.3.29",
+"3.6.3.17",
+"3.6.3.50",
+"3.6.3.39",
+"3.6.3.19",
+"3.6.3.4",
+"3.6.3.35",
+"3.6.3.16",
+"3.6.4.4",
+"3.6.3.37",
+"3.6.4.8",
+"3.6.3.31",
+"3.6.3.6",
+"3.6.4.5",
+"3.6.3.52",
+"3.6.3.2",
+"3.6.3.14",
+"3.6.3.51",
+"3.6.3.25",
+"3.6.3.38",
+"3.6.3.33",
+"3.6.3.43",
+"3.6.4.10",
+"3.6.4.13",
+"3.6.3.3",
+"3.6.3.10",
+"3.6.3.24",
+"3.6.3.44",
+"3.6.3.15",
+"3.6.3.5",
+"3.6.1.3",
+"3.6.1.15",
+"3.6.4.2",
+"3.6.4.3",
+"3.6.3.42",
+"3.6.3.11",
+"3.6.3.28",
+"3.6.3.30",
+"3.6.4.1",
+"3.6.4.11",
+"3.6.3.47",
+"3.6.4.6",
+"3.6.3.36",
+"3.6.3.21",
+"3.6.3.12",
+"3.6.3.18",
+"3.6.3.26",
+"3.6.3.27",
+"3.6.3.7",
+"3.6.4.9",
+"3.6.4.7",
+"3.6.3.46",
+"3.6.3.41",
+"3.6.3.49"
+],
+"kegg.reaction":[
+"R00086"
+],
+"metanetx.reaction":[
+"MNXR96131"
+],
+"rhea":[
+"13066",
+"13065",
+"13068",
+"13067"
+],
+"sabiork":[
+"75"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn11300",
+"rxn09694",
+"rxn00062"
+]
+}
+},
+{
+"id":"PPCK",
+"name":"Phosphoenolpyruvate carboxykinase",
+"metabolites":{
+"adp_c":1.0,
+"atp_c":-1.0,
+"co2_c":1.0,
+"oaa_c":-1.0,
+"pep_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3403",
+"subsystem":"Anaplerotic reactions",
+"notes":{
+"original_bigg_ids":[
+"PPCK"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PPCK"
+],
+"biocyc":[
+"META:PEPCARBOXYKIN-RXN"
+],
+"ec-code":[
+"4.1.1.49"
+],
+"kegg.reaction":[
+"R00341"
+],
+"metanetx.reaction":[
+"MNXR103099"
+],
+"rhea":[
+"18620",
+"18618",
+"18617",
+"18619"
+],
+"sabiork":[
+"151"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00247"
+]
+}
+},
+{
+"id":"ACt2r",
+"name":"Acetate reversible transport via proton symport",
+"metabolites":{
+"ac_c":1.0,
+"ac_e":-1.0,
+"h_c":1.0,
+"h_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"ACt2r"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ACt2r"
+],
+"biocyc":[
+"META:TRANS-RXN0-571"
+],
+"metanetx.reaction":[
+"MNXR95429"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn08061",
+"rxn05488"
+]
+}
+},
+{
+"id":"PPS",
+"name":"Phosphoenolpyruvate synthase",
+"metabolites":{
+"amp_c":1.0,
+"atp_c":-1.0,
+"h2o_c":-1.0,
+"h_c":2.0,
+"pep_c":1.0,
+"pi_c":1.0,
+"pyr_c":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b1702",
+"subsystem":"Glycolysis/Gluconeogenesis",
+"notes":{
+"original_bigg_ids":[
+"PPS"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PPS"
+],
+"biocyc":[
+"META:PEPSYNTH-RXN"
+],
+"ec-code":[
+"2.7.9.2"
+],
+"kegg.reaction":[
+"R00199"
+],
+"metanetx.reaction":[
+"MNXR103140"
+],
+"rhea":[
+"11364",
+"11367",
+"11366",
+"11365"
+],
+"sabiork":[
+"148"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00147"
+]
+}
+},
+{
+"id":"ADK1",
+"name":"Adenylate kinase",
+"metabolites":{
+"adp_c":2.0,
+"amp_c":-1.0,
+"atp_c":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0474",
+"subsystem":"Oxidative Phosphorylation",
+"notes":{
+"original_bigg_ids":[
+"ADK1"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ADK1"
+],
+"biocyc":[
+"META:ADENYL-KIN-RXN"
+],
+"ec-code":[
+"2.7.4.3"
+],
+"kegg.reaction":[
+"R00127"
+],
+"metanetx.reaction":[
+"MNXR95450"
+],
+"reactome.reaction":[
+"R-ATH-110145",
+"R-SSC-110144",
+"R-ATH-110144",
+"R-SSC-110145",
+"R-GGA-110145",
+"R-PFA-110144",
+"R-HSA-110145",
+"R-RNO-110144",
+"R-OSA-110145",
+"R-SCE-110145",
+"R-RNO-110145",
+"R-XTR-110144",
+"R-SCE-110144",
+"R-PFA-110145",
+"R-OSA-110144",
+"R-HSA-110144",
+"R-BTA-110144",
+"R-DRE-110145",
+"R-DRE-110144",
+"R-SPO-110145",
+"R-CEL-110144",
+"R-CFA-110144",
+"R-XTR-110145",
+"R-MMU-110144",
+"R-DME-110144",
+"R-SPO-110144",
+"R-DDI-110145",
+"R-GGA-110144",
+"R-TGU-110144",
+"R-BTA-110145",
+"R-CEL-110145",
+"R-CFA-110145",
+"R-DME-110145",
+"R-TGU-110145",
+"R-DDI-110144",
+"R-MMU-110145"
+],
+"rhea":[
+"12975",
+"12973",
+"12976",
+"12974"
+],
+"sabiork":[
+"82"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00097"
+]
+}
+},
+{
+"id":"AKGDH",
+"name":"2-Oxogluterate dehydrogenase",
+"metabolites":{
+"akg_c":-1.0,
+"co2_c":1.0,
+"coa_c":-1.0,
+"nad_c":-1.0,
+"nadh_c":1.0,
+"succoa_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0116 and b0726 and b0727",
+"subsystem":"Citric Acid Cycle",
+"notes":{
+"original_bigg_ids":[
+"AKGDH"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"AKGDH"
+],
+"biocyc":[
+"META:2OXOGLUTARATEDEH-RXN"
+],
+"ec-code":[
+"1.2.1.52",
+"2.3.1.61",
+"1.8.1.4",
+"1.2.4.2"
+],
+"kegg.reaction":[
+"R08549"
+],
+"metanetx.reaction":[
+"MNXR95655"
+],
+"reactome.reaction":[
+"R-PFA-71401",
+"R-XTR-71401",
+"R-SCE-71401",
+"R-SSC-71401",
+"R-TGU-71401",
+"R-ATH-71401",
+"R-OSA-71401",
+"R-SPO-71401",
+"R-CEL-71401",
+"R-RNO-71401",
+"R-DRE-71401",
+"R-GGA-373042",
+"R-DDI-71401",
+"R-CFA-71401",
+"R-HSA-71401",
+"R-BTA-71401",
+"R-DME-71401",
+"R-MMU-71401",
+"R-GGA-71401"
+],
+"rhea":[
+"27789",
+"27788",
+"27786",
+"27787"
+],
+"sabiork":[
+"8163"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn08094"
+]
+}
+},
+{
+"id":"ATPS4r",
+"name":"ATP synthase (four protons for one ATP)",
+"metabolites":{
+"adp_c":-1.0,
+"atp_c":1.0,
+"h2o_c":1.0,
+"h_c":3.0,
+"h_e":-4.0,
+"pi_c":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"((b3736 and b3737 and b3738) and (b3731 and b3732 and b3733 and b3734 and b3735)) or ((b3736 and b3737 and b3738) and (b3731 and b3732 and b3733 and b3734 and b3735) and b3739)",
+"subsystem":"Oxidative Phosphorylation",
+"notes":{
+"original_bigg_ids":[
+"ATPS4r"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ATPS4r"
+],
+"biocyc":[
+"META:ATPSYN-RXN"
+],
+"ec-code":[
+"3.6.3.14"
+],
+"metanetx.reaction":[
+"MNXR96136"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn08173",
+"rxn10042"
+]
+}
+},
+{
+"id":"PTAr",
+"name":"Phosphotransacetylase",
+"metabolites":{
+"accoa_c":-1.0,
+"actp_c":1.0,
+"coa_c":1.0,
+"pi_c":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2297 or b2458",
+"subsystem":"Pyruvate Metabolism",
+"notes":{
+"original_bigg_ids":[
+"PTAr"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PTAr"
+],
+"biocyc":[
+"META:PHOSACETYLTRANS-RXN"
+],
+"ec-code":[
+"2.3.1.8"
+],
+"kegg.reaction":[
+"R00230"
+],
+"metanetx.reaction":[
+"MNXR103319"
+],
+"rhea":[
+"19521",
+"19523",
+"19522",
+"19524"
+],
+"sabiork":[
+"72"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00173"
+]
+}
+},
+{
+"id":"PYK",
+"name":"Pyruvate kinase",
+"metabolites":{
+"adp_c":-1.0,
+"atp_c":1.0,
+"h_c":-1.0,
+"pep_c":-1.0,
+"pyr_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b1854 or b1676",
+"subsystem":"Glycolysis/Gluconeogenesis",
+"notes":{
+"original_bigg_ids":[
+"PYK"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PYK"
+],
+"biocyc":[
+"META:PEPDEPHOS-RXN"
+],
+"ec-code":[
+"2.7.1.40"
+],
+"kegg.reaction":[
+"R00200"
+],
+"metanetx.reaction":[
+"MNXR103371"
+],
+"reactome.reaction":[
+"R-SSC-71670",
+"R-GGA-353056",
+"R-DRE-71670",
+"R-OSA-71670",
+"R-SPO-71670",
+"R-DDI-71670",
+"R-SCE-71670",
+"R-CEL-71670",
+"R-PFA-71670",
+"R-HSA-71670",
+"R-TGU-71670",
+"R-DME-71670",
+"R-ATH-71670",
+"R-BTA-71670",
+"R-MMU-71670",
+"R-RNO-71670",
+"R-GGA-71670",
+"R-CFA-71670",
+"R-XTR-71670"
+],
+"rhea":[
+"18160",
+"18159",
+"18158",
+"18157"
+],
+"sabiork":[
+"9"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00148"
+]
+}
+},
+{
+"id":"BIOMASS_Ecoli_core_w_GAM",
+"name":"Biomass Objective Function with GAM",
+"metabolites":{
+"3pg_c":-1.496,
+"accoa_c":-3.7478,
+"adp_c":59.81,
+"akg_c":4.1182,
+"atp_c":-59.81,
+"coa_c":3.7478,
+"e4p_c":-0.361,
+"f6p_c":-0.0709,
+"g3p_c":-0.129,
+"g6p_c":-0.205,
+"gln__L_c":-0.2557,
+"glu__L_c":-4.9414,
+"h2o_c":-59.81,
+"h_c":59.81,
+"nad_c":-3.547,
+"nadh_c":3.547,
+"nadp_c":13.0279,
+"nadph_c":-13.0279,
+"oaa_c":-1.7867,
+"pep_c":-0.5191,
+"pi_c":59.81,
+"pyr_c":-2.8328,
+"r5p_c":-0.8977
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"objective_coefficient":1.0,
+"subsystem":"Biomass and maintenance functions",
+"notes":{
+"original_bigg_ids":[
+"Biomass_Ecoli_core_w_GAM"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"BIOMASS_Ecoli_core_w_GAM"
+],
+"metanetx.reaction":[
+"MNXR96280"
+],
+"sbo":"SBO:0000629"
+}
+},
+{
+"id":"PYRt2",
+"name":"Pyruvate transport in via proton symport",
+"metabolites":{
+"h_c":1.0,
+"h_e":-1.0,
+"pyr_c":1.0,
+"pyr_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"PYRt2r"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PYRt2"
+],
+"metanetx.reaction":[
+"MNXR103385"
+],
+"reactome.reaction":[
+"R-RNO-372347",
+"R-HSA-372342",
+"R-GGA-372359"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn05469",
+"rxn09832",
+"rxn09717",
+"rxn09217"
+]
+}
+},
+{
+"id":"CO2t",
+"name":"CO2 transporter via diffusion",
+"metabolites":{
+"co2_c":1.0,
+"co2_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"s0001",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"CO2t"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"CO2t"
+],
+"biocyc":[
+"META:TRANS-RXN0-545"
+],
+"metanetx.reaction":[
+"MNXR96810"
+],
+"reactome.reaction":[
+"R-DDI-1247645",
+"R-CFA-1237069",
+"R-TGU-1247649",
+"R-CFA-1237042",
+"R-CEL-1247645",
+"R-XTR-1237069",
+"R-HSA-1247645",
+"R-OSA-1237042",
+"R-GGA-1237042",
+"R-BTA-1247645",
+"R-GGA-1247649",
+"R-RNO-1247645",
+"R-XTR-1247645",
+"R-TGU-1237042",
+"R-SCE-1247649",
+"R-MMU-1247649",
+"R-CFA-1247649",
+"R-GGA-1247645",
+"R-SSC-1247645",
+"R-BTA-1237069",
+"R-RNO-1237069",
+"R-SCE-1237042",
+"R-DDI-1247649",
+"R-SSC-1237042",
+"R-DRE-1247649",
+"R-DRE-1237042",
+"R-DDI-1237042",
+"R-DME-1237042",
+"R-MMU-1237042",
+"R-SSC-1247649",
+"R-TGU-1237069",
+"R-BTA-1247649",
+"R-CFA-1247645",
+"R-RNO-1247649",
+"R-HSA-1237069",
+"R-CEL-1237069",
+"R-DDI-1237069",
+"R-MMU-1237069",
+"R-DME-1247645",
+"R-ATH-1237042",
+"R-OSA-1247649",
+"R-HSA-1237042",
+"R-DRE-1247645",
+"R-HSA-1247649",
+"R-MMU-1247645",
+"R-DME-1237069",
+"R-RNO-1237042",
+"R-TGU-1247645",
+"R-BTA-1237042",
+"R-GGA-1237069",
+"R-DME-1247649",
+"R-SSC-1237069",
+"R-DRE-1237069",
+"R-ATH-1247649"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn05467",
+"rxn08237",
+"rxn09706",
+"rxn09821",
+"rxn09775",
+"rxn09876",
+"rxn08238",
+"rxn09860"
+]
+}
+},
+{
+"id":"RPE",
+"name":"Ribulose 5-phosphate 3-epimerase",
+"metabolites":{
+"ru5p__D_c":-1.0,
+"xu5p__D_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3386 or b4301",
+"subsystem":"Pentose Phosphate Pathway",
+"notes":{
+"original_bigg_ids":[
+"RPE"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"RPE"
+],
+"biocyc":[
+"META:RIBULP3EPIM-RXN"
+],
+"ec-code":[
+"5.1.3.1"
+],
+"kegg.reaction":[
+"R01529"
+],
+"metanetx.reaction":[
+"MNXR104083"
+],
+"reactome.reaction":[
+"R-SPO-71303",
+"R-CFA-199803",
+"R-ATH-71303",
+"R-SCE-71303",
+"R-CFA-71303",
+"R-DME-199803",
+"R-XTR-199803",
+"R-SSC-199803",
+"R-GGA-199803",
+"R-TGU-71303",
+"R-OSA-199803",
+"R-SSC-71303",
+"R-MMU-71303",
+"R-OSA-71303",
+"R-HSA-71303",
+"R-MMU-199803",
+"R-XTR-71303",
+"R-SPO-199803",
+"R-SCE-199803",
+"R-DDI-71303",
+"R-RNO-71303",
+"R-DME-71303",
+"R-HSA-199803",
+"R-DRE-71303",
+"R-PFA-199803",
+"R-CEL-199803",
+"R-RNO-199803",
+"R-PFA-71303",
+"R-CEL-71303",
+"R-TGU-199803",
+"R-GGA-71303",
+"R-DDI-199803",
+"R-BTA-71303",
+"R-ATH-199803",
+"R-DRE-199803",
+"R-BTA-199803"
+],
+"rhea":[
+"13677",
+"13680",
+"13678",
+"13679"
+],
+"sabiork":[
+"62"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn01116"
+]
+}
+},
+{
+"id":"CS",
+"name":"Citrate synthase",
+"metabolites":{
+"accoa_c":-1.0,
+"cit_c":1.0,
+"coa_c":1.0,
+"h2o_c":-1.0,
+"h_c":1.0,
+"oaa_c":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0720",
+"subsystem":"Citric Acid Cycle",
+"notes":{
+"original_bigg_ids":[
+"CS"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"CS"
+],
+"biocyc":[
+"META:CITSYN-RXN",
+"META:RXN-14905"
+],
+"ec-code":[
+"2.3.3.16",
+"2.3.3.1",
+"2.3.3.3"
+],
+"kegg.reaction":[
+"R00351"
+],
+"metanetx.reaction":[
+"MNXR96920"
+],
+"reactome.reaction":[
+"R-GGA-373006",
+"R-GGA-70975",
+"R-CEL-70975",
+"R-HSA-70975",
+"R-DRE-70975",
+"R-MMU-70975",
+"R-ATH-70975",
+"R-SPO-70975",
+"R-OSA-70975",
+"R-SCE-70975",
+"R-SSC-70975",
+"R-DDI-70975",
+"R-RNO-70975",
+"R-DME-70975",
+"R-PFA-70975",
+"R-XTR-70975",
+"R-CFA-70975",
+"R-BTA-70975"
+],
+"rhea":[
+"16847",
+"16846",
+"16845",
+"16848"
+],
+"sabiork":[
+"267"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00256"
+]
+}
+},
+{
+"id":"RPI",
+"name":"Ribose-5-phosphate isomerase",
+"metabolites":{
+"r5p_c":-1.0,
+"ru5p__D_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2914 or b4090",
+"subsystem":"Pentose Phosphate Pathway",
+"notes":{
+"original_bigg_ids":[
+"RPI"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"RPI"
+],
+"ec-code":[
+"5.3.1.6"
+],
+"metanetx.reaction":[
+"MNXR104084"
+],
+"sbo":"SBO:0000176"
+}
+},
+{
+"id":"SUCCt2_2",
+"name":"Succinate transport via proton symport (2 H)",
+"metabolites":{
+"h_c":2.0,
+"h_e":-2.0,
+"succ_c":1.0,
+"succ_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3528",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"SUCCt2_2"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"SUCCt2_2"
+],
+"biocyc":[
+"META:TRANS-RXN-121"
+],
+"metanetx.reaction":[
+"MNXR104620"
+],
+"rhea":[
+"29305",
+"29306",
+"29304",
+"29303"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn10154",
+"rxn09269"
+]
+}
+},
+{
+"id":"CYTBD",
+"name":"Cytochrome oxidase bd (ubiquinol-8: 2 protons)",
+"metabolites":{
+"h2o_c":1.0,
+"h_c":-2.0,
+"h_e":2.0,
+"o2_c":-0.5,
+"q8_c":1.0,
+"q8h2_c":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"(b0978 and b0979) or (b0733 and b0734)",
+"subsystem":"Oxidative Phosphorylation",
+"notes":{
+"original_bigg_ids":[
+"CYTBD"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"CYTBD"
+],
+"metanetx.reaction":[
+"MNXR97031"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn12494",
+"rxn10112",
+"rxn08288"
+]
+}
+},
+{
+"id":"D_LACt2",
+"name":"D lactate transport via proton symport",
+"metabolites":{
+"h_c":1.0,
+"h_e":-1.0,
+"lac__D_c":1.0,
+"lac__D_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2975 or b3603",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"D_LACt2"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"D_LACt2"
+],
+"biocyc":[
+"META:TRANS-RXN0-515"
+],
+"metanetx.reaction":[
+"MNXR97838"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn10171",
+"rxn09772",
+"rxn08350"
+]
+}
+},
+{
+"id":"ENO",
+"name":"Enolase",
+"metabolites":{
+"2pg_c":-1.0,
+"h2o_c":1.0,
+"pep_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2779",
+"subsystem":"Glycolysis/Gluconeogenesis",
+"notes":{
+"original_bigg_ids":[
+"ENO"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ENO"
+],
+"biocyc":[
+"META:2PGADEHYDRAT-RXN"
+],
+"ec-code":[
+"4.2.1.11"
+],
+"kegg.reaction":[
+"R00658"
+],
+"metanetx.reaction":[
+"MNXR97932"
+],
+"reactome.reaction":[
+"R-BTA-71660",
+"R-RNO-70494",
+"R-TGU-71660",
+"R-SSC-71660",
+"R-GGA-352981",
+"R-DME-70494",
+"R-CFA-70494",
+"R-OSA-70494",
+"R-SCE-71660",
+"R-GGA-353044",
+"R-CFA-71660",
+"R-GGA-70494",
+"R-PFA-71660",
+"R-SPO-71660",
+"R-SPO-70494",
+"R-DDI-70494",
+"R-RNO-71660",
+"R-MMU-70494",
+"R-ATH-70494",
+"R-SCE-70494",
+"R-SSC-70494",
+"R-HSA-70494",
+"R-DME-71660",
+"R-CEL-71660",
+"R-HSA-71660",
+"R-TGU-70494",
+"R-XTR-71660",
+"R-DRE-70494",
+"R-DRE-71660",
+"R-MMU-71660",
+"R-ATH-71660",
+"R-BTA-70494",
+"R-CEL-70494",
+"R-XTR-70494",
+"R-DDI-71660",
+"R-OSA-71660",
+"R-PFA-70494",
+"R-GGA-71660"
+],
+"rhea":[
+"10166",
+"10165",
+"10164",
+"10167"
+],
+"sabiork":[
+"8"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00459"
+]
+}
+},
+{
+"id":"SUCCt3",
+"name":"Succinate transport out via proton antiport",
+"metabolites":{
+"h_c":1.0,
+"h_e":-1.0,
+"succ_c":-1.0,
+"succ_e":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"SUCCt3"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"SUCCt3"
+],
+"metanetx.reaction":[
+"MNXR104623"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn09270"
+]
+}
+},
+{
+"id":"ETOHt2r",
+"name":"Ethanol reversible transport via proton symport",
+"metabolites":{
+"etoh_c":1.0,
+"etoh_e":-1.0,
+"h_c":1.0,
+"h_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"ETOHt2r"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ETOHt2r"
+],
+"metanetx.reaction":[
+"MNXR97981"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn10146",
+"rxn08427"
+]
+}
+},
+{
+"id":"SUCDi",
+"name":"Succinate dehydrogenase (irreversible)",
+"metabolites":{
+"fum_c":1.0,
+"q8_c":-1.0,
+"q8h2_c":1.0,
+"succ_c":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0721 and b0722 and b0723 and b0724",
+"subsystem":"Oxidative Phosphorylation",
+"notes":{
+"original_bigg_ids":[
+"SUCDi"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"SUCDi"
+],
+"metanetx.reaction":[
+"MNXR99641"
+],
+"rhea":[
+"29190",
+"29189",
+"29187",
+"29188"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn09272"
+]
+}
+},
+{
+"id":"SUCOAS",
+"name":"Succinyl-CoA synthetase (ADP-forming)",
+"metabolites":{
+"adp_c":1.0,
+"atp_c":-1.0,
+"coa_c":-1.0,
+"pi_c":1.0,
+"succ_c":-1.0,
+"succoa_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0728 and b0729",
+"subsystem":"Citric Acid Cycle",
+"notes":{
+"original_bigg_ids":[
+"SUCOAS"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"SUCOAS"
+],
+"biocyc":[
+"META:SUCCCOASYN-RXN"
+],
+"ec-code":[
+"6.2.1.5"
+],
+"kegg.reaction":[
+"R00405"
+],
+"metanetx.reaction":[
+"MNXR104635"
+],
+"reactome.reaction":[
+"R-BTA-70997",
+"R-GGA-372977",
+"R-PFA-70997",
+"R-GGA-373134",
+"R-TGU-70997",
+"R-XTR-70997",
+"R-SSC-70997",
+"R-HSA-70997",
+"R-DRE-70997",
+"R-SCE-70997",
+"R-SPO-70997",
+"R-DDI-70997",
+"R-CFA-70997",
+"R-OSA-70997",
+"R-GGA-70997",
+"R-RNO-70997",
+"R-ATH-70997",
+"R-MMU-70997"
+],
+"rhea":[
+"17664",
+"17663",
+"17662",
+"17661"
+],
+"sabiork":[
+"260"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00285"
+]
+}
+},
+{
+"id":"TALA",
+"name":"Transaldolase",
+"metabolites":{
+"e4p_c":1.0,
+"f6p_c":1.0,
+"g3p_c":-1.0,
+"s7p_c":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2464 or b0008",
+"subsystem":"Pentose Phosphate Pathway",
+"notes":{
+"original_bigg_ids":[
+"TALA"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"TALA"
+],
+"biocyc":[
+"META:TRANSALDOL-RXN"
+],
+"ec-code":[
+"2.2.1.2"
+],
+"kegg.reaction":[
+"R01827"
+],
+"metanetx.reaction":[
+"MNXR104715"
+],
+"rhea":[
+"17056",
+"17055",
+"17054",
+"17053"
+],
+"sbo":"SBO:0000176"
+}
+},
+{
+"id":"THD2",
+"name":"NAD(P) transhydrogenase",
+"metabolites":{
+"h_c":2.0,
+"h_e":-2.0,
+"nad_c":1.0,
+"nadh_c":-1.0,
+"nadp_c":-1.0,
+"nadph_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b1602 and b1603",
+"subsystem":"Oxidative Phosphorylation",
+"notes":{
+"original_bigg_ids":[
+"THD2"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"THD2"
+],
+"ec-code":[
+"1.6.1.1"
+],
+"metanetx.reaction":[
+"MNXR104805"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn10125",
+"rxn09295"
+]
+}
+},
+{
+"id":"TKT1",
+"name":"Transketolase",
+"metabolites":{
+"g3p_c":1.0,
+"r5p_c":-1.0,
+"s7p_c":1.0,
+"xu5p__D_c":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2935 or b2465",
+"subsystem":"Pentose Phosphate Pathway",
+"notes":{
+"original_bigg_ids":[
+"TKT1"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"TKT1"
+],
+"ec-code":[
+"2.2.1.1"
+],
+"metanetx.reaction":[
+"MNXR104868"
+],
+"sbo":"SBO:0000176"
+}
+},
+{
+"id":"TKT2",
+"name":"Transketolase",
+"metabolites":{
+"e4p_c":-1.0,
+"f6p_c":1.0,
+"g3p_c":1.0,
+"xu5p__D_c":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2935 or b2465",
+"subsystem":"Pentose Phosphate Pathway",
+"notes":{
+"original_bigg_ids":[
+"TKT2"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"TKT2"
+],
+"biocyc":[
+"META:2TRANSKETO-RXN"
+],
+"ec-code":[
+"2.2.1.1"
+],
+"kegg.reaction":[
+"R01830"
+],
+"metanetx.reaction":[
+"MNXR104869"
+],
+"rhea":[
+"27627",
+"27628",
+"27626",
+"27629"
+],
+"sbo":"SBO:0000176"
+}
+},
+{
+"id":"TPI",
+"name":"Triose-phosphate isomerase",
+"metabolites":{
+"dhap_c":-1.0,
+"g3p_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3919",
+"subsystem":"Glycolysis/Gluconeogenesis",
+"notes":{
+"original_bigg_ids":[
+"TPI"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"TPI"
+],
+"biocyc":[
+"META:TRIOSEPISOMERIZATION-RXN"
+],
+"ec-code":[
+"5.3.1.1"
+],
+"kegg.reaction":[
+"R01015"
+],
+"metanetx.reaction":[
+"MNXR104918"
+],
+"reactome.reaction":[
+"R-RNO-70481",
+"R-MMU-70481",
+"R-XTR-70481",
+"R-SSC-70481",
+"R-GGA-352927",
+"R-SCE-70454",
+"R-CEL-70481",
+"R-PFA-70454",
+"R-XTR-70454",
+"R-BTA-70481",
+"R-BTA-70454",
+"R-GGA-352914",
+"R-ATH-70481",
+"R-CFA-70454",
+"R-OSA-70454",
+"R-HSA-70481",
+"R-DRE-70454",
+"R-DME-70481",
+"R-OSA-70481",
+"R-DRE-70481",
+"R-ATH-70454",
+"R-HSA-70454",
+"R-SSC-70454",
+"R-DDI-70454",
+"R-SCE-70481",
+"R-CFA-70481",
+"R-PFA-70481",
+"R-DDI-70481",
+"R-SPO-70454",
+"R-SPO-70481",
+"R-RNO-70454",
+"R-MMU-70454",
+"R-CEL-70454",
+"R-GGA-70481",
+"R-GGA-70454",
+"R-DME-70454"
+],
+"rhea":[
+"18587",
+"18588",
+"18586",
+"18585"
+],
+"sabiork":[
+"4"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00747"
+]
+}
+},
+{
+"id":"EX_ac_e",
+"name":"Acetate exchange",
+"metabolites":{
+"ac_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_ac_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_ac_e"
+],
+"biocyc":[
+"META:RXN0-1981",
+"META:TRANS-RXN0-567"
+],
+"metanetx.reaction":[
+"MNXR95431"
+],
+"rhea":[
+"27817",
+"27814",
+"27816",
+"27815"
+],
+"sabiork":[
+"12184"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn09787",
+"rxn09866",
+"rxn10904",
+"rxn08063"
+]
+}
+},
+{
+"id":"EX_acald_e",
+"name":"Acetaldehyde exchange",
+"metabolites":{
+"acald_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_acald_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_acald_e"
+],
+"metanetx.reaction":[
+"MNXR95212"
+],
+"reactome.reaction":[
+"R-HSA-449872"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn09700",
+"rxn08033",
+"rxn13212",
+"rxn08032"
+]
+}
+},
+{
+"id":"EX_akg_e",
+"name":"2-Oxoglutarate exchange",
+"metabolites":{
+"akg_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_akg_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_akg_e"
+],
+"metanetx.reaction":[
+"MNXR95663"
+],
+"sabiork":[
+"13794"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn10923",
+"rxn08096",
+"rxn13220"
+]
+}
+},
+{
+"id":"EX_co2_e",
+"name":"CO2 exchange",
+"metabolites":{
+"co2_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_co2_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_co2_e"
+],
+"biocyc":[
+"META:TRANS-RXN0-545"
+],
+"metanetx.reaction":[
+"MNXR96810"
+],
+"reactome.reaction":[
+"R-DDI-1247645",
+"R-CFA-1237069",
+"R-TGU-1247649",
+"R-CFA-1237042",
+"R-CEL-1247645",
+"R-XTR-1237069",
+"R-HSA-1247645",
+"R-OSA-1237042",
+"R-GGA-1237042",
+"R-BTA-1247645",
+"R-GGA-1247649",
+"R-RNO-1247645",
+"R-XTR-1247645",
+"R-TGU-1237042",
+"R-SCE-1247649",
+"R-MMU-1247649",
+"R-CFA-1247649",
+"R-GGA-1247645",
+"R-SSC-1247645",
+"R-BTA-1237069",
+"R-RNO-1237069",
+"R-SCE-1237042",
+"R-DDI-1247649",
+"R-SSC-1237042",
+"R-DRE-1247649",
+"R-DRE-1237042",
+"R-DDI-1237042",
+"R-DME-1237042",
+"R-MMU-1237042",
+"R-SSC-1247649",
+"R-TGU-1237069",
+"R-BTA-1247649",
+"R-CFA-1247645",
+"R-RNO-1247649",
+"R-HSA-1237069",
+"R-CEL-1237069",
+"R-DDI-1237069",
+"R-MMU-1237069",
+"R-DME-1247645",
+"R-ATH-1237042",
+"R-OSA-1247649",
+"R-HSA-1237042",
+"R-DRE-1247645",
+"R-HSA-1247649",
+"R-MMU-1247645",
+"R-DME-1237069",
+"R-RNO-1237042",
+"R-TGU-1247645",
+"R-BTA-1237042",
+"R-GGA-1237069",
+"R-DME-1247649",
+"R-SSC-1237069",
+"R-DRE-1237069",
+"R-ATH-1247649"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn05467",
+"rxn08237",
+"rxn09706",
+"rxn09821",
+"rxn09775",
+"rxn09876",
+"rxn08238",
+"rxn09860"
+]
+}
+},
+{
+"id":"EX_etoh_e",
+"name":"Ethanol exchange",
+"metabolites":{
+"etoh_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_etoh_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_etoh_e"
+],
+"biocyc":[
+"META:TRANS-RXN0-546"
+],
+"metanetx.reaction":[
+"MNXR97980"
+],
+"rhea":[
+"35269",
+"35267",
+"35270",
+"35268"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn09683",
+"rxn08428",
+"rxn09764"
+]
+}
+},
+{
+"id":"EX_for_e",
+"name":"Formate exchange",
+"metabolites":{
+"for_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_for_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_for_e"
+],
+"biocyc":[
+"META:TRANS-RXN-1"
+],
+"metanetx.reaction":[
+"MNXR99620"
+],
+"reactome.reaction":[
+"R-HSA-6803255"
+],
+"rhea":[
+"29681",
+"29680",
+"29682",
+"29679"
+],
+"sabiork":[
+"12483"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn09754",
+"rxn08525",
+"rxn09682",
+"rxn08526"
+]
+}
+},
+{
+"id":"EX_fru_e",
+"name":"D-Fructose exchange",
+"metabolites":{
+"fru_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_fru_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_fru_e"
+],
+"metanetx.reaction":[
+"MNXR99663"
+],
+"reactome.reaction":[
+"R-OSA-189222",
+"R-XTR-189222",
+"R-SCE-189222",
+"R-ATH-189222",
+"R-RNO-189222",
+"R-DME-189222",
+"R-TGU-189222",
+"R-SSC-189222",
+"R-CFA-189222",
+"R-DRE-189222",
+"R-HSA-189222",
+"R-GGA-189222",
+"R-BTA-189222",
+"R-MMU-189222",
+"R-DDI-189222"
+],
+"sabiork":[
+"13415"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn12996",
+"rxn08537"
+]
+}
+},
+{
+"id":"EX_fum_e",
+"name":"Fumarate exchange",
+"metabolites":{
+"fum_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_fum_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_fum_e"
+],
+"biocyc":[
+"META:TRANS-RXN0-553"
+],
+"metanetx.reaction":[
+"MNXR99715"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn08544",
+"rxn11013"
+]
+}
+},
+{
+"id":"EX_glc__D_e",
+"name":"D-Glucose exchange",
+"metabolites":{
+"glc__D_e":-1.0
+},
+"lower_bound":-10.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_glc_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_glc__D_e"
+],
+"biocyc":[
+"META:TRANS-RXN0-574"
+],
+"metanetx.reaction":[
+"MNXR100188"
+],
+"sabiork":[
+"7002",
+"601"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn09875",
+"rxn09679",
+"rxn08617"
+]
+}
+},
+{
+"id":"EX_gln__L_e",
+"name":"L-Glutamine exchange",
+"metabolites":{
+"gln__L_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_gln_L_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_gln__L_e"
+],
+"biocyc":[
+"META:TRANS-RXN-233"
+],
+"metanetx.reaction":[
+"MNXR100259"
+],
+"reactome.reaction":[
+"R-HSA-212651",
+"R-BTA-212614",
+"R-RNO-212614",
+"R-SSC-212614",
+"R-MMU-212614",
+"R-HSA-212614",
+"R-GGA-212614",
+"R-CFA-212614",
+"R-TGU-212614",
+"R-SCE-212614"
+],
+"sabiork":[
+"13421"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn08625",
+"rxn10928"
+]
+}
+},
+{
+"id":"EX_glu__L_e",
+"name":"L-Glutamate exchange",
+"metabolites":{
+"glu__L_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_glu_L_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_glu__L_e"
+],
+"biocyc":[
+"META:TRANS-RXN-234",
+"META:TRANS-RXN-232"
+],
+"metanetx.reaction":[
+"MNXR100301"
+],
+"reactome.reaction":[
+"R-HSA-212658",
+"R-TGU-210439",
+"R-GGA-210439",
+"R-XTR-210439",
+"R-RNO-210439",
+"R-CFA-210439",
+"R-CEL-210439",
+"R-DME-210439",
+"R-SSC-210439",
+"R-HSA-210439",
+"R-DRE-210439",
+"R-MMU-210439",
+"R-BTA-210439"
+],
+"sabiork":[
+"12283"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn08633",
+"rxn09750",
+"rxn13304",
+"rxn13120",
+"rxn10917"
+]
+}
+},
+{
+"id":"EX_h_e",
+"name":"H+ exchange",
+"metabolites":{
+"h_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_h_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_h_e"
+],
+"biocyc":[
+"META:RXN-14452"
+],
+"metanetx.reaction":[
+"MNXR100765"
+],
+"reactome.reaction":[
+"R-HSA-2534378",
+"R-DDI-74723",
+"R-BTA-170026",
+"R-CFA-170026",
+"R-SCE-74723",
+"R-DRE-74723",
+"R-HSA-170026",
+"R-TGU-2534378",
+"R-HSA-74723",
+"R-CFA-2534378",
+"R-TGU-74723",
+"R-OSA-170026",
+"R-RNO-2534378",
+"R-GGA-2534378",
+"R-MMU-2534378",
+"R-BTA-2534378",
+"R-SSC-2534378",
+"R-DRE-170026",
+"R-TGU-170026",
+"R-GGA-170026",
+"R-SCE-170026",
+"R-DRE-2534378",
+"R-BTA-74723",
+"R-SPO-74723",
+"R-XTR-74723",
+"R-RNO-74723",
+"R-XTR-2534378",
+"R-MMU-74723",
+"R-CFA-74723",
+"R-GGA-74723",
+"R-CEL-170026",
+"R-MMU-170026",
+"R-ATH-74723",
+"R-DME-74723",
+"R-PFA-74723",
+"R-SSC-74723",
+"R-XTR-170026",
+"R-SSC-170026",
+"R-CEL-74723",
+"R-ATH-170026",
+"R-RNO-170026",
+"R-DME-170026"
+],
+"rhea":[
+"34980",
+"34981",
+"34982",
+"34979"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn11009",
+"rxn08730"
+]
+}
+},
+{
+"id":"EX_h2o_e",
+"name":"H2O exchange",
+"metabolites":{
+"h2o_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_h2o_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_h2o_e"
+],
+"biocyc":[
+"META:TRANS-RXN-145",
+"META:TRANS-RXN0-547"
+],
+"metanetx.reaction":[
+"MNXR98641"
+],
+"reactome.reaction":[
+"R-ATH-507868",
+"R-CFA-432054",
+"R-CFA-432010",
+"R-RNO-507868",
+"R-OSA-432065",
+"R-GGA-432010",
+"R-SPO-445714",
+"R-PFA-445714",
+"R-CFA-432065",
+"R-GGA-432067",
+"R-TGU-432054",
+"R-TGU-445714",
+"R-OSA-507868",
+"R-DRE-507868",
+"R-SPO-507868",
+"R-BTA-432054",
+"R-GGA-507870",
+"R-OSA-432010",
+"R-DME-432065",
+"R-DRE-432067",
+"R-PFA-507868",
+"R-SSC-432054",
+"R-HSA-432065",
+"R-OSA-507870",
+"R-HSA-432054",
+"R-SSC-432065",
+"R-CEL-507868",
+"R-XTR-507868",
+"R-ATH-507870",
+"R-SCE-432065",
+"R-BTA-507870",
+"R-DME-432010",
+"R-CFA-445714",
+"R-DRE-445714",
+"R-BTA-507868",
+"R-GGA-507868",
+"R-RNO-432054",
+"R-RNO-432010",
+"R-SSC-432067",
+"R-CEL-445714",
+"R-DDI-432065",
+"R-ATH-432010",
+"R-SCE-432054",
+"R-MMU-432065",
+"R-MMU-445714",
+"R-GGA-432065",
+"R-HSA-432067",
+"R-SSC-507870",
+"R-SCE-432067",
+"R-RNO-507870",
+"R-DME-432054",
+"R-ATH-432067",
+"R-BTA-445714",
+"R-DRE-507870",
+"R-DME-507868",
+"R-DME-507870",
+"R-DRE-432010",
+"R-MMU-432010",
+"R-HSA-445714",
+"R-OSA-432054",
+"R-RNO-432067",
+"R-TGU-432010",
+"R-TGU-507868",
+"R-DDI-432054",
+"R-PFA-507870",
+"R-HSA-507870",
+"R-XTR-432067",
+"R-HSA-432010",
+"R-SSC-507868",
+"R-SCE-507870",
+"R-CEL-507870",
+"R-DDI-507868",
+"R-DRE-432054",
+"R-XTR-507870",
+"R-DDI-432010",
+"R-BTA-432065",
+"R-CFA-432067",
+"R-OSA-432067",
+"R-ATH-432065",
+"R-GGA-445714",
+"R-SCE-507868",
+"R-TGU-432065",
+"R-MMU-432067",
+"R-TGU-507870",
+"R-CFA-507870",
+"R-RNO-432065",
+"R-MMU-432054",
+"R-MMU-507868",
+"R-SPO-507870",
+"R-SCE-432010",
+"R-MMU-507870",
+"R-SSC-445714",
+"R-HSA-507868",
+"R-DME-432067",
+"R-SSC-432010",
+"R-TGU-432067",
+"R-GGA-432054",
+"R-BTA-432010",
+"R-SCE-445714",
+"R-DDI-507870",
+"R-ATH-432054",
+"R-DDI-432067",
+"R-XTR-445714",
+"R-BTA-432067",
+"R-CFA-507868",
+"R-RNO-445714"
+],
+"rhea":[
+"29668",
+"29669",
+"29667",
+"29670"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn08687",
+"rxn08686",
+"rxn09745",
+"rxn09838",
+"rxn09874",
+"rxn09812",
+"rxn09643",
+"rxn05319"
+]
+}
+},
+{
+"id":"EX_lac__D_e",
+"name":"D-lactate exchange",
+"metabolites":{
+"lac__D_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_lac_D_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_lac__D_e"
+],
+"metanetx.reaction":[
+"MNXR97840"
+],
+"sabiork":[
+"12471"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn08351"
+]
+}
+},
+{
+"id":"EX_mal__L_e",
+"name":"L-Malate exchange",
+"metabolites":{
+"mal__L_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_mal_L_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_mal__L_e"
+],
+"biocyc":[
+"META:TRANS-RXN-225",
+"META:TRANS-RXN-224"
+],
+"metanetx.reaction":[
+"MNXR101367"
+],
+"sabiork":[
+"13793"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn10967",
+"rxn08868"
+]
+}
+},
+{
+"id":"EX_nh4_e",
+"name":"Ammonia exchange",
+"metabolites":{
+"nh4_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_nh4_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_nh4_e"
+],
+"biocyc":[
+"META:TRANS-RXN0-206",
+"META:RXN-9615",
+"META:TRANS-RXN0-544"
+],
+"metanetx.reaction":[
+"MNXR101950"
+],
+"reactome.reaction":[
+"R-CEL-444416",
+"R-SSC-444416",
+"R-DDI-444416",
+"R-MMU-444416",
+"R-DRE-444416",
+"R-GGA-444416",
+"R-CFA-444416",
+"R-HSA-444416",
+"R-XTR-444416",
+"R-BTA-444416",
+"R-RNO-444416",
+"R-TGU-444416",
+"R-DME-444416"
+],
+"rhea":[
+"28749",
+"28748",
+"28750",
+"28747"
+],
+"sabiork":[
+"11683"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn13364",
+"rxn09835",
+"rxn05466",
+"rxn08987",
+"rxn08986",
+"rxn09736"
+]
+}
+},
+{
+"id":"EX_o2_e",
+"name":"O2 exchange",
+"metabolites":{
+"o2_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_o2_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_o2_e"
+],
+"biocyc":[
+"META:TRANS-RXN0-474"
+],
+"metanetx.reaction":[
+"MNXR102090"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn09641",
+"rxn05468",
+"rxn09031",
+"rxn09032",
+"rxn09734"
+]
+}
+},
+{
+"id":"EX_pi_e",
+"name":"Phosphate exchange",
+"metabolites":{
+"pi_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_pi_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_pi_e"
+],
+"biocyc":[
+"META:TRANS-RXN0-470"
+],
+"metanetx.reaction":[
+"MNXR102871"
+],
+"rhea":[
+"32824",
+"32826",
+"32825",
+"32823"
+],
+"sabiork":[
+"10985"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn10838",
+"rxn09722",
+"rxn09121",
+"rxn13178"
+]
+}
+},
+{
+"id":"EX_pyr_e",
+"name":"Pyruvate exchange",
+"metabolites":{
+"pyr_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_pyr_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_pyr_e"
+],
+"biocyc":[
+"META:TRANS-RXN0-506",
+"META:TRANS-RXN0-570"
+],
+"metanetx.reaction":[
+"MNXR103384"
+],
+"sabiork":[
+"12168"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn10929",
+"rxn09218"
+]
+}
+},
+{
+"id":"EX_succ_e",
+"name":"Succinate exchange",
+"metabolites":{
+"succ_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"",
+"subsystem":"Extracellular exchange",
+"notes":{
+"original_bigg_ids":[
+"EX_succ_e"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"EX_succ_e"
+],
+"biocyc":[
+"META:TRANS-RXN0-552"
+],
+"metanetx.reaction":[
+"MNXR104619"
+],
+"sbo":"SBO:0000627",
+"seed.reaction":[
+"rxn10952",
+"rxn09271"
+]
+}
+},
+{
+"id":"FBA",
+"name":"Fructose-bisphosphate aldolase",
+"metabolites":{
+"dhap_c":1.0,
+"fdp_c":-1.0,
+"g3p_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2097 or b1773 or b2925",
+"subsystem":"Glycolysis/Gluconeogenesis",
+"notes":{
+"original_bigg_ids":[
+"FBA"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"FBA"
+],
+"ec-code":[
+"4.1.2.13"
+],
+"kegg.reaction":[
+"R01068"
+],
+"metanetx.reaction":[
+"MNXR99459"
+],
+"rhea":[
+"14729",
+"14732",
+"14731",
+"14730"
+],
+"sabiork":[
+"1338"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00786"
+]
+}
+},
+{
+"id":"FBP",
+"name":"Fructose-bisphosphatase",
+"metabolites":{
+"f6p_c":1.0,
+"fdp_c":-1.0,
+"h2o_c":-1.0,
+"pi_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3925 or b4232",
+"subsystem":"Glycolysis/Gluconeogenesis",
+"notes":{
+"original_bigg_ids":[
+"FBP"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"FBP"
+],
+"ec-code":[
+"3.1.3.11"
+],
+"metanetx.reaction":[
+"MNXR99465"
+],
+"rhea":[
+"11067",
+"11065",
+"11066",
+"11064"
+],
+"sabiork":[
+"2084"
+],
+"sbo":"SBO:0000176"
+}
+},
+{
+"id":"FORt2",
+"name":"Formate transport in via proton symport",
+"metabolites":{
+"for_c":1.0,
+"for_e":-1.0,
+"h_c":1.0,
+"h_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0904 or b2492",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"FORt2"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"FORt2"
+],
+"metanetx.reaction":[
+"MNXR99621"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn08524",
+"rxn05559"
+]
+}
+},
+{
+"id":"FORt",
+"name":"Formate transport via diffusion",
+"metabolites":{
+"for_c":1.0,
+"for_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":0.0,
+"gene_reaction_rule":"b0904 or b2492",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"FORti"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"FORt"
+],
+"biocyc":[
+"META:TRANS-RXN-1"
+],
+"metanetx.reaction":[
+"MNXR99620"
+],
+"reactome.reaction":[
+"R-HSA-6803255"
+],
+"rhea":[
+"29681",
+"29680",
+"29682",
+"29679"
+],
+"sabiork":[
+"12483"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn09754",
+"rxn08525",
+"rxn09682",
+"rxn08526"
+]
+}
+},
+{
+"id":"FRD7",
+"name":"Fumarate reductase",
+"metabolites":{
+"fum_c":-1.0,
+"q8_c":1.0,
+"q8h2_c":-1.0,
+"succ_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b4151 and b4152 and b4153 and b4154",
+"subsystem":"Oxidative Phosphorylation",
+"notes":{
+"original_bigg_ids":[
+"FRD7"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"FRD7"
+],
+"metanetx.reaction":[
+"MNXR99641"
+],
+"rhea":[
+"29190",
+"29189",
+"29187",
+"29188"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn09272"
+]
+}
+},
+{
+"id":"FRUpts2",
+"name":"Fructose transport via PEP:Pyr PTS (f6p generating)",
+"metabolites":{
+"f6p_c":1.0,
+"fru_e":-1.0,
+"pep_c":-1.0,
+"pyr_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b1817 and b1818 and b1819 and b2415 and b2416",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"FRUpts2"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"FRUpts2"
+],
+"metanetx.reaction":[
+"MNXR99662"
+],
+"sbo":"SBO:0000185"
+}
+},
+{
+"id":"FUM",
+"name":"Fumarase",
+"metabolites":{
+"fum_c":-1.0,
+"h2o_c":-1.0,
+"mal__L_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b1612 or b4122 or b1611",
+"subsystem":"Citric Acid Cycle",
+"notes":{
+"original_bigg_ids":[
+"FUM"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"FUM"
+],
+"biocyc":[
+"META:FUMHYDR-RXN"
+],
+"ec-code":[
+"4.2.1.2"
+],
+"kegg.reaction":[
+"R01082"
+],
+"metanetx.reaction":[
+"MNXR99705"
+],
+"reactome.reaction":[
+"R-TGU-451033",
+"R-TGU-70982",
+"R-HSA-70982",
+"R-ATH-451033",
+"R-SPO-70982",
+"R-SPO-451033",
+"R-XTR-451033",
+"R-MMU-70982",
+"R-DRE-70982",
+"R-DME-70982",
+"R-DME-451033",
+"R-HSA-451033",
+"R-SCE-451033",
+"R-DDI-451033",
+"R-OSA-451033",
+"R-CFA-70982",
+"R-XTR-70982",
+"R-MMU-451033",
+"R-OSA-70982",
+"R-BTA-70982",
+"R-DRE-451033",
+"R-GGA-373141",
+"R-RNO-451033",
+"R-CEL-451033",
+"R-ATH-70982",
+"R-GGA-373145",
+"R-CEL-70982",
+"R-BTA-451033",
+"R-SSC-451033",
+"R-SCE-70982",
+"R-CFA-451033",
+"R-RNO-70982",
+"R-GGA-70982",
+"R-DDI-70982",
+"R-GGA-451033",
+"R-SSC-70982"
+],
+"rhea":[
+"12463",
+"12461",
+"12462",
+"12460"
+],
+"sabiork":[
+"256"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00799"
+]
+}
+},
+{
+"id":"FUMt2_2",
+"name":"Fumarate transport via proton symport (2 H)",
+"metabolites":{
+"fum_c":1.0,
+"fum_e":-1.0,
+"h_c":2.0,
+"h_e":-2.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3528",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"FUMt2_2"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"FUMt2_2"
+],
+"biocyc":[
+"META:TRANS-RXN-121B"
+],
+"metanetx.reaction":[
+"MNXR99711"
+],
+"rhea":[
+"29332",
+"29334",
+"29333",
+"29331"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn08542",
+"rxn10152"
+]
+}
+},
+{
+"id":"G6PDH2r",
+"name":"Glucose 6-phosphate dehydrogenase",
+"metabolites":{
+"6pgl_c":1.0,
+"g6p_c":-1.0,
+"h_c":1.0,
+"nadp_c":-1.0,
+"nadph_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b1852",
+"subsystem":"Pentose Phosphate Pathway",
+"notes":{
+"original_bigg_ids":[
+"G6PDH2r"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"G6PDH2r"
+],
+"biocyc":[
+"META:GLU6PDEHYDROG-RXN"
+],
+"ec-code":[
+"1.1.1.363",
+"1.1.1.49"
+],
+"kegg.reaction":[
+"R00835"
+],
+"metanetx.reaction":[
+"MNXR99907"
+],
+"rhea":[
+"15842",
+"15843",
+"15841",
+"15844"
+],
+"sabiork":[
+"1176",
+"6509"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00604"
+]
+}
+},
+{
+"id":"GAPD",
+"name":"Glyceraldehyde-3-phosphate dehydrogenase",
+"metabolites":{
+"13dpg_c":1.0,
+"g3p_c":-1.0,
+"h_c":1.0,
+"nad_c":-1.0,
+"nadh_c":1.0,
+"pi_c":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b1779",
+"subsystem":"Glycolysis/Gluconeogenesis",
+"notes":{
+"original_bigg_ids":[
+"GAPD"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"GAPD"
+],
+"biocyc":[
+"META:GAPOXNPHOSPHN-RXN"
+],
+"ec-code":[
+"1.2.1.12",
+"1.2.1.59"
+],
+"kegg.reaction":[
+"R01061"
+],
+"metanetx.reaction":[
+"MNXR100040"
+],
+"reactome.reaction":[
+"R-ATH-70482",
+"R-DME-70449",
+"R-PFA-70482",
+"R-SPO-70449",
+"R-DRE-70449",
+"R-CEL-70449",
+"R-CEL-70482",
+"R-CFA-70449",
+"R-MMU-70482",
+"R-HSA-70449",
+"R-OSA-70482",
+"R-GGA-352956",
+"R-RNO-70449",
+"R-SCE-70449",
+"R-SSC-70482",
+"R-ATH-70449",
+"R-GGA-70482",
+"R-OSA-70449",
+"R-GGA-352921",
+"R-DDI-70449",
+"R-SPO-70482",
+"R-TGU-70482",
+"R-SCE-70482",
+"R-HSA-70482",
+"R-DME-70482",
+"R-PFA-70449",
+"R-XTR-70449",
+"R-DRE-70482",
+"R-XTR-70482",
+"R-GGA-70449",
+"R-RNO-70482",
+"R-SSC-70449",
+"R-DDI-70482",
+"R-TGU-70449",
+"R-MMU-70449",
+"R-CFA-70482",
+"R-BTA-70449",
+"R-BTA-70482"
+],
+"rhea":[
+"10303",
+"10300",
+"10302",
+"10301"
+],
+"sabiork":[
+"7844"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00781"
+]
+}
+},
+{
+"id":"GLCpts",
+"name":"D-glucose transport via PEP:Pyr PTS",
+"metabolites":{
+"g6p_c":1.0,
+"glc__D_e":-1.0,
+"pep_c":-1.0,
+"pyr_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"(b2417 and b1101 and b2415 and b2416) or (b1817 and b1818 and b1819 and b2415 and b2416) or (b2417 and b1621 and b2415 and b2416)",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"GLCpts"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"GLCpts"
+],
+"metanetx.reaction":[
+"MNXR100237"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn08612",
+"rxn05226"
+]
+}
+},
+{
+"id":"GLNS",
+"name":"Glutamine synthetase",
+"metabolites":{
+"adp_c":1.0,
+"atp_c":-1.0,
+"gln__L_c":1.0,
+"glu__L_c":-1.0,
+"h_c":1.0,
+"nh4_c":-1.0,
+"pi_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3870 or b1297",
+"subsystem":"Glutamate Metabolism",
+"notes":{
+"original_bigg_ids":[
+"GLNS"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"GLNS"
+],
+"biocyc":[
+"META:GLUTAMINESYN-RXN"
+],
+"ec-code":[
+"6.3.1.2"
+],
+"kegg.reaction":[
+"R00253"
+],
+"metanetx.reaction":[
+"MNXR100024"
+],
+"reactome.reaction":[
+"R-GGA-70606",
+"R-RNO-70606",
+"R-TGU-70606",
+"R-DME-70606",
+"R-CEL-70606",
+"R-DRE-70606",
+"R-XTR-70606",
+"R-SPO-70606",
+"R-ATH-70606",
+"R-CFA-70606",
+"R-BTA-70606",
+"R-OSA-70606",
+"R-SSC-70606",
+"R-MMU-70606",
+"R-HSA-70606",
+"R-SCE-70606"
+],
+"rhea":[
+"16172",
+"16171",
+"16169",
+"16170"
+],
+"sabiork":[
+"760"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00187"
+]
+}
+},
+{
+"id":"GLNabc",
+"name":"L-glutamine transport via ABC system",
+"metabolites":{
+"adp_c":1.0,
+"atp_c":-1.0,
+"gln__L_c":1.0,
+"gln__L_e":-1.0,
+"h2o_c":-1.0,
+"h_c":1.0,
+"pi_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0811 and b0810 and b0809",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"GLNabc"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"GLNabc"
+],
+"biocyc":[
+"META:ABC-12-RXN"
+],
+"ec-code":[
+"3.6.3.21"
+],
+"metanetx.reaction":[
+"MNXR100258"
+],
+"rhea":[
+"29895#1",
+"29897#1",
+"29898#1",
+"29896#1"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn11233",
+"rxn05196",
+"rxn05155",
+"rxn11101",
+"rxn08624"
+]
+}
+},
+{
+"id":"GLUDy",
+"name":"Glutamate dehydrogenase (NADP)",
+"metabolites":{
+"akg_c":1.0,
+"glu__L_c":-1.0,
+"h2o_c":-1.0,
+"h_c":1.0,
+"nadp_c":-1.0,
+"nadph_c":1.0,
+"nh4_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b1761",
+"subsystem":"Glutamate Metabolism",
+"notes":{
+"original_bigg_ids":[
+"GLUDy"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"GLUDy"
+],
+"biocyc":[
+"META:GLUTDEHYD-RXN"
+],
+"ec-code":[
+"1.4.1.13",
+"1.4.1.3",
+"1.4.1.4"
+],
+"kegg.reaction":[
+"R00248"
+],
+"metanetx.reaction":[
+"MNXR100086"
+],
+"rhea":[
+"11613",
+"11614",
+"11612",
+"11615"
+],
+"sabiork":[
+"757"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00184"
+]
+}
+},
+{
+"id":"GLUN",
+"name":"Glutaminase",
+"metabolites":{
+"gln__L_c":-1.0,
+"glu__L_c":1.0,
+"h2o_c":-1.0,
+"nh4_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b1812 or b0485 or b1524",
+"subsystem":"Glutamate Metabolism",
+"notes":{
+"original_bigg_ids":[
+"GLUN"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"GLUN"
+],
+"biocyc":[
+"META:GLUTAMIN-RXN"
+],
+"ec-code":[
+"6.3.5.2",
+"4.3.3.6",
+"6.3.5.5",
+"1.4.7.1",
+"6.3.5.4",
+"3.5.1.2",
+"6.3.4.2",
+"1.4.1.13",
+"3.5.1.38"
+],
+"kegg.reaction":[
+"R00256"
+],
+"metanetx.reaction":[
+"MNXR100030"
+],
+"reactome.reaction":[
+"R-TGU-70609",
+"R-XTR-70609",
+"R-SSC-70609",
+"R-GGA-70609",
+"R-DDI-70609",
+"R-MMU-70609",
+"R-DME-70609",
+"R-RNO-70609",
+"R-CEL-70609",
+"R-BTA-70609",
+"R-DRE-70609",
+"R-HSA-70609",
+"R-CFA-70609"
+],
+"rhea":[
+"15892",
+"15889",
+"15891",
+"15890"
+],
+"sabiork":[
+"762"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00189"
+]
+}
+},
+{
+"id":"GLUSy",
+"name":"Glutamate synthase (NADPH)",
+"metabolites":{
+"akg_c":-1.0,
+"gln__L_c":-1.0,
+"glu__L_c":2.0,
+"h_c":-1.0,
+"nadp_c":1.0,
+"nadph_c":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3212 and b3213",
+"subsystem":"Glutamate Metabolism",
+"notes":{
+"original_bigg_ids":[
+"GLUSy"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"GLUSy"
+],
+"biocyc":[
+"META:GLUTAMATESYN-RXN"
+],
+"ec-code":[
+"1.4.1.13"
+],
+"kegg.reaction":[
+"R00114"
+],
+"metanetx.reaction":[
+"MNXR100291"
+],
+"rhea":[
+"15503",
+"15501",
+"15504",
+"15502"
+],
+"sabiork":[
+"694"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00085"
+]
+}
+},
+{
+"id":"GLUt2r",
+"name":"L glutamate transport via proton symport reversible",
+"metabolites":{
+"glu__L_c":1.0,
+"glu__L_e":-1.0,
+"h_c":1.0,
+"h_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b4077",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"GLUt2r"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"GLUt2r"
+],
+"metanetx.reaction":[
+"MNXR100300"
+],
+"reactome.reaction":[
+"R-SCE-8875623",
+"R-MMU-8875623",
+"R-TGU-8875623",
+"R-XTR-8875623",
+"R-SSC-8875623",
+"R-DME-8875623",
+"R-CEL-8875623",
+"R-DRE-8875623",
+"R-GGA-8875623",
+"R-HSA-8875623",
+"R-RNO-8875623",
+"R-DDI-8875623",
+"R-CFA-8875623",
+"R-BTA-8875623"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn05297",
+"rxn09813",
+"rxn13303",
+"rxn09751",
+"rxn08631"
+]
+}
+},
+{
+"id":"GND",
+"name":"Phosphogluconate dehydrogenase",
+"metabolites":{
+"6pgc_c":-1.0,
+"co2_c":1.0,
+"nadp_c":-1.0,
+"nadph_c":1.0,
+"ru5p__D_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2029",
+"subsystem":"Pentose Phosphate Pathway",
+"notes":{
+"original_bigg_ids":[
+"GND"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"GND"
+],
+"biocyc":[
+"META:RXN-9952"
+],
+"ec-code":[
+"1.1.1.44",
+"1.1.1.351"
+],
+"kegg.reaction":[
+"R01528"
+],
+"metanetx.reaction":[
+"MNXR100389"
+],
+"reactome.reaction":[
+"R-PFA-71299",
+"R-GGA-71299",
+"R-HSA-71299",
+"R-SPO-71299",
+"R-XTR-71299",
+"R-ATH-71299",
+"R-TGU-71299",
+"R-OSA-71299",
+"R-MMU-71299",
+"R-DRE-71299",
+"R-SCE-71299",
+"R-SSC-71299",
+"R-DDI-71299",
+"R-CFA-71299",
+"R-DME-71299",
+"R-BTA-71299",
+"R-CEL-71299"
+],
+"rhea":[
+"10116",
+"10117",
+"10118",
+"10119"
+],
+"sabiork":[
+"108"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn01115"
+]
+}
+},
+{
+"id":"H2Ot",
+"name":"H2O transport via diffusion",
+"metabolites":{
+"h2o_c":1.0,
+"h2o_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0875 or s0001",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"H2Ot"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"H2Ot"
+],
+"biocyc":[
+"META:TRANS-RXN-145",
+"META:TRANS-RXN0-547"
+],
+"metanetx.reaction":[
+"MNXR98641"
+],
+"reactome.reaction":[
+"R-ATH-507868",
+"R-CFA-432054",
+"R-CFA-432010",
+"R-RNO-507868",
+"R-OSA-432065",
+"R-GGA-432010",
+"R-SPO-445714",
+"R-PFA-445714",
+"R-CFA-432065",
+"R-GGA-432067",
+"R-TGU-432054",
+"R-TGU-445714",
+"R-OSA-507868",
+"R-DRE-507868",
+"R-SPO-507868",
+"R-BTA-432054",
+"R-GGA-507870",
+"R-OSA-432010",
+"R-DME-432065",
+"R-DRE-432067",
+"R-PFA-507868",
+"R-SSC-432054",
+"R-HSA-432065",
+"R-OSA-507870",
+"R-HSA-432054",
+"R-SSC-432065",
+"R-CEL-507868",
+"R-XTR-507868",
+"R-ATH-507870",
+"R-SCE-432065",
+"R-BTA-507870",
+"R-DME-432010",
+"R-CFA-445714",
+"R-DRE-445714",
+"R-BTA-507868",
+"R-GGA-507868",
+"R-RNO-432054",
+"R-RNO-432010",
+"R-SSC-432067",
+"R-CEL-445714",
+"R-DDI-432065",
+"R-ATH-432010",
+"R-SCE-432054",
+"R-MMU-432065",
+"R-MMU-445714",
+"R-GGA-432065",
+"R-HSA-432067",
+"R-SSC-507870",
+"R-SCE-432067",
+"R-RNO-507870",
+"R-DME-432054",
+"R-ATH-432067",
+"R-BTA-445714",
+"R-DRE-507870",
+"R-DME-507868",
+"R-DME-507870",
+"R-DRE-432010",
+"R-MMU-432010",
+"R-HSA-445714",
+"R-OSA-432054",
+"R-RNO-432067",
+"R-TGU-432010",
+"R-TGU-507868",
+"R-DDI-432054",
+"R-PFA-507870",
+"R-HSA-507870",
+"R-XTR-432067",
+"R-HSA-432010",
+"R-SSC-507868",
+"R-SCE-507870",
+"R-CEL-507870",
+"R-DDI-507868",
+"R-DRE-432054",
+"R-XTR-507870",
+"R-DDI-432010",
+"R-BTA-432065",
+"R-CFA-432067",
+"R-OSA-432067",
+"R-ATH-432065",
+"R-GGA-445714",
+"R-SCE-507868",
+"R-TGU-432065",
+"R-MMU-432067",
+"R-TGU-507870",
+"R-CFA-507870",
+"R-RNO-432065",
+"R-MMU-432054",
+"R-MMU-507868",
+"R-SPO-507870",
+"R-SCE-432010",
+"R-MMU-507870",
+"R-SSC-445714",
+"R-HSA-507868",
+"R-DME-432067",
+"R-SSC-432010",
+"R-TGU-432067",
+"R-GGA-432054",
+"R-BTA-432010",
+"R-SCE-445714",
+"R-DDI-507870",
+"R-ATH-432054",
+"R-DDI-432067",
+"R-XTR-445714",
+"R-BTA-432067",
+"R-CFA-507868",
+"R-RNO-445714"
+],
+"rhea":[
+"29668",
+"29669",
+"29667",
+"29670"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn08687",
+"rxn08686",
+"rxn09745",
+"rxn09838",
+"rxn09874",
+"rxn09812",
+"rxn09643",
+"rxn05319"
+]
+}
+},
+{
+"id":"ICDHyr",
+"name":"Isocitrate dehydrogenase (NADP)",
+"metabolites":{
+"akg_c":1.0,
+"co2_c":1.0,
+"icit_c":-1.0,
+"nadp_c":-1.0,
+"nadph_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b1136",
+"subsystem":"Citric Acid Cycle",
+"notes":{
+"original_bigg_ids":[
+"ICDHyr"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ICDHyr"
+],
+"ec-code":[
+"1.1.1.42"
+],
+"kegg.reaction":[
+"R00267"
+],
+"metanetx.reaction":[
+"MNXR100781"
+],
+"rhea":[
+"19629",
+"19630",
+"19631",
+"19632"
+],
+"sabiork":[
+"269"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00198"
+]
+}
+},
+{
+"id":"ICL",
+"name":"Isocitrate lyase",
+"metabolites":{
+"glx_c":1.0,
+"icit_c":-1.0,
+"succ_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b4015",
+"subsystem":"Anaplerotic reactions",
+"notes":{
+"original_bigg_ids":[
+"ICL"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ICL"
+],
+"ec-code":[
+"4.1.3.1"
+],
+"kegg.reaction":[
+"R00479"
+],
+"metanetx.reaction":[
+"MNXR100789"
+],
+"rhea":[
+"13248",
+"13245",
+"13246",
+"13247"
+],
+"sabiork":[
+"911"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00336"
+]
+}
+},
+{
+"id":"LDH_D",
+"name":"D-lactate dehydrogenase",
+"metabolites":{
+"h_c":1.0,
+"lac__D_c":-1.0,
+"nad_c":-1.0,
+"nadh_c":1.0,
+"pyr_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2133 or b1380",
+"subsystem":"Pyruvate Metabolism",
+"notes":{
+"original_bigg_ids":[
+"LDH_D"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"LDH_D"
+],
+"biocyc":[
+"META:DLACTDEHYDROGNAD-RXN"
+],
+"ec-code":[
+"1.1.1.28"
+],
+"kegg.reaction":[
+"R00704"
+],
+"metanetx.reaction":[
+"MNXR101037"
+],
+"rhea":[
+"16370",
+"16371",
+"16372",
+"16369"
+],
+"sabiork":[
+"155"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00500"
+]
+}
+},
+{
+"id":"MALS",
+"name":"Malate synthase",
+"metabolites":{
+"accoa_c":-1.0,
+"coa_c":1.0,
+"glx_c":-1.0,
+"h2o_c":-1.0,
+"h_c":1.0,
+"mal__L_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b4014 or b2976",
+"subsystem":"Anaplerotic reactions",
+"notes":{
+"original_bigg_ids":[
+"MALS"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"MALS"
+],
+"biocyc":[
+"META:MALSYN-RXN"
+],
+"ec-code":[
+"2.3.3.9"
+],
+"kegg.reaction":[
+"R00472"
+],
+"metanetx.reaction":[
+"MNXR101347"
+],
+"rhea":[
+"18181",
+"18182",
+"18184",
+"18183"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00330"
+]
+}
+},
+{
+"id":"MALt2_2",
+"name":"Malate transport via proton symport (2 H)",
+"metabolites":{
+"h_c":2.0,
+"h_e":-2.0,
+"mal__L_c":1.0,
+"mal__L_e":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3528",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"MALt2_2"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"MALt2_2"
+],
+"biocyc":[
+"META:TRANS-RXN-121A"
+],
+"metanetx.reaction":[
+"MNXR101370"
+],
+"rhea":[
+"29341",
+"29340",
+"29342",
+"29339"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn08865",
+"rxn10153"
+]
+}
+},
+{
+"id":"MDH",
+"name":"Malate dehydrogenase",
+"metabolites":{
+"h_c":1.0,
+"mal__L_c":-1.0,
+"nad_c":-1.0,
+"nadh_c":1.0,
+"oaa_c":1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3236",
+"subsystem":"Citric Acid Cycle",
+"notes":{
+"original_bigg_ids":[
+"MDH"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"MDH"
+],
+"biocyc":[
+"META:MALATE-DEH-RXN"
+],
+"ec-code":[
+"1.1.1.37",
+"1.1.1.299"
+],
+"kegg.reaction":[
+"R00342"
+],
+"metanetx.reaction":[
+"MNXR101439"
+],
+"reactome.reaction":[
+"R-BTA-70979",
+"R-BTA-198508",
+"R-SCE-70979",
+"R-GGA-70979",
+"R-MMU-71783",
+"R-RNO-71783",
+"R-DDI-198508",
+"R-CFA-71783",
+"R-CFA-198508",
+"R-ATH-70979",
+"R-DME-198508",
+"R-TGU-71783",
+"R-HSA-71783",
+"R-BTA-71783",
+"R-DRE-198508",
+"R-SPO-70979",
+"R-GGA-71783",
+"R-TGU-198508",
+"R-GGA-372422",
+"R-CEL-71783",
+"R-XTR-70979",
+"R-RNO-198508",
+"R-MMU-70979",
+"R-SPO-71783",
+"R-ATH-71783",
+"R-MMU-198508",
+"R-DME-70979",
+"R-TGU-70979",
+"R-CEL-198508",
+"R-DME-71783",
+"R-DRE-70979",
+"R-OSA-71783",
+"R-SSC-198508",
+"R-GGA-372855",
+"R-SSC-70979",
+"R-OSA-70979",
+"R-GGA-373047",
+"R-GGA-198508",
+"R-SSC-71783",
+"R-HSA-70979",
+"R-CFA-70979",
+"R-XTR-71783",
+"R-HSA-198508",
+"R-XTR-198508",
+"R-SCE-71783",
+"R-RNO-70979",
+"R-DRE-71783",
+"R-CEL-70979"
+],
+"rhea":[
+"21432",
+"21433",
+"21434",
+"21435"
+],
+"sabiork":[
+"113"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00248"
+]
+}
+},
+{
+"id":"ME1",
+"name":"Malic enzyme (NAD)",
+"metabolites":{
+"co2_c":1.0,
+"mal__L_c":-1.0,
+"nad_c":-1.0,
+"nadh_c":1.0,
+"pyr_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b1479",
+"subsystem":"Anaplerotic reactions",
+"notes":{
+"original_bigg_ids":[
+"ME1"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ME1"
+],
+"biocyc":[
+"META:1.1.1.39-RXN"
+],
+"ec-code":[
+"1.1.1.38",
+"1.1.1.39"
+],
+"kegg.reaction":[
+"R00214"
+],
+"metanetx.reaction":[
+"MNXR101446"
+],
+"rhea":[
+"12655",
+"12654",
+"12653",
+"12656"
+],
+"sabiork":[
+"141"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00159"
+]
+}
+},
+{
+"id":"ME2",
+"name":"Malic enzyme (NADP)",
+"metabolites":{
+"co2_c":1.0,
+"mal__L_c":-1.0,
+"nadp_c":-1.0,
+"nadph_c":1.0,
+"pyr_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2463",
+"subsystem":"Anaplerotic reactions",
+"notes":{
+"original_bigg_ids":[
+"ME2"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"ME2"
+],
+"biocyc":[
+"META:MALIC-NADP-RXN"
+],
+"ec-code":[
+"1.1.1.40"
+],
+"kegg.reaction":[
+"R00216"
+],
+"metanetx.reaction":[
+"MNXR101443"
+],
+"rhea":[
+"18255",
+"18256",
+"18254",
+"18253"
+],
+"sabiork":[
+"142"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00161"
+]
+}
+},
+{
+"id":"NADH16",
+"name":"NADH dehydrogenase (ubiquinone-8 & 3 protons)",
+"metabolites":{
+"h_c":-4.0,
+"h_e":3.0,
+"nad_c":1.0,
+"nadh_c":-1.0,
+"q8_c":-1.0,
+"q8h2_c":1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b2276 and b2277 and b2278 and b2279 and b2280 and b2281 and b2282 and b2283 and b2284 and b2285 and b2286 and b2287 and b2288",
+"subsystem":"Oxidative Phosphorylation",
+"notes":{
+"original_bigg_ids":[
+"NADH16"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"NADH16"
+],
+"ec-code":[
+"1.6.5.3"
+],
+"metanetx.reaction":[
+"MNXR101864"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn08972"
+]
+}
+},
+{
+"id":"NADTRHD",
+"name":"NAD transhydrogenase",
+"metabolites":{
+"nad_c":-1.0,
+"nadh_c":1.0,
+"nadp_c":1.0,
+"nadph_c":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b3962 or (b1602 and b1603)",
+"subsystem":"Oxidative Phosphorylation",
+"notes":{
+"original_bigg_ids":[
+"NADTRHD"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"NADTRHD"
+],
+"biocyc":[
+"META:PYRNUTRANSHYDROGEN-RXN"
+],
+"ec-code":[
+"1.6.1.3",
+"1.6.1.2",
+"1.6.1.1"
+],
+"kegg.reaction":[
+"R00112"
+],
+"metanetx.reaction":[
+"MNXR101898"
+],
+"rhea":[
+"11692",
+"11695",
+"11694",
+"11693"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00083"
+]
+}
+},
+{
+"id":"NH4t",
+"name":"Ammonia reversible transport",
+"metabolites":{
+"nh4_c":1.0,
+"nh4_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"s0001 or b0451",
+"subsystem":"Inorganic Ion Transport and Metabolism",
+"notes":{
+"original_bigg_ids":[
+"NH4t"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"NH4t"
+],
+"biocyc":[
+"META:TRANS-RXN0-206",
+"META:RXN-9615",
+"META:TRANS-RXN0-544"
+],
+"metanetx.reaction":[
+"MNXR101950"
+],
+"reactome.reaction":[
+"R-CEL-444416",
+"R-SSC-444416",
+"R-DDI-444416",
+"R-MMU-444416",
+"R-DRE-444416",
+"R-GGA-444416",
+"R-CFA-444416",
+"R-HSA-444416",
+"R-XTR-444416",
+"R-BTA-444416",
+"R-RNO-444416",
+"R-TGU-444416",
+"R-DME-444416"
+],
+"rhea":[
+"28749",
+"28748",
+"28750",
+"28747"
+],
+"sabiork":[
+"11683"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn13364",
+"rxn09835",
+"rxn05466",
+"rxn08987",
+"rxn08986",
+"rxn09736"
+]
+}
+},
+{
+"id":"O2t",
+"name":"O2 transport diffusion ",
+"metabolites":{
+"o2_c":1.0,
+"o2_e":-1.0
+},
+"lower_bound":-1000.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"s0001",
+"subsystem":"Transport, Extracellular",
+"notes":{
+"original_bigg_ids":[
+"O2t"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"O2t"
+],
+"biocyc":[
+"META:TRANS-RXN0-474"
+],
+"metanetx.reaction":[
+"MNXR102090"
+],
+"sbo":"SBO:0000185",
+"seed.reaction":[
+"rxn09641",
+"rxn05468",
+"rxn09031",
+"rxn09032",
+"rxn09734"
+]
+}
+},
+{
+"id":"PDH",
+"name":"Pyruvate dehydrogenase",
+"metabolites":{
+"accoa_c":1.0,
+"co2_c":1.0,
+"coa_c":-1.0,
+"nad_c":-1.0,
+"nadh_c":1.0,
+"pyr_c":-1.0
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":"b0114 and b0115 and b0116",
+"subsystem":"Glycolysis/Gluconeogenesis",
+"notes":{
+"original_bigg_ids":[
+"PDH"
+]
+},
+"annotation":{
+"bigg.reaction":[
+"PDH"
+],
+"biocyc":[
+"META:PYRUVDEH-RXN"
+],
+"ec-code":[
+"1.2.1",
+"1.8.1.4",
+"1.2.1.51",
+"1.2.4.1",
+"2.3.1.12"
+],
+"kegg.reaction":[
+"R00209"
+],
+"metanetx.reaction":[
+"MNXR102425"
+],
+"reactome.reaction":[
+"R-RNO-71397",
+"R-OSA-71397",
+"R-GGA-373177",
+"R-DME-71397",
+"R-TGU-71397",
+"R-XTR-71397",
+"R-CFA-71397",
+"R-BTA-71397",
+"R-HSA-71397",
+"R-GGA-71397",
+"R-SPO-71397",
+"R-CEL-71397",
+"R-DDI-71397",
+"R-DRE-71397",
+"R-SSC-71397",
+"R-SCE-71397",
+"R-ATH-71397",
+"R-MMU-71397"
+],
+"rhea":[
+"28043",
+"28045",
+"28044",
+"28042"
+],
+"sabiork":[
+"523"
+],
+"sbo":"SBO:0000176",
+"seed.reaction":[
+"rxn00154"
+]
+}
+}
+],
+"genes":[
+{
+"id":"b1241",
+"name":"adhE",
+"notes":{
+"original_bigg_ids":[
+"b1241"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0004164"
+],
+"ecogene":[
+"EG10031"
+],
+"ncbigene":[
+"945837"
+],
+"ncbigi":[
+"16129202"
+],
+"refseq_locus_tag":[
+"b1241"
+],
+"refseq_name":[
+"adhE"
+],
+"refseq_synonym":[
+"JW1228",
+"ECK1235",
+"adhC",
+"ana"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A9Q7"
+]
+}
+},
+{
+"id":"b0351",
+"name":"mhpF",
+"notes":{
+"original_bigg_ids":[
+"b0351"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0001207"
+],
+"ecogene":[
+"EG13625"
+],
+"ncbigene":[
+"945008"
+],
+"ncbigi":[
+"16128336"
+],
+"refseq_locus_tag":[
+"b0351"
+],
+"refseq_name":[
+"mhpF"
+],
+"refseq_synonym":[
+"JW0342",
+"ECK0348"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P77580"
+]
+}
+},
+{
+"id":"s0001",
+"name":"",
+"notes":{
+"original_bigg_ids":[
+"s0001"
+]
+},
+"annotation":{
+"sbo":"SBO:0000243"
+}
+},
+{
+"id":"b1849",
+"name":"purT",
+"notes":{
+"original_bigg_ids":[
+"b1849"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0006162"
+],
+"ecogene":[
+"EG11809"
+],
+"ncbigene":[
+"946368"
+],
+"ncbigi":[
+"16129802"
+],
+"refseq_locus_tag":[
+"b1849"
+],
+"refseq_name":[
+"purT"
+],
+"refseq_synonym":[
+"JW1838",
+"ECK1850"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P33221"
+]
+}
+},
+{
+"id":"b3115",
+"name":"tdcD",
+"notes":{
+"original_bigg_ids":[
+"b3115"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0010245"
+],
+"ecogene":[
+"EG11172"
+],
+"ncbigene":[
+"947635"
+],
+"ncbigi":[
+"145698313"
+],
+"refseq_locus_tag":[
+"b3115"
+],
+"refseq_name":[
+"tdcD"
+],
+"refseq_synonym":[
+"JW5806",
+"ECK3104",
+"yhaA"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P11868"
+]
+}
+},
+{
+"id":"b2296",
+"name":"ackA",
+"notes":{
+"original_bigg_ids":[
+"b2296"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007579"
+],
+"ecogene":[
+"EG10027"
+],
+"ncbigene":[
+"946775"
+],
+"ncbigi":[
+"16130231"
+],
+"refseq_locus_tag":[
+"b2296"
+],
+"refseq_name":[
+"ackA"
+],
+"refseq_synonym":[
+"JW2293",
+"ECK2290"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A6A3"
+]
+}
+},
+{
+"id":"b1276",
+"name":"acnA",
+"notes":{
+"original_bigg_ids":[
+"b1276"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0004283"
+],
+"ecogene":[
+"EG11325"
+],
+"ncbigene":[
+"946724"
+],
+"ncbigi":[
+"16129237"
+],
+"refseq_locus_tag":[
+"b1276"
+],
+"refseq_name":[
+"acnA"
+],
+"refseq_synonym":[
+"JW1268",
+"ECK1271",
+"acn"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P25516"
+]
+}
+},
+{
+"id":"b0118",
+"name":"acnB",
+"notes":{
+"original_bigg_ids":[
+"b0118"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0000411"
+],
+"ecogene":[
+"EG12316"
+],
+"ncbigene":[
+"944864"
+],
+"ncbigi":[
+"16128111"
+],
+"refseq_locus_tag":[
+"b0118"
+],
+"refseq_name":[
+"acnB"
+],
+"refseq_synonym":[
+"ECK0117",
+"JW0114",
+"yacJ",
+"yacI"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P36683"
+]
+}
+},
+{
+"id":"b0474",
+"name":"adk",
+"notes":{
+"original_bigg_ids":[
+"b0474"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0001645"
+],
+"ecogene":[
+"EG10032"
+],
+"ncbigene":[
+"945097"
+],
+"ncbigi":[
+"16128458"
+],
+"refseq_locus_tag":[
+"b0474"
+],
+"refseq_name":[
+"adk"
+],
+"refseq_synonym":[
+"plsA",
+"JW0463",
+"ECK0468",
+"dnaW"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P69441"
+]
+}
+},
+{
+"id":"b0116",
+"name":"lpd",
+"notes":{
+"original_bigg_ids":[
+"b0116"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0000404"
+],
+"ecogene":[
+"EG10543"
+],
+"ncbigene":[
+"944854"
+],
+"ncbigi":[
+"16128109"
+],
+"refseq_locus_tag":[
+"b0116"
+],
+"refseq_name":[
+"lpd"
+],
+"refseq_synonym":[
+"dhl",
+"lpdA",
+"ECK0115",
+"JW0112"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A9P0"
+]
+}
+},
+{
+"id":"b0727",
+"name":"sucB",
+"notes":{
+"original_bigg_ids":[
+"b0727"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002480"
+],
+"ecogene":[
+"EG10980"
+],
+"ncbigene":[
+"945307"
+],
+"ncbigi":[
+"16128702"
+],
+"refseq_locus_tag":[
+"b0727"
+],
+"refseq_name":[
+"sucB"
+],
+"refseq_synonym":[
+"JW0716",
+"ECK0715"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AFG6"
+]
+}
+},
+{
+"id":"b0726",
+"name":"sucA",
+"notes":{
+"original_bigg_ids":[
+"b0726"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002478"
+],
+"ecogene":[
+"EG10979"
+],
+"ncbigene":[
+"945303"
+],
+"ncbigi":[
+"16128701"
+],
+"refseq_locus_tag":[
+"b0726"
+],
+"refseq_name":[
+"sucA"
+],
+"refseq_synonym":[
+"lys",
+"JW0715",
+"ECK0714"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AFG3"
+]
+}
+},
+{
+"id":"b2587",
+"name":"kgtP",
+"notes":{
+"original_bigg_ids":[
+"b2587"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0008515"
+],
+"ecogene":[
+"EG10522"
+],
+"ncbigene":[
+"947069"
+],
+"ncbigi":[
+"16130512"
+],
+"refseq_locus_tag":[
+"b2587"
+],
+"refseq_name":[
+"kgtP"
+],
+"refseq_synonym":[
+"ECK2585",
+"JW2571",
+"witA"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AEX3"
+]
+}
+},
+{
+"id":"b0356",
+"name":"frmA",
+"notes":{
+"original_bigg_ids":[
+"b0356"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0001221"
+],
+"ecogene":[
+"EG50010"
+],
+"ncbigene":[
+"944988"
+],
+"ncbigi":[
+"16128341"
+],
+"refseq_locus_tag":[
+"b0356"
+],
+"refseq_name":[
+"frmA"
+],
+"refseq_synonym":[
+"ECK0353",
+"adhC",
+"JW0347"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P25437"
+]
+}
+},
+{
+"id":"b1478",
+"name":"adhP",
+"notes":{
+"original_bigg_ids":[
+"b1478"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0004928"
+],
+"ecogene":[
+"EG12622"
+],
+"ncbigene":[
+"946036"
+],
+"ncbigi":[
+"90111280"
+],
+"refseq_locus_tag":[
+"b1478"
+],
+"refseq_name":[
+"adhP"
+],
+"refseq_synonym":[
+"yddN",
+"ECK1472",
+"JW1474"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P39451"
+]
+}
+},
+{
+"id":"b3734",
+"name":"atpA",
+"notes":{
+"original_bigg_ids":[
+"b3734"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012213"
+],
+"ecogene":[
+"EG10098"
+],
+"ncbigene":[
+"948242"
+],
+"ncbigi":[
+"16131602"
+],
+"refseq_locus_tag":[
+"b3734"
+],
+"refseq_name":[
+"atpA"
+],
+"refseq_synonym":[
+"uncA",
+"papA",
+"ECK3727",
+"JW3712"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0ABB0"
+]
+}
+},
+{
+"id":"b3733",
+"name":"atpG",
+"notes":{
+"original_bigg_ids":[
+"b3733"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012211"
+],
+"ecogene":[
+"EG10104"
+],
+"ncbigene":[
+"948243"
+],
+"ncbigi":[
+"16131601"
+],
+"refseq_locus_tag":[
+"b3733"
+],
+"refseq_name":[
+"atpG"
+],
+"refseq_synonym":[
+"uncG",
+"ECK3726",
+"papC",
+"JW3711"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0ABA6"
+]
+}
+},
+{
+"id":"b3736",
+"name":"atpF",
+"notes":{
+"original_bigg_ids":[
+"b3736"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012217"
+],
+"ecogene":[
+"EG10103"
+],
+"ncbigene":[
+"948247"
+],
+"ncbigi":[
+"16131604"
+],
+"refseq_locus_tag":[
+"b3736"
+],
+"refseq_name":[
+"atpF"
+],
+"refseq_synonym":[
+"uncF",
+"JW3714",
+"papF",
+"ECK3729"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0ABA0"
+]
+}
+},
+{
+"id":"b3737",
+"name":"atpE",
+"notes":{
+"original_bigg_ids":[
+"b3737"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012220"
+],
+"ecogene":[
+"EG10102"
+],
+"ncbigene":[
+"948253"
+],
+"ncbigi":[
+"16131605"
+],
+"refseq_locus_tag":[
+"b3737"
+],
+"refseq_name":[
+"atpE"
+],
+"refseq_synonym":[
+"uncE",
+"JW3715",
+"ECK3730",
+"papH"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P68699"
+]
+}
+},
+{
+"id":"b3739",
+"name":"atpI",
+"notes":{
+"original_bigg_ids":[
+"b3739"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012224"
+],
+"ecogene":[
+"EG10106"
+],
+"ncbigene":[
+"948251"
+],
+"ncbigi":[
+"90111645"
+],
+"refseq_locus_tag":[
+"b3739"
+],
+"refseq_name":[
+"atpI"
+],
+"refseq_synonym":[
+"uncI",
+"JW5611",
+"ECK3732"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0ABC0"
+]
+}
+},
+{
+"id":"b3738",
+"name":"atpB",
+"notes":{
+"original_bigg_ids":[
+"b3738"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012222"
+],
+"ecogene":[
+"EG10099"
+],
+"ncbigene":[
+"948252"
+],
+"ncbigi":[
+"16131606"
+],
+"refseq_locus_tag":[
+"b3738"
+],
+"refseq_name":[
+"atpB"
+],
+"refseq_synonym":[
+"JW3716",
+"ECK3731",
+"uncB",
+"papD"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AB98"
+]
+}
+},
+{
+"id":"b3735",
+"name":"atpH",
+"notes":{
+"original_bigg_ids":[
+"b3735"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012215"
+],
+"ecogene":[
+"EG10105"
+],
+"ncbigene":[
+"948254"
+],
+"ncbigi":[
+"16131603"
+],
+"refseq_locus_tag":[
+"b3735"
+],
+"refseq_name":[
+"atpH"
+],
+"refseq_synonym":[
+"JW3713",
+"papE",
+"ECK3728",
+"uncH"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0ABA4"
+]
+}
+},
+{
+"id":"b3731",
+"name":"atpC",
+"notes":{
+"original_bigg_ids":[
+"b3731"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012206"
+],
+"ecogene":[
+"EG10100"
+],
+"ncbigene":[
+"948245"
+],
+"ncbigi":[
+"16131599"
+],
+"refseq_locus_tag":[
+"b3731"
+],
+"refseq_name":[
+"atpC"
+],
+"refseq_synonym":[
+"uncC",
+"ECK3724",
+"papG",
+"JW3709"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A6E6"
+]
+}
+},
+{
+"id":"b3732",
+"name":"atpD",
+"notes":{
+"original_bigg_ids":[
+"b3732"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012208"
+],
+"ecogene":[
+"EG10101"
+],
+"ncbigene":[
+"948244"
+],
+"ncbigi":[
+"16131600"
+],
+"refseq_locus_tag":[
+"b3732"
+],
+"refseq_name":[
+"atpD"
+],
+"refseq_synonym":[
+"papB",
+"ECK3725",
+"JW3710",
+"uncD"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0ABB4"
+]
+}
+},
+{
+"id":"b0720",
+"name":"gltA",
+"notes":{
+"original_bigg_ids":[
+"b0720"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002451"
+],
+"ecogene":[
+"EG10402"
+],
+"ncbigene":[
+"945323"
+],
+"ncbigi":[
+"16128695"
+],
+"refseq_locus_tag":[
+"b0720"
+],
+"refseq_name":[
+"gltA"
+],
+"refseq_synonym":[
+"JW0710",
+"gluT",
+"ECK0709",
+"icdB"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0ABH7"
+]
+}
+},
+{
+"id":"b0733",
+"name":"cydA",
+"notes":{
+"original_bigg_ids":[
+"b0733"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002499"
+],
+"ecogene":[
+"EG10173"
+],
+"ncbigene":[
+"945341"
+],
+"ncbigi":[
+"90111166"
+],
+"refseq_locus_tag":[
+"b0733"
+],
+"refseq_name":[
+"cydA"
+],
+"refseq_synonym":[
+"ECK0721",
+"JW0722"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0ABJ9"
+]
+}
+},
+{
+"id":"b0734",
+"name":"cydB",
+"notes":{
+"original_bigg_ids":[
+"b0734"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002501"
+],
+"ecogene":[
+"EG10174"
+],
+"ncbigene":[
+"945347"
+],
+"ncbigi":[
+"16128709"
+],
+"refseq_locus_tag":[
+"b0734"
+],
+"refseq_name":[
+"cydB"
+],
+"refseq_synonym":[
+"ECK0722",
+"JW0723"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0ABK2"
+]
+}
+},
+{
+"id":"b0979",
+"name":"cbdB",
+"notes":{
+"original_bigg_ids":[
+"b0979"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0003302"
+],
+"ecogene":[
+"EG11379"
+],
+"ncbigene":[
+"947547"
+],
+"ncbigi":[
+"16128945"
+],
+"refseq_locus_tag":[
+"b0979"
+],
+"refseq_name":[
+"cbdB"
+],
+"refseq_synonym":[
+"JW0961",
+"appB",
+"cyxB",
+"ECK0970"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P26458"
+]
+}
+},
+{
+"id":"b0978",
+"name":"cbdA",
+"notes":{
+"original_bigg_ids":[
+"b0978"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0003300"
+],
+"ecogene":[
+"EG11380"
+],
+"ncbigene":[
+"945585"
+],
+"ncbigi":[
+"16128944"
+],
+"refseq_locus_tag":[
+"b0978"
+],
+"refseq_name":[
+"cbdA"
+],
+"refseq_synonym":[
+"JW0960",
+"ECK0969",
+"cyxA",
+"appC"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P26459"
+]
+}
+},
+{
+"id":"b3603",
+"name":"lldP",
+"notes":{
+"original_bigg_ids":[
+"b3603"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0011777"
+],
+"ecogene":[
+"EG11961"
+],
+"ncbigene":[
+"948114"
+],
+"ncbigi":[
+"16131474"
+],
+"refseq_locus_tag":[
+"b3603"
+],
+"refseq_name":[
+"lldP"
+],
+"refseq_synonym":[
+"JW3578",
+"ECK3593",
+"lct",
+"lctP"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P33231"
+]
+}
+},
+{
+"id":"b2975",
+"name":"glcA",
+"notes":{
+"original_bigg_ids":[
+"b2975"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0009763"
+],
+"ecogene":[
+"EG12995"
+],
+"ncbigene":[
+"947259"
+],
+"ncbigi":[
+"16130875"
+],
+"refseq_locus_tag":[
+"b2975"
+],
+"refseq_name":[
+"glcA"
+],
+"refseq_synonym":[
+"ECK2969",
+"JW2942",
+"yghK"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"Q46839"
+]
+}
+},
+{
+"id":"b2779",
+"name":"eno",
+"notes":{
+"original_bigg_ids":[
+"b2779"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0009110"
+],
+"ecogene":[
+"EG10258"
+],
+"ncbigene":[
+"945032"
+],
+"ncbigi":[
+"16130686"
+],
+"refseq_locus_tag":[
+"b2779"
+],
+"refseq_name":[
+"eno"
+],
+"refseq_synonym":[
+"JW2750",
+"ECK2773"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A6P9"
+]
+}
+},
+{
+"id":"b2925",
+"name":"fbaA",
+"notes":{
+"original_bigg_ids":[
+"b2925"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0009600"
+],
+"ecogene":[
+"EG10282"
+],
+"ncbigene":[
+"947415"
+],
+"ncbigi":[
+"16130826"
+],
+"refseq_locus_tag":[
+"b2925"
+],
+"refseq_name":[
+"fbaA"
+],
+"refseq_synonym":[
+"fba",
+"ald",
+"fda",
+"ECK2921",
+"JW2892"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AB71"
+]
+}
+},
+{
+"id":"b1773",
+"name":"ydjI",
+"notes":{
+"original_bigg_ids":[
+"b1773"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0005906"
+],
+"ecogene":[
+"EG13485"
+],
+"ncbigene":[
+"946291"
+],
+"ncbigi":[
+"16129727"
+],
+"refseq_locus_tag":[
+"b1773"
+],
+"refseq_name":[
+"ydjI"
+],
+"refseq_synonym":[
+"ECK1771",
+"JW1762"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P77704"
+]
+}
+},
+{
+"id":"b2097",
+"name":"fbaB",
+"notes":{
+"original_bigg_ids":[
+"b2097"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0006941"
+],
+"ecogene":[
+"EG14062"
+],
+"ncbigene":[
+"946632"
+],
+"ncbigi":[
+"90111385"
+],
+"refseq_locus_tag":[
+"b2097"
+],
+"refseq_name":[
+"fbaB"
+],
+"refseq_synonym":[
+"dhnA",
+"JW5344",
+"ECK2090"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A991"
+]
+}
+},
+{
+"id":"b3925",
+"name":"glpX",
+"notes":{
+"original_bigg_ids":[
+"b3925"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012821"
+],
+"ecogene":[
+"EG11517"
+],
+"ncbigene":[
+"948424"
+],
+"ncbigi":[
+"16131763"
+],
+"refseq_locus_tag":[
+"b3925"
+],
+"refseq_name":[
+"glpX"
+],
+"refseq_synonym":[
+"JW3896",
+"ECK3917"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A9C9"
+]
+}
+},
+{
+"id":"b4232",
+"name":"fbp",
+"notes":{
+"original_bigg_ids":[
+"b4232"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0013842"
+],
+"ecogene":[
+"EG10283"
+],
+"ncbigene":[
+"948753"
+],
+"ncbigi":[
+"16132054"
+],
+"refseq_locus_tag":[
+"b4232"
+],
+"refseq_name":[
+"fbp"
+],
+"refseq_synonym":[
+"JW4191",
+"ECK4227",
+"fdp"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A993"
+]
+}
+},
+{
+"id":"b2492",
+"name":"focB",
+"notes":{
+"original_bigg_ids":[
+"b2492"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0008206"
+],
+"ecogene":[
+"EG14220"
+],
+"ncbigene":[
+"949032"
+],
+"ncbigi":[
+"16130417"
+],
+"refseq_locus_tag":[
+"b2492"
+],
+"refseq_name":[
+"focB"
+],
+"refseq_synonym":[
+"JW2477",
+"ECK2488"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P77733"
+]
+}
+},
+{
+"id":"b0904",
+"name":"focA",
+"notes":{
+"original_bigg_ids":[
+"b0904"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0003073"
+],
+"ecogene":[
+"EG11258"
+],
+"ncbigene":[
+"945513"
+],
+"ncbigi":[
+"16128871"
+],
+"refseq_locus_tag":[
+"b0904"
+],
+"refseq_name":[
+"focA"
+],
+"refseq_synonym":[
+"ycaE",
+"ECK0895",
+"JW0887"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AC23"
+]
+}
+},
+{
+"id":"b4152",
+"name":"frdC",
+"notes":{
+"original_bigg_ids":[
+"b4152"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0013598"
+],
+"ecogene":[
+"EG10332"
+],
+"ncbigene":[
+"948680"
+],
+"ncbigi":[
+"16131977"
+],
+"refseq_locus_tag":[
+"b4152"
+],
+"refseq_name":[
+"frdC"
+],
+"refseq_synonym":[
+"ECK4148",
+"JW4113"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A8Q0"
+]
+}
+},
+{
+"id":"b4154",
+"name":"frdA",
+"notes":{
+"original_bigg_ids":[
+"b4154"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0013604"
+],
+"ecogene":[
+"EG10330"
+],
+"ncbigene":[
+"948667"
+],
+"ncbigi":[
+"16131979"
+],
+"refseq_locus_tag":[
+"b4154"
+],
+"refseq_name":[
+"frdA"
+],
+"refseq_synonym":[
+"ECK4150",
+"JW4115"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P00363"
+]
+}
+},
+{
+"id":"b4153",
+"name":"frdB",
+"notes":{
+"original_bigg_ids":[
+"b4153"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0013602"
+],
+"ecogene":[
+"EG10331"
+],
+"ncbigene":[
+"948666"
+],
+"ncbigi":[
+"16131978"
+],
+"refseq_locus_tag":[
+"b4153"
+],
+"refseq_name":[
+"frdB"
+],
+"refseq_synonym":[
+"JW4114",
+"ECK4149"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AC47"
+]
+}
+},
+{
+"id":"b4151",
+"name":"frdD",
+"notes":{
+"original_bigg_ids":[
+"b4151"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0013595"
+],
+"ecogene":[
+"EG10333"
+],
+"ncbigene":[
+"948668"
+],
+"ncbigi":[
+"16131976"
+],
+"refseq_locus_tag":[
+"b4151"
+],
+"refseq_name":[
+"frdD"
+],
+"refseq_synonym":[
+"JW4112",
+"ECK4147"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A8Q3"
+]
+}
+},
+{
+"id":"b1819",
+"name":"manZ",
+"notes":{
+"original_bigg_ids":[
+"b1819"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0006058"
+],
+"ecogene":[
+"EG10569"
+],
+"ncbigene":[
+"946342"
+],
+"ncbigi":[
+"345452720"
+],
+"refseq_locus_tag":[
+"b1819"
+],
+"refseq_name":[
+"manZ"
+],
+"refseq_synonym":[
+"ptsM",
+"ECK1817",
+"ptsX",
+"gptB",
+"mpt",
+"JW1808"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P69805"
+]
+}
+},
+{
+"id":"b1817",
+"name":"manX",
+"notes":{
+"original_bigg_ids":[
+"b1817"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0006054"
+],
+"ecogene":[
+"EG10567"
+],
+"ncbigene":[
+"946334"
+],
+"ncbigi":[
+"16129771"
+],
+"refseq_locus_tag":[
+"b1817"
+],
+"refseq_name":[
+"manX"
+],
+"refseq_synonym":[
+"ECK1815",
+"ptsX",
+"gptB",
+"mpt",
+"JW1806",
+"ptsL"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P69797"
+]
+}
+},
+{
+"id":"b2416",
+"name":"ptsI",
+"notes":{
+"original_bigg_ids":[
+"b2416"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007967"
+],
+"ecogene":[
+"EG10789"
+],
+"ncbigene":[
+"946879"
+],
+"ncbigi":[
+"16130342"
+],
+"refseq_locus_tag":[
+"b2416"
+],
+"refseq_name":[
+"ptsI"
+],
+"refseq_synonym":[
+"ECK2411",
+"ctr",
+"JW2409"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P08839"
+]
+}
+},
+{
+"id":"b2415",
+"name":"ptsH",
+"notes":{
+"original_bigg_ids":[
+"b2415"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007962"
+],
+"ecogene":[
+"EG10788"
+],
+"ncbigene":[
+"946886"
+],
+"ncbigi":[
+"16130341"
+],
+"refseq_locus_tag":[
+"b2415"
+],
+"refseq_name":[
+"ptsH"
+],
+"refseq_synonym":[
+"ctr",
+"hpr",
+"JW2408",
+"ECK2410",
+"iex?"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AA04"
+]
+}
+},
+{
+"id":"b1818",
+"name":"manY",
+"notes":{
+"original_bigg_ids":[
+"b1818"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0006056"
+],
+"ecogene":[
+"EG10568"
+],
+"ncbigene":[
+"946332"
+],
+"ncbigi":[
+"16129772"
+],
+"refseq_locus_tag":[
+"b1818"
+],
+"refseq_name":[
+"manY"
+],
+"refseq_synonym":[
+"ptsX",
+"pel",
+"ECK1816",
+"JW1807",
+"ptsP"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P69801"
+]
+}
+},
+{
+"id":"b1611",
+"name":"fumC",
+"notes":{
+"original_bigg_ids":[
+"b1611"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0005380"
+],
+"ecogene":[
+"EG10358"
+],
+"ncbigene":[
+"946147"
+],
+"ncbigi":[
+"16129569"
+],
+"refseq_locus_tag":[
+"b1611"
+],
+"refseq_name":[
+"fumC"
+],
+"refseq_synonym":[
+"JW1603",
+"ECK1606"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P05042"
+]
+}
+},
+{
+"id":"b4122",
+"name":"fumB",
+"notes":{
+"original_bigg_ids":[
+"b4122"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0013501"
+],
+"ecogene":[
+"EG10357"
+],
+"ncbigene":[
+"948642"
+],
+"ncbigi":[
+"16131948"
+],
+"refseq_locus_tag":[
+"b4122"
+],
+"refseq_name":[
+"fumB"
+],
+"refseq_synonym":[
+"JW4083",
+"ECK4115"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P14407"
+]
+}
+},
+{
+"id":"b1612",
+"name":"fumA",
+"notes":{
+"original_bigg_ids":[
+"b1612"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0005392"
+],
+"ecogene":[
+"EG10356"
+],
+"ncbigene":[
+"946826"
+],
+"ncbigi":[
+"16129570"
+],
+"refseq_locus_tag":[
+"b1612"
+],
+"refseq_name":[
+"fumA"
+],
+"refseq_synonym":[
+"JW1604",
+"ECK1607"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AC33"
+]
+}
+},
+{
+"id":"b3528",
+"name":"dctA",
+"notes":{
+"original_bigg_ids":[
+"b3528"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0011527"
+],
+"ecogene":[
+"EG20044"
+],
+"ncbigene":[
+"948039"
+],
+"ncbigi":[
+"16131400"
+],
+"refseq_locus_tag":[
+"b3528"
+],
+"refseq_name":[
+"dctA"
+],
+"refseq_synonym":[
+"JW3496",
+"ECK3513",
+"out"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A830"
+]
+}
+},
+{
+"id":"b1852",
+"name":"zwf",
+"notes":{
+"original_bigg_ids":[
+"b1852"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0006171"
+],
+"ecogene":[
+"EG11221"
+],
+"ncbigene":[
+"946370"
+],
+"ncbigi":[
+"16129805"
+],
+"refseq_locus_tag":[
+"b1852"
+],
+"refseq_name":[
+"zwf"
+],
+"refseq_synonym":[
+"JW1841",
+"ECK1853"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AC53"
+]
+}
+},
+{
+"id":"b1779",
+"name":"gapA",
+"notes":{
+"original_bigg_ids":[
+"b1779"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0005920"
+],
+"ecogene":[
+"EG10367"
+],
+"ncbigene":[
+"947679"
+],
+"ncbigi":[
+"16129733"
+],
+"refseq_locus_tag":[
+"b1779"
+],
+"refseq_name":[
+"gapA"
+],
+"refseq_synonym":[
+"ECK1777",
+"JW1768"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A9B2"
+]
+}
+},
+{
+"id":"b1101",
+"name":"ptsG",
+"notes":{
+"original_bigg_ids":[
+"b1101"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0003722"
+],
+"ecogene":[
+"EG10787"
+],
+"ncbigene":[
+"945651"
+],
+"ncbigi":[
+"16129064"
+],
+"refseq_locus_tag":[
+"b1101"
+],
+"refseq_name":[
+"ptsG"
+],
+"refseq_synonym":[
+"car",
+"JW1087",
+"umg",
+"glcA",
+"umgC",
+"cat",
+"CR",
+"tgl",
+"ECK1087"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P69786"
+]
+}
+},
+{
+"id":"b2417",
+"name":"crr",
+"notes":{
+"original_bigg_ids":[
+"b2417"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007971"
+],
+"ecogene":[
+"EG10165"
+],
+"ncbigene":[
+"946880"
+],
+"ncbigi":[
+"16130343"
+],
+"refseq_locus_tag":[
+"b2417"
+],
+"refseq_name":[
+"crr"
+],
+"refseq_synonym":[
+"gsr",
+"JW2410",
+"ECK2412",
+"treD",
+"tgs",
+"iex"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P69783"
+]
+}
+},
+{
+"id":"b1621",
+"name":"malX",
+"notes":{
+"original_bigg_ids":[
+"b1621"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0005429"
+],
+"ecogene":[
+"EG10563"
+],
+"ncbigene":[
+"946009"
+],
+"ncbigi":[
+"16129579"
+],
+"refseq_locus_tag":[
+"b1621"
+],
+"refseq_name":[
+"malX"
+],
+"refseq_synonym":[
+"ECK1616",
+"JW1613"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P19642"
+]
+}
+},
+{
+"id":"b1297",
+"name":"puuA",
+"notes":{
+"original_bigg_ids":[
+"b1297"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0004365"
+],
+"ecogene":[
+"EG13908"
+],
+"ncbigene":[
+"946202"
+],
+"ncbigi":[
+"90111244"
+],
+"refseq_locus_tag":[
+"b1297"
+],
+"refseq_name":[
+"puuA"
+],
+"refseq_synonym":[
+"ECK1292",
+"JW5201",
+"ycjK"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P78061"
+]
+}
+},
+{
+"id":"b3870",
+"name":"glnA",
+"notes":{
+"original_bigg_ids":[
+"b3870"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012640"
+],
+"ecogene":[
+"EG10383"
+],
+"ncbigene":[
+"948370"
+],
+"ncbigi":[
+"16131710"
+],
+"refseq_locus_tag":[
+"b3870"
+],
+"refseq_name":[
+"glnA"
+],
+"refseq_synonym":[
+"ECK3863",
+"JW3841"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A9C5"
+]
+}
+},
+{
+"id":"b0809",
+"name":"glnQ",
+"notes":{
+"original_bigg_ids":[
+"b0809"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002764"
+],
+"ecogene":[
+"EG10389"
+],
+"ncbigene":[
+"945435"
+],
+"ncbigi":[
+"16128777"
+],
+"refseq_locus_tag":[
+"b0809"
+],
+"refseq_name":[
+"glnQ"
+],
+"refseq_synonym":[
+"JW0794",
+"ECK0798"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P10346"
+]
+}
+},
+{
+"id":"b0811",
+"name":"glnH",
+"notes":{
+"original_bigg_ids":[
+"b0811"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002771"
+],
+"ecogene":[
+"EG10386"
+],
+"ncbigene":[
+"944872"
+],
+"ncbigi":[
+"16128779"
+],
+"refseq_locus_tag":[
+"b0811"
+],
+"refseq_name":[
+"glnH"
+],
+"refseq_synonym":[
+"JW0796",
+"ECK0800"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AEQ3"
+]
+}
+},
+{
+"id":"b0810",
+"name":"glnP",
+"notes":{
+"original_bigg_ids":[
+"b0810"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002766"
+],
+"ecogene":[
+"EG10388"
+],
+"ncbigene":[
+"945621"
+],
+"ncbigi":[
+"16128778"
+],
+"refseq_locus_tag":[
+"b0810"
+],
+"refseq_name":[
+"glnP"
+],
+"refseq_synonym":[
+"JW0795",
+"ECK0799"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AEQ6"
+]
+}
+},
+{
+"id":"b1761",
+"name":"gdhA",
+"notes":{
+"original_bigg_ids":[
+"b1761"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0005865"
+],
+"ecogene":[
+"EG10372"
+],
+"ncbigene":[
+"946802"
+],
+"ncbigi":[
+"16129715"
+],
+"refseq_locus_tag":[
+"b1761"
+],
+"refseq_name":[
+"gdhA"
+],
+"refseq_synonym":[
+"ECK1759",
+"JW1750"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P00370"
+]
+}
+},
+{
+"id":"b1524",
+"name":"glsB",
+"notes":{
+"original_bigg_ids":[
+"b1524"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0005086"
+],
+"ecogene":[
+"EG13816"
+],
+"ncbigene":[
+"944973"
+],
+"ncbigi":[
+"16129483"
+],
+"refseq_locus_tag":[
+"b1524"
+],
+"refseq_name":[
+"glsB"
+],
+"refseq_synonym":[
+"glsA2",
+"yneH",
+"JW1517",
+"ECK1517"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A6W0"
+]
+}
+},
+{
+"id":"b0485",
+"name":"glsA",
+"notes":{
+"original_bigg_ids":[
+"b0485"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0001688"
+],
+"ecogene":[
+"EG13247"
+],
+"ncbigene":[
+"946187"
+],
+"ncbigi":[
+"16128469"
+],
+"refseq_locus_tag":[
+"b0485"
+],
+"refseq_name":[
+"glsA"
+],
+"refseq_synonym":[
+"glsA1",
+"ECK0479",
+"ybaS",
+"JW0474"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P77454"
+]
+}
+},
+{
+"id":"b1812",
+"name":"pabB",
+"notes":{
+"original_bigg_ids":[
+"b1812"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0006031"
+],
+"ecogene":[
+"EG10683"
+],
+"ncbigene":[
+"946337"
+],
+"ncbigi":[
+"16129766"
+],
+"refseq_locus_tag":[
+"b1812"
+],
+"refseq_name":[
+"pabB"
+],
+"refseq_synonym":[
+"ECK1810",
+"JW1801"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P05041"
+]
+}
+},
+{
+"id":"b3213",
+"name":"gltD",
+"notes":{
+"original_bigg_ids":[
+"b3213"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0010547"
+],
+"ecogene":[
+"EG10404"
+],
+"ncbigene":[
+"947723"
+],
+"ncbigi":[
+"16131103"
+],
+"refseq_locus_tag":[
+"b3213"
+],
+"refseq_name":[
+"gltD"
+],
+"refseq_synonym":[
+"psiQ",
+"aspB",
+"ossB",
+"JW3180",
+"ECK3203"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P09832"
+]
+}
+},
+{
+"id":"b3212",
+"name":"gltB",
+"notes":{
+"original_bigg_ids":[
+"b3212"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0010545"
+],
+"ecogene":[
+"EG10403"
+],
+"ncbigene":[
+"947724"
+],
+"ncbigi":[
+"308209621"
+],
+"refseq_locus_tag":[
+"b3212"
+],
+"refseq_name":[
+"gltB"
+],
+"refseq_synonym":[
+"psiQ",
+"aspB",
+"ECK3202",
+"ossB",
+"JW3179"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P09831"
+]
+}
+},
+{
+"id":"b4077",
+"name":"gltP",
+"notes":{
+"original_bigg_ids":[
+"b4077"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0013357"
+],
+"ecogene":[
+"EG10405"
+],
+"ncbigene":[
+"948591"
+],
+"ncbigi":[
+"16131903"
+],
+"refseq_locus_tag":[
+"b4077"
+],
+"refseq_name":[
+"gltP"
+],
+"refseq_synonym":[
+"ECK4070",
+"JW4038"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P21345"
+]
+}
+},
+{
+"id":"b2029",
+"name":"gnd",
+"notes":{
+"original_bigg_ids":[
+"b2029"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0006737"
+],
+"ecogene":[
+"EG10411"
+],
+"ncbigene":[
+"946554"
+],
+"ncbigi":[
+"16129970"
+],
+"refseq_locus_tag":[
+"b2029"
+],
+"refseq_name":[
+"gnd"
+],
+"refseq_synonym":[
+"JW2011",
+"ECK2024"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P00350"
+]
+}
+},
+{
+"id":"b0875",
+"name":"aqpZ",
+"notes":{
+"original_bigg_ids":[
+"b0875"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002976"
+],
+"ecogene":[
+"EG13270"
+],
+"ncbigene":[
+"945497"
+],
+"ncbigi":[
+"16128843"
+],
+"refseq_locus_tag":[
+"b0875"
+],
+"refseq_name":[
+"aqpZ"
+],
+"refseq_synonym":[
+"bniP",
+"JW0859",
+"ECK0866"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P60844"
+]
+}
+},
+{
+"id":"b1136",
+"name":"icd",
+"notes":{
+"original_bigg_ids":[
+"b1136"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0003823"
+],
+"ecogene":[
+"EG10489"
+],
+"ncbigene":[
+"945702"
+],
+"ncbigi":[
+"16129099"
+],
+"refseq_locus_tag":[
+"b1136"
+],
+"refseq_name":[
+"icd"
+],
+"refseq_synonym":[
+"icdA",
+"icdE",
+"JW1122",
+"ECK1122"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P08200"
+]
+}
+},
+{
+"id":"b4015",
+"name":"aceA",
+"notes":{
+"original_bigg_ids":[
+"b4015"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0013128"
+],
+"ecogene":[
+"EG10022"
+],
+"ncbigene":[
+"948517"
+],
+"ncbigi":[
+"16131841"
+],
+"refseq_locus_tag":[
+"b4015"
+],
+"refseq_name":[
+"aceA"
+],
+"refseq_synonym":[
+"JW3975",
+"icl",
+"ECK4007"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A9G6"
+]
+}
+},
+{
+"id":"b1380",
+"name":"ldhA",
+"notes":{
+"original_bigg_ids":[
+"b1380"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0004619"
+],
+"ecogene":[
+"EG13186"
+],
+"ncbigene":[
+"946315"
+],
+"ncbigi":[
+"16129341"
+],
+"refseq_locus_tag":[
+"b1380"
+],
+"refseq_name":[
+"ldhA"
+],
+"refseq_synonym":[
+"ECK1377",
+"JW1375",
+"hslI",
+"htpH",
+"hslF"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P52643"
+]
+}
+},
+{
+"id":"b2133",
+"name":"dld",
+"notes":{
+"original_bigg_ids":[
+"b2133"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007048"
+],
+"ecogene":[
+"EG10231"
+],
+"ncbigene":[
+"946653"
+],
+"ncbigi":[
+"16130071"
+],
+"refseq_locus_tag":[
+"b2133"
+],
+"refseq_name":[
+"dld"
+],
+"refseq_synonym":[
+"JW2121",
+"ECK2126"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P06149"
+]
+}
+},
+{
+"id":"b4014",
+"name":"aceB",
+"notes":{
+"original_bigg_ids":[
+"b4014"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0013125"
+],
+"ecogene":[
+"EG10023"
+],
+"ncbigene":[
+"948512"
+],
+"ncbigi":[
+"16131840"
+],
+"refseq_locus_tag":[
+"b4014"
+],
+"refseq_name":[
+"aceB"
+],
+"refseq_synonym":[
+"ECK4006",
+"mas",
+"JW3974"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P08997"
+]
+}
+},
+{
+"id":"b2976",
+"name":"glcB",
+"notes":{
+"original_bigg_ids":[
+"b2976"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0009767"
+],
+"ecogene":[
+"EG20080"
+],
+"ncbigene":[
+"948857"
+],
+"ncbigi":[
+"16130876"
+],
+"refseq_locus_tag":[
+"b2976"
+],
+"refseq_name":[
+"glcB"
+],
+"refseq_synonym":[
+"JW2943",
+"glc",
+"ECK2970"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P37330"
+]
+}
+},
+{
+"id":"b3236",
+"name":"mdh",
+"notes":{
+"original_bigg_ids":[
+"b3236"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0010613"
+],
+"ecogene":[
+"EG10576"
+],
+"ncbigene":[
+"947854"
+],
+"ncbigi":[
+"16131126"
+],
+"refseq_locus_tag":[
+"b3236"
+],
+"refseq_name":[
+"mdh"
+],
+"refseq_synonym":[
+"ECK3225",
+"JW3205"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P61889"
+]
+}
+},
+{
+"id":"b1479",
+"name":"maeA",
+"notes":{
+"original_bigg_ids":[
+"b1479"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0004931"
+],
+"ecogene":[
+"EG10948"
+],
+"ncbigene":[
+"946031"
+],
+"ncbigi":[
+"90111281"
+],
+"refseq_locus_tag":[
+"b1479"
+],
+"refseq_name":[
+"maeA"
+],
+"refseq_synonym":[
+"JW5238",
+"sfcA",
+"ECK1473"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P26616"
+]
+}
+},
+{
+"id":"b2463",
+"name":"maeB",
+"notes":{
+"original_bigg_ids":[
+"b2463"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0008111"
+],
+"ecogene":[
+"EG14193"
+],
+"ncbigene":[
+"946947"
+],
+"ncbigi":[
+"16130388"
+],
+"refseq_locus_tag":[
+"b2463"
+],
+"refseq_name":[
+"maeB"
+],
+"refseq_synonym":[
+"ECK2458",
+"JW2447",
+"ypfF"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P76558"
+]
+}
+},
+{
+"id":"b2281",
+"name":"nuoI",
+"notes":{
+"original_bigg_ids":[
+"b2281"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007539"
+],
+"ecogene":[
+"EG12089"
+],
+"ncbigene":[
+"946757"
+],
+"ncbigi":[
+"16130216"
+],
+"refseq_locus_tag":[
+"b2281"
+],
+"refseq_name":[
+"nuoI"
+],
+"refseq_synonym":[
+"ECK2275",
+"JW2276"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AFD6"
+]
+}
+},
+{
+"id":"b2277",
+"name":"nuoM",
+"notes":{
+"original_bigg_ids":[
+"b2277"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007529"
+],
+"ecogene":[
+"EG11773"
+],
+"ncbigene":[
+"947731"
+],
+"ncbigi":[
+"16130212"
+],
+"refseq_locus_tag":[
+"b2277"
+],
+"refseq_name":[
+"nuoM"
+],
+"refseq_synonym":[
+"JW2272",
+"nuoA",
+"ECK2271"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AFE8"
+]
+}
+},
+{
+"id":"b2280",
+"name":"nuoJ",
+"notes":{
+"original_bigg_ids":[
+"b2280"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007536"
+],
+"ecogene":[
+"EG12090"
+],
+"ncbigene":[
+"946756"
+],
+"ncbigi":[
+"16130215"
+],
+"refseq_locus_tag":[
+"b2280"
+],
+"refseq_name":[
+"nuoJ"
+],
+"refseq_synonym":[
+"ECK2274",
+"JW2275"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AFE0"
+]
+}
+},
+{
+"id":"b2286",
+"name":"nuoC",
+"notes":{
+"original_bigg_ids":[
+"b2286"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007549"
+],
+"ecogene":[
+"EG12084"
+],
+"ncbigene":[
+"946759"
+],
+"ncbigi":[
+"145698291"
+],
+"refseq_locus_tag":[
+"b2286"
+],
+"refseq_name":[
+"nuoC"
+],
+"refseq_synonym":[
+"ECK2280",
+"nuoD",
+"nuoCD",
+"JW5375"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P33599"
+]
+}
+},
+{
+"id":"b2287",
+"name":"nuoB",
+"notes":{
+"original_bigg_ids":[
+"b2287"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007551"
+],
+"ecogene":[
+"EG12083"
+],
+"ncbigene":[
+"946738"
+],
+"ncbigi":[
+"16130222"
+],
+"refseq_locus_tag":[
+"b2287"
+],
+"refseq_name":[
+"nuoB"
+],
+"refseq_synonym":[
+"JW5875",
+"ECK2281"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AFC7"
+]
+}
+},
+{
+"id":"b2284",
+"name":"nuoF",
+"notes":{
+"original_bigg_ids":[
+"b2284"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007545"
+],
+"ecogene":[
+"EG11774"
+],
+"ncbigene":[
+"946753"
+],
+"ncbigi":[
+"16130219"
+],
+"refseq_locus_tag":[
+"b2284"
+],
+"refseq_name":[
+"nuoF"
+],
+"refseq_synonym":[
+"ECK2278",
+"nuoB",
+"JW2279"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P31979"
+]
+}
+},
+{
+"id":"b2276",
+"name":"nuoN",
+"notes":{
+"original_bigg_ids":[
+"b2276"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007526"
+],
+"ecogene":[
+"EG12093"
+],
+"ncbigene":[
+"945136"
+],
+"ncbigi":[
+"145698289"
+],
+"refseq_locus_tag":[
+"b2276"
+],
+"refseq_name":[
+"nuoN"
+],
+"refseq_synonym":[
+"JW2271",
+"ECK2270"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AFF0"
+]
+}
+},
+{
+"id":"b2282",
+"name":"nuoH",
+"notes":{
+"original_bigg_ids":[
+"b2282"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007541"
+],
+"ecogene":[
+"EG12088"
+],
+"ncbigene":[
+"946761"
+],
+"ncbigi":[
+"16130217"
+],
+"refseq_locus_tag":[
+"b2282"
+],
+"refseq_name":[
+"nuoH"
+],
+"refseq_synonym":[
+"JW2277",
+"ECK2276"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AFD4"
+]
+}
+},
+{
+"id":"b2279",
+"name":"nuoK",
+"notes":{
+"original_bigg_ids":[
+"b2279"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007534"
+],
+"ecogene":[
+"EG12091"
+],
+"ncbigene":[
+"947580"
+],
+"ncbigi":[
+"16130214"
+],
+"refseq_locus_tag":[
+"b2279"
+],
+"refseq_name":[
+"nuoK"
+],
+"refseq_synonym":[
+"JW2274",
+"ECK2273"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AFE4"
+]
+}
+},
+{
+"id":"b2283",
+"name":"nuoG",
+"notes":{
+"original_bigg_ids":[
+"b2283"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007543"
+],
+"ecogene":[
+"EG12087"
+],
+"ncbigene":[
+"946762"
+],
+"ncbigi":[
+"145698290"
+],
+"refseq_locus_tag":[
+"b2283"
+],
+"refseq_name":[
+"nuoG"
+],
+"refseq_synonym":[
+"JW2278",
+"ECK2277"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P33602"
+]
+}
+},
+{
+"id":"b2285",
+"name":"nuoE",
+"notes":{
+"original_bigg_ids":[
+"b2285"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007547"
+],
+"ecogene":[
+"EG12086"
+],
+"ncbigene":[
+"946746"
+],
+"ncbigi":[
+"16130220"
+],
+"refseq_locus_tag":[
+"b2285"
+],
+"refseq_name":[
+"nuoE"
+],
+"refseq_synonym":[
+"JW2280",
+"ECK2279"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AFD1"
+]
+}
+},
+{
+"id":"b2288",
+"name":"nuoA",
+"notes":{
+"original_bigg_ids":[
+"b2288"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007553"
+],
+"ecogene":[
+"EG12082"
+],
+"ncbigene":[
+"946764"
+],
+"ncbigi":[
+"49176207"
+],
+"refseq_locus_tag":[
+"b2288"
+],
+"refseq_name":[
+"nuoA"
+],
+"refseq_synonym":[
+"JW2283",
+"ECK2282"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AFC3"
+]
+}
+},
+{
+"id":"b2278",
+"name":"nuoL",
+"notes":{
+"original_bigg_ids":[
+"b2278"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007532"
+],
+"ecogene":[
+"EG12092"
+],
+"ncbigene":[
+"945540"
+],
+"ncbigi":[
+"16130213"
+],
+"refseq_locus_tag":[
+"b2278"
+],
+"refseq_name":[
+"nuoL"
+],
+"refseq_synonym":[
+"ECK2272",
+"JW2273"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P33607"
+]
+}
+},
+{
+"id":"b1603",
+"name":"pntA",
+"notes":{
+"original_bigg_ids":[
+"b1603"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0005354"
+],
+"ecogene":[
+"EG10744"
+],
+"ncbigene":[
+"946628"
+],
+"ncbigi":[
+"16129561"
+],
+"refseq_locus_tag":[
+"b1603"
+],
+"refseq_name":[
+"pntA"
+],
+"refseq_synonym":[
+"JW1595",
+"ECK1598"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P07001"
+]
+}
+},
+{
+"id":"b3962",
+"name":"sthA",
+"notes":{
+"original_bigg_ids":[
+"b3962"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012975"
+],
+"ecogene":[
+"EG11428"
+],
+"ncbigene":[
+"948461"
+],
+"ncbigi":[
+"90111670"
+],
+"refseq_locus_tag":[
+"b3962"
+],
+"refseq_name":[
+"sthA"
+],
+"refseq_synonym":[
+"ECK3954",
+"udhA",
+"JW5551",
+"sth"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P27306"
+]
+}
+},
+{
+"id":"b1602",
+"name":"pntB",
+"notes":{
+"original_bigg_ids":[
+"b1602"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0005352"
+],
+"ecogene":[
+"EG10745"
+],
+"ncbigene":[
+"946144"
+],
+"ncbigi":[
+"16129560"
+],
+"refseq_locus_tag":[
+"b1602"
+],
+"refseq_name":[
+"pntB"
+],
+"refseq_synonym":[
+"ECK1597",
+"JW1594"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AB67"
+]
+}
+},
+{
+"id":"b0451",
+"name":"amtB",
+"notes":{
+"original_bigg_ids":[
+"b0451"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0001564"
+],
+"ecogene":[
+"EG11821"
+],
+"ncbigene":[
+"945084"
+],
+"ncbigi":[
+"16128436"
+],
+"refseq_locus_tag":[
+"b0451"
+],
+"refseq_name":[
+"amtB"
+],
+"refseq_synonym":[
+"JW0441",
+"ECK0445",
+"ybaG"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P69681"
+]
+}
+},
+{
+"id":"b0114",
+"name":"aceE",
+"notes":{
+"original_bigg_ids":[
+"b0114"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0000397"
+],
+"ecogene":[
+"EG10024"
+],
+"ncbigene":[
+"944834"
+],
+"ncbigi":[
+"16128107"
+],
+"refseq_locus_tag":[
+"b0114"
+],
+"refseq_name":[
+"aceE"
+],
+"refseq_synonym":[
+"ECK0113",
+"JW0110"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AFG8"
+]
+}
+},
+{
+"id":"b0115",
+"name":"aceF",
+"notes":{
+"original_bigg_ids":[
+"b0115"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0000400"
+],
+"ecogene":[
+"EG10025"
+],
+"ncbigene":[
+"944794"
+],
+"ncbigi":[
+"16128108"
+],
+"refseq_locus_tag":[
+"b0115"
+],
+"refseq_name":[
+"aceF"
+],
+"refseq_synonym":[
+"ECK0114",
+"JW0111"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P06959"
+]
+}
+},
+{
+"id":"b3916",
+"name":"pfkA",
+"notes":{
+"original_bigg_ids":[
+"b3916"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012789"
+],
+"ecogene":[
+"EG10699"
+],
+"ncbigene":[
+"948412"
+],
+"ncbigi":[
+"16131754"
+],
+"refseq_locus_tag":[
+"b3916"
+],
+"refseq_name":[
+"pfkA"
+],
+"refseq_synonym":[
+"JW3887",
+"ECK3908"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A796"
+]
+}
+},
+{
+"id":"b1723",
+"name":"pfkB",
+"notes":{
+"original_bigg_ids":[
+"b1723"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0005748"
+],
+"ecogene":[
+"EG10700"
+],
+"ncbigene":[
+"946230"
+],
+"ncbigi":[
+"49176138"
+],
+"refseq_locus_tag":[
+"b1723"
+],
+"refseq_name":[
+"pfkB"
+],
+"refseq_synonym":[
+"JW5280",
+"ECK1721"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P06999"
+]
+}
+},
+{
+"id":"b3114",
+"name":"tdcE",
+"notes":{
+"original_bigg_ids":[
+"b3114"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0010242"
+],
+"ecogene":[
+"EG12758"
+],
+"ncbigene":[
+"947623"
+],
+"ncbigi":[
+"49176316"
+],
+"refseq_locus_tag":[
+"b3114"
+],
+"refseq_name":[
+"tdcE"
+],
+"refseq_synonym":[
+"JW5522",
+"ECK3103",
+"yhaS"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P42632"
+]
+}
+},
+{
+"id":"b2579",
+"name":"grcA",
+"notes":{
+"original_bigg_ids":[
+"b2579"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0008489"
+],
+"ecogene":[
+"EG11784"
+],
+"ncbigene":[
+"947068"
+],
+"ncbigi":[
+"16130504"
+],
+"refseq_locus_tag":[
+"b2579"
+],
+"refseq_name":[
+"grcA"
+],
+"refseq_synonym":[
+"ECK2577",
+"yfiD",
+"JW2563"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P68066"
+]
+}
+},
+{
+"id":"b3951",
+"name":"pflD",
+"notes":{
+"original_bigg_ids":[
+"b3951"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012934"
+],
+"ecogene":[
+"EG11910"
+],
+"ncbigene":[
+"948454"
+],
+"ncbigi":[
+"16131789"
+],
+"refseq_locus_tag":[
+"b3951"
+],
+"refseq_name":[
+"pflD"
+],
+"refseq_synonym":[
+"ECK3942",
+"yijL",
+"JW3923"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P32674"
+]
+}
+},
+{
+"id":"b0902",
+"name":"pflA",
+"notes":{
+"original_bigg_ids":[
+"b0902"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0003068"
+],
+"ecogene":[
+"EG10028"
+],
+"ncbigene":[
+"945517"
+],
+"ncbigi":[
+"16128869"
+],
+"refseq_locus_tag":[
+"b0902"
+],
+"refseq_name":[
+"pflA"
+],
+"refseq_synonym":[
+"ECK0893",
+"JW0885",
+"act"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A9N4"
+]
+}
+},
+{
+"id":"b3952",
+"name":"pflC",
+"notes":{
+"original_bigg_ids":[
+"b3952"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012937"
+],
+"ecogene":[
+"EG11911"
+],
+"ncbigene":[
+"948453"
+],
+"ncbigi":[
+"49176447"
+],
+"refseq_locus_tag":[
+"b3952"
+],
+"refseq_name":[
+"pflC"
+],
+"refseq_synonym":[
+"ECK3943",
+"JW3924",
+"yijM"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P32675"
+]
+}
+},
+{
+"id":"b0903",
+"name":"pflB",
+"notes":{
+"original_bigg_ids":[
+"b0903"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0003071"
+],
+"ecogene":[
+"EG10701"
+],
+"ncbigene":[
+"945514"
+],
+"ncbigi":[
+"16128870"
+],
+"refseq_locus_tag":[
+"b0903"
+],
+"refseq_name":[
+"pflB"
+],
+"refseq_synonym":[
+"pfl",
+"ECK0894",
+"JW0886"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P09373"
+]
+}
+},
+{
+"id":"b4025",
+"name":"pgi",
+"notes":{
+"original_bigg_ids":[
+"b4025"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0013163"
+],
+"ecogene":[
+"EG10702"
+],
+"ncbigene":[
+"948535"
+],
+"ncbigi":[
+"16131851"
+],
+"refseq_locus_tag":[
+"b4025"
+],
+"refseq_name":[
+"pgi"
+],
+"refseq_synonym":[
+"JW3985",
+"ECK4017"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A6T1"
+]
+}
+},
+{
+"id":"b2926",
+"name":"pgk",
+"notes":{
+"original_bigg_ids":[
+"b2926"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0009605"
+],
+"ecogene":[
+"EG10703"
+],
+"ncbigene":[
+"947414"
+],
+"ncbigi":[
+"16130827"
+],
+"refseq_locus_tag":[
+"b2926"
+],
+"refseq_name":[
+"pgk"
+],
+"refseq_synonym":[
+"ECK2922",
+"JW2893"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A799"
+]
+}
+},
+{
+"id":"b0767",
+"name":"pgl",
+"notes":{
+"original_bigg_ids":[
+"b0767"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002611"
+],
+"ecogene":[
+"EG13231"
+],
+"ncbigene":[
+"946398"
+],
+"ncbigi":[
+"16128735"
+],
+"refseq_locus_tag":[
+"b0767"
+],
+"refseq_name":[
+"pgl"
+],
+"refseq_synonym":[
+"JW0750",
+"ybhE",
+"ECK0756",
+"blu"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P52697"
+]
+}
+},
+{
+"id":"b3612",
+"name":"gpmM",
+"notes":{
+"original_bigg_ids":[
+"b3612"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0011818"
+],
+"ecogene":[
+"EG12296"
+],
+"ncbigene":[
+"948130"
+],
+"ncbigi":[
+"16131483"
+],
+"refseq_locus_tag":[
+"b3612"
+],
+"refseq_name":[
+"gpmM"
+],
+"refseq_synonym":[
+"JW3587",
+"yibO",
+"ECK3602",
+"pgmI",
+"gpmC",
+"gpmI"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P37689"
+]
+}
+},
+{
+"id":"b4395",
+"name":"ytjC",
+"notes":{
+"original_bigg_ids":[
+"b4395"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0014416"
+],
+"ecogene":[
+"EG12164"
+],
+"ncbigene":[
+"948918"
+],
+"ncbigi":[
+"16132212"
+],
+"refseq_locus_tag":[
+"b4395"
+],
+"refseq_name":[
+"ytjC"
+],
+"refseq_synonym":[
+"gpmB",
+"JW4358",
+"ECK4387"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A7A2"
+]
+}
+},
+{
+"id":"b0755",
+"name":"gpmA",
+"notes":{
+"original_bigg_ids":[
+"b0755"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002563"
+],
+"ecogene":[
+"EG11699"
+],
+"ncbigene":[
+"945068"
+],
+"ncbigi":[
+"16128723"
+],
+"refseq_locus_tag":[
+"b0755"
+],
+"refseq_name":[
+"gpmA"
+],
+"refseq_synonym":[
+"JW0738",
+"gpm",
+"ECK0744"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P62707"
+]
+}
+},
+{
+"id":"b3493",
+"name":"pitA",
+"notes":{
+"original_bigg_ids":[
+"b3493"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0011407"
+],
+"ecogene":[
+"EG12230"
+],
+"ncbigene":[
+"948009"
+],
+"ncbigi":[
+"16131365"
+],
+"refseq_locus_tag":[
+"b3493"
+],
+"refseq_name":[
+"pitA"
+],
+"refseq_synonym":[
+"pit",
+"ECK3478",
+"JW3460"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AFJ7"
+]
+}
+},
+{
+"id":"b2987",
+"name":"pitB",
+"notes":{
+"original_bigg_ids":[
+"b2987"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0009800"
+],
+"ecogene":[
+"EG12883"
+],
+"ncbigene":[
+"947475"
+],
+"ncbigi":[
+"16130887"
+],
+"refseq_locus_tag":[
+"b2987"
+],
+"refseq_name":[
+"pitB"
+],
+"refseq_synonym":[
+"ECK2981",
+"JW2955"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P43676"
+]
+}
+},
+{
+"id":"b3956",
+"name":"ppc",
+"notes":{
+"original_bigg_ids":[
+"b3956"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012950"
+],
+"ecogene":[
+"EG10756"
+],
+"ncbigene":[
+"948457"
+],
+"ncbigi":[
+"16131794"
+],
+"refseq_locus_tag":[
+"b3956"
+],
+"refseq_name":[
+"ppc"
+],
+"refseq_synonym":[
+"glu",
+"ECK3947",
+"asp",
+"JW3928"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P00864"
+]
+}
+},
+{
+"id":"b3403",
+"name":"pck",
+"notes":{
+"original_bigg_ids":[
+"b3403"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0011106"
+],
+"ecogene":[
+"EG10688"
+],
+"ncbigene":[
+"945667"
+],
+"ncbigi":[
+"16131280"
+],
+"refseq_locus_tag":[
+"b3403"
+],
+"refseq_name":[
+"pck"
+],
+"refseq_synonym":[
+"JW3366",
+"pckA",
+"ECK3390"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P22259"
+]
+}
+},
+{
+"id":"b1702",
+"name":"ppsA",
+"notes":{
+"original_bigg_ids":[
+"b1702"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0005678"
+],
+"ecogene":[
+"EG10759"
+],
+"ncbigene":[
+"946209"
+],
+"ncbigi":[
+"16129658"
+],
+"refseq_locus_tag":[
+"b1702"
+],
+"refseq_name":[
+"ppsA"
+],
+"refseq_synonym":[
+"pps",
+"ECK1700",
+"JW1692"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P23538"
+]
+}
+},
+{
+"id":"b2297",
+"name":"pta",
+"notes":{
+"original_bigg_ids":[
+"b2297"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0007582"
+],
+"ecogene":[
+"EG20173"
+],
+"ncbigene":[
+"946778"
+],
+"ncbigi":[
+"16130232"
+],
+"refseq_locus_tag":[
+"b2297"
+],
+"refseq_name":[
+"pta"
+],
+"refseq_synonym":[
+"JW2294",
+"ECK2291"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A9M8"
+]
+}
+},
+{
+"id":"b2458",
+"name":"eutD",
+"notes":{
+"original_bigg_ids":[
+"b2458"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0008097"
+],
+"ecogene":[
+"EG14188"
+],
+"ncbigene":[
+"946940"
+],
+"ncbigi":[
+"16130383"
+],
+"refseq_locus_tag":[
+"b2458"
+],
+"refseq_name":[
+"eutD"
+],
+"refseq_synonym":[
+"eutI",
+"ypfA",
+"ECK2453",
+"JW2442"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P77218"
+]
+}
+},
+{
+"id":"b1676",
+"name":"pykF",
+"notes":{
+"original_bigg_ids":[
+"b1676"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0005600"
+],
+"ecogene":[
+"EG10804"
+],
+"ncbigene":[
+"946179"
+],
+"ncbigi":[
+"16129632"
+],
+"refseq_locus_tag":[
+"b1676"
+],
+"refseq_name":[
+"pykF"
+],
+"refseq_synonym":[
+"ECK1672",
+"JW1666"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AD61"
+]
+}
+},
+{
+"id":"b1854",
+"name":"pykA",
+"notes":{
+"original_bigg_ids":[
+"b1854"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0006182"
+],
+"ecogene":[
+"EG10803"
+],
+"ncbigene":[
+"946527"
+],
+"ncbigi":[
+"16129807"
+],
+"refseq_locus_tag":[
+"b1854"
+],
+"refseq_name":[
+"pykA"
+],
+"refseq_synonym":[
+"JW1843",
+"ECK1855"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P21599"
+]
+}
+},
+{
+"id":"b3386",
+"name":"rpe",
+"notes":{
+"original_bigg_ids":[
+"b3386"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0011061"
+],
+"ecogene":[
+"EG11960"
+],
+"ncbigene":[
+"947896"
+],
+"ncbigi":[
+"16131264"
+],
+"refseq_locus_tag":[
+"b3386"
+],
+"refseq_name":[
+"rpe"
+],
+"refseq_synonym":[
+"yhfD",
+"ECK3373",
+"JW3349",
+"dod"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AG07"
+]
+}
+},
+{
+"id":"b4301",
+"name":"sgcE",
+"notes":{
+"original_bigg_ids":[
+"b4301"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0014097"
+],
+"ecogene":[
+"EG12553"
+],
+"ncbigene":[
+"948829"
+],
+"ncbigi":[
+"16132122"
+],
+"refseq_locus_tag":[
+"b4301"
+],
+"refseq_name":[
+"sgcE"
+],
+"refseq_synonym":[
+"JW4263",
+"ECK4290",
+"yjhK"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P39362"
+]
+}
+},
+{
+"id":"b2914",
+"name":"rpiA",
+"notes":{
+"original_bigg_ids":[
+"b2914"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0009567"
+],
+"ecogene":[
+"EG11443"
+],
+"ncbigene":[
+"947407"
+],
+"ncbigi":[
+"16130815"
+],
+"refseq_locus_tag":[
+"b2914"
+],
+"refseq_name":[
+"rpiA"
+],
+"refseq_synonym":[
+"ECK2910",
+"JW5475",
+"ygfC"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A7Z0"
+]
+}
+},
+{
+"id":"b4090",
+"name":"rpiB",
+"notes":{
+"original_bigg_ids":[
+"b4090"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0013405"
+],
+"ecogene":[
+"EG11827"
+],
+"ncbigene":[
+"948602"
+],
+"ncbigi":[
+"16131916"
+],
+"refseq_locus_tag":[
+"b4090"
+],
+"refseq_name":[
+"rpiB"
+],
+"refseq_synonym":[
+"JW4051",
+"alsB",
+"alsI",
+"yjcA",
+"ECK4083"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P37351"
+]
+}
+},
+{
+"id":"b0721",
+"name":"sdhC",
+"notes":{
+"original_bigg_ids":[
+"b0721"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002460"
+],
+"ecogene":[
+"EG10933"
+],
+"ncbigene":[
+"945316"
+],
+"ncbigi":[
+"16128696"
+],
+"refseq_locus_tag":[
+"b0721"
+],
+"refseq_name":[
+"sdhC"
+],
+"refseq_synonym":[
+"JW0711",
+"ECK0710",
+"cybA"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P69054"
+]
+}
+},
+{
+"id":"b0722",
+"name":"sdhD",
+"notes":{
+"original_bigg_ids":[
+"b0722"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002464"
+],
+"ecogene":[
+"EG10934"
+],
+"ncbigene":[
+"945322"
+],
+"ncbigi":[
+"16128697"
+],
+"refseq_locus_tag":[
+"b0722"
+],
+"refseq_name":[
+"sdhD"
+],
+"refseq_synonym":[
+"JW0712",
+"ECK0711"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AC44"
+]
+}
+},
+{
+"id":"b0724",
+"name":"sdhB",
+"notes":{
+"original_bigg_ids":[
+"b0724"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002468"
+],
+"ecogene":[
+"EG10932"
+],
+"ncbigene":[
+"945300"
+],
+"ncbigi":[
+"16128699"
+],
+"refseq_locus_tag":[
+"b0724"
+],
+"refseq_name":[
+"sdhB"
+],
+"refseq_synonym":[
+"ECK0713",
+"JW0714"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P07014"
+]
+}
+},
+{
+"id":"b0723",
+"name":"sdhA",
+"notes":{
+"original_bigg_ids":[
+"b0723"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002466"
+],
+"ecogene":[
+"EG10931"
+],
+"ncbigene":[
+"945402"
+],
+"ncbigi":[
+"16128698"
+],
+"refseq_locus_tag":[
+"b0723"
+],
+"refseq_name":[
+"sdhA"
+],
+"refseq_synonym":[
+"JW0713",
+"ECK0712"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AC41"
+]
+}
+},
+{
+"id":"b0729",
+"name":"sucD",
+"notes":{
+"original_bigg_ids":[
+"b0729"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002485"
+],
+"ecogene":[
+"EG10982"
+],
+"ncbigene":[
+"945314"
+],
+"ncbigi":[
+"16128704"
+],
+"refseq_locus_tag":[
+"b0729"
+],
+"refseq_name":[
+"sucD"
+],
+"refseq_synonym":[
+"JW0718",
+"ECK0717"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AGE9"
+]
+}
+},
+{
+"id":"b0728",
+"name":"sucC",
+"notes":{
+"original_bigg_ids":[
+"b0728"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002483"
+],
+"ecogene":[
+"EG10981"
+],
+"ncbigene":[
+"945312"
+],
+"ncbigi":[
+"16128703"
+],
+"refseq_locus_tag":[
+"b0728"
+],
+"refseq_name":[
+"sucC"
+],
+"refseq_synonym":[
+"JW0717",
+"ECK0716"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A836"
+]
+}
+},
+{
+"id":"b0008",
+"name":"talB",
+"notes":{
+"original_bigg_ids":[
+"b0008"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0000027"
+],
+"ecogene":[
+"EG11556"
+],
+"ncbigene":[
+"944748"
+],
+"ncbigi":[
+"16128002"
+],
+"refseq_locus_tag":[
+"b0008"
+],
+"refseq_name":[
+"talB"
+],
+"refseq_synonym":[
+"yaaK",
+"JW0007",
+"ECK0008"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A870"
+]
+}
+},
+{
+"id":"b2464",
+"name":"talA",
+"notes":{
+"original_bigg_ids":[
+"b2464"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0008115"
+],
+"ecogene":[
+"EG11797"
+],
+"ncbigene":[
+"947006"
+],
+"ncbigi":[
+"16130389"
+],
+"refseq_locus_tag":[
+"b2464"
+],
+"refseq_name":[
+"talA"
+],
+"refseq_synonym":[
+"ECK2459",
+"JW2448"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A867"
+]
+}
+},
+{
+"id":"b2465",
+"name":"tktB",
+"notes":{
+"original_bigg_ids":[
+"b2465"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0008117"
+],
+"ecogene":[
+"EG12100"
+],
+"ncbigene":[
+"945865"
+],
+"ncbigi":[
+"16130390"
+],
+"refseq_locus_tag":[
+"b2465"
+],
+"refseq_name":[
+"tktB"
+],
+"refseq_synonym":[
+"JW2449",
+"ECK2460"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P33570"
+]
+}
+},
+{
+"id":"b2935",
+"name":"tktA",
+"notes":{
+"original_bigg_ids":[
+"b2935"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0009625"
+],
+"ecogene":[
+"EG11427"
+],
+"ncbigene":[
+"947420"
+],
+"ncbigi":[
+"49176286"
+],
+"refseq_locus_tag":[
+"b2935"
+],
+"refseq_name":[
+"tktA"
+],
+"refseq_synonym":[
+"JW5478",
+"tkt",
+"ECK2930"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P27302"
+]
+}
+},
+{
+"id":"b3919",
+"name":"tpiA",
+"notes":{
+"original_bigg_ids":[
+"b3919"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012799"
+],
+"ecogene":[
+"EG11015"
+],
+"ncbigene":[
+"948409"
+],
+"ncbigi":[
+"16131757"
+],
+"refseq_locus_tag":[
+"b3919"
+],
+"refseq_name":[
+"tpiA"
+],
+"refseq_synonym":[
+"JW3890",
+"ECK3911",
+"tpi"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A858"
+]
+}
+}
+],
+"id":"e_coli_core",
+"compartments":{
+"c":"cytosol",
+"e":"extracellular space"
+},
+"version":"1"
+}
\ No newline at end of file
diff --git a/tests/data/e_coli_core_for_annotation.xml b/tests/data/e_coli_core_for_annotation.xml
new file mode 100644
index 000000000..5658f8fdb
--- /dev/null
+++ b/tests/data/e_coli_core_for_annotation.xml
@@ -0,0 +1,8367 @@
+
+
+
+
+
+
+
Key1 : Value1
+
+
+
e_coli_core - Escherichia coli str. K-12 substr. MG1655
+
+
+
Description
+
+
This is a metabolism model of Escherichia coli str. K-12 substr. MG1655 in
+ SBML format.
+
The content of this model has been carefully created in a manual research effort. This file has been exported from the software
+
COBRApy and further processed with the
+
JSBML-based
+
ModelPolisher application.
Terms of use
+ Copyright © 2017 The Regents of the University of California.
+
+
Redistribution and use of any part of this model from BiGG Models knowledge-base, with or without modification, are permitted provided that the following conditions are met:
+
+ - Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
+ - Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
For specific licensing terms about this particular model and regulations of commercial use, see
+ this model in BiGG Models knowledge-base.
+
References
When using content from BiGG Models knowledge-base in your research works, please cite
+
+ - King ZA, Lu JS, Dräger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, and Lewis NE. (2015).
+
- BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models.
+ Nucl Acids Res.
+ doi:10.1093/nar/gkv1049
+
+
+
+
+
+
+
+
+
+ Koenig
+ Matthias
+
+ koenigmx@hu-berlin.de
+
+ Humboldt-University Berlin, Institute for Theoretical Biology
+
+
+
+
+ Koenig
+ Matthias
+
+ koenigmx@hu-berlin.de
+
+
+
+ Koenig
+ Matthias
+
+
+ Humboldt-University Berlin, Institute for Theoretical Biology
+
+
+
+
+ Koenig
+ Matthias
+
+
+
+
+
+ 2019-03-06T14:40:55Z
+
+
+ 2019-03-06T14:40:55Z
+
+
+ 2019-03-06T14:41:55Z
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Key1 : Value1
+
Key2 : Value2
+
+
A Heading
+
e_coli_core - Escherichia coli str. K-12 substr. MG1655
+
+
Key3 : Value3
+
\n - Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
\n - Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided\n with the distribution.
\n
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.",
+ "This is a metabolism model of Escherichia coli str. K-12 substr. MG1655 in\n SBML\u00a0format."
+ },
+ "metadata": {
+ "standardized": [
+ {
+ "qualifier": "bqb_hasTaxon",
+ "resources": ["http://identifiers.org/taxonomy/511145"]
+ },
+ {
+ "qualifier": "bqm_is",
+ "resources": ["http://identifiers.org/bigg.model/e_coli_core"]
+ },
+ {
+ "qualifier": "bqm_isDescribedBy",
+ "resources": ["http://identifiers.org/doi/10.1128/ecosalplus.10.2.1"]
+ }
+ ]
+ },
+ "version": "1"
+}
diff --git a/tests/data/example_notes.xml b/tests/data/example_notes.xml
index 13fcdff15..ccbb3b9fd 100644
--- a/tests/data/example_notes.xml
+++ b/tests/data/example_notes.xml
@@ -46,7 +46,6 @@
-
@@ -72,7 +71,6 @@
-
diff --git a/tests/data/iJO1366.pickle b/tests/data/iJO1366.pickle
index 3856b85be..14178f2a2 100644
Binary files a/tests/data/iJO1366.pickle and b/tests/data/iJO1366.pickle differ
diff --git a/tests/data/mini.json b/tests/data/mini.json
new file mode 100644
index 000000000..3ecf28e0d
--- /dev/null
+++ b/tests/data/mini.json
@@ -0,0 +1,1641 @@
+{
+ "compartments": {
+ "c": "cytosol",
+ "e": "extracellular"
+ },
+ "genes": [
+ {
+ "id": "G_b0755",
+ "name": "gpmA"
+ },
+ {
+ "id": "G_b0875",
+ "name": "aqpZ"
+ },
+ {
+ "id": "G_b1101",
+ "name": "ptsG"
+ },
+ {
+ "id": "G_b1380",
+ "name": "ldhA"
+ },
+ {
+ "id": "G_b1621",
+ "name": "malX"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/ncbiprotein/1208453",
+ "http://identifiers.org/ncbiprotein/1652654"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "id": "G_b1676",
+ "name": "pykF"
+ },
+ {
+ "id": "G_b1723",
+ "name": "pfkB"
+ },
+ {
+ "id": "G_b1773",
+ "name": "ydjI"
+ },
+ {
+ "id": "G_b1779",
+ "name": "gapA"
+ },
+ {
+ "id": "G_b1817",
+ "name": "manX"
+ },
+ {
+ "id": "G_b1818",
+ "name": "manY"
+ },
+ {
+ "id": "G_b1819",
+ "name": "manZ"
+ },
+ {
+ "id": "G_b1854",
+ "name": "pykA"
+ },
+ {
+ "id": "G_b2097",
+ "name": "fbaB"
+ },
+ {
+ "id": "G_b2133",
+ "name": "dld"
+ },
+ {
+ "id": "G_b2415",
+ "name": "ptsH"
+ },
+ {
+ "id": "G_b2416",
+ "name": "ptsI"
+ },
+ {
+ "id": "G_b2417",
+ "name": "crr"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/ncbiprotein/1653839"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "id": "G_b2779",
+ "name": "eno"
+ },
+ {
+ "id": "G_b2925",
+ "name": "fbaA"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/ncbiprotein/1653609"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "id": "G_b2926",
+ "name": "pgk"
+ },
+ {
+ "id": "G_b2987",
+ "name": "pitB"
+ },
+ {
+ "id": "G_b3493",
+ "name": "pitA"
+ },
+ {
+ "id": "G_b3612",
+ "name": "gpmM"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/ncbiprotein/1006614",
+ "http://identifiers.org/ncbiprotein/1651919"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "id": "G_b3916",
+ "name": "pfkA"
+ },
+ {
+ "id": "G_b3919",
+ "name": "tpiA"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/ncbiprotein/1653253"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "id": "G_b4025",
+ "name": "pgi"
+ },
+ {
+ "id": "G_b4395",
+ "name": "ytjC"
+ },
+ {
+ "id": "G_s0001",
+ "name": "G_s0001"
+ }
+ ],
+ "groups": [],
+ "id": "mini_textbook",
+ "metabolites": [
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/13dpg",
+ "http://identifiers.org/biocyc/DPG",
+ "http://identifiers.org/chebi/CHEBI:11881",
+ "http://identifiers.org/chebi/CHEBI:16001",
+ "http://identifiers.org/chebi/CHEBI:1658",
+ "http://identifiers.org/chebi/CHEBI:20189",
+ "http://identifiers.org/chebi/CHEBI:57604",
+ "http://identifiers.org/hmdb/HMDB01270",
+ "http://identifiers.org/kegg.compound/C00236",
+ "http://identifiers.org/pubchem.substance/3535",
+ "http://identifiers.org/reactome/REACT_29800",
+ "http://identifiers.org/seed.compound/cpd00203",
+ "http://identifiers.org/unipathway.compound/UPC00236"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -4,
+ "compartment": "c",
+ "formula": "C3H4O10P2",
+ "id": "M_13dpg_c",
+ "name": "3-Phospho-D-glyceroyl phosphate"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/2pg",
+ "http://identifiers.org/biocyc/2-PG",
+ "http://identifiers.org/chebi/CHEBI:11651",
+ "http://identifiers.org/chebi/CHEBI:1267",
+ "http://identifiers.org/chebi/CHEBI:12986",
+ "http://identifiers.org/chebi/CHEBI:17835",
+ "http://identifiers.org/chebi/CHEBI:21028",
+ "http://identifiers.org/chebi/CHEBI:24344",
+ "http://identifiers.org/chebi/CHEBI:39868",
+ "http://identifiers.org/chebi/CHEBI:58289",
+ "http://identifiers.org/hmdb/HMDB00362",
+ "http://identifiers.org/hmdb/HMDB03391",
+ "http://identifiers.org/kegg.compound/C00631",
+ "http://identifiers.org/pubchem.substance/3904",
+ "http://identifiers.org/reactome/REACT_30485",
+ "http://identifiers.org/seed.compound/cpd00482",
+ "http://identifiers.org/unipathway.compound/UPC00631"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -3,
+ "compartment": "c",
+ "formula": "C3H4O7P",
+ "id": "M_2pg_c",
+ "name": "D-Glycerate 2-phosphate"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/3pg",
+ "http://identifiers.org/biocyc/G3P",
+ "http://identifiers.org/chebi/CHEBI:11879",
+ "http://identifiers.org/chebi/CHEBI:11880",
+ "http://identifiers.org/chebi/CHEBI:11882",
+ "http://identifiers.org/chebi/CHEBI:12987",
+ "http://identifiers.org/chebi/CHEBI:1657",
+ "http://identifiers.org/chebi/CHEBI:1659",
+ "http://identifiers.org/chebi/CHEBI:17050",
+ "http://identifiers.org/chebi/CHEBI:17794",
+ "http://identifiers.org/chebi/CHEBI:21029",
+ "http://identifiers.org/chebi/CHEBI:24345",
+ "http://identifiers.org/chebi/CHEBI:40016",
+ "http://identifiers.org/chebi/CHEBI:57998",
+ "http://identifiers.org/chebi/CHEBI:58272",
+ "http://identifiers.org/hmdb/HMDB00807",
+ "http://identifiers.org/kegg.compound/C00197",
+ "http://identifiers.org/kegg.compound/C00597",
+ "http://identifiers.org/pubchem.substance/3497",
+ "http://identifiers.org/reactome/REACT_29728",
+ "http://identifiers.org/seed.compound/cpd00169",
+ "http://identifiers.org/unipathway.compound/UPC00197",
+ "http://identifiers.org/unipathway.compound/UPC00597"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -3,
+ "compartment": "c",
+ "formula": "C3H4O7P",
+ "id": "M_3pg_c",
+ "name": "3-Phospho-D-glycerate"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/adp",
+ "http://identifiers.org/biocyc/ADP",
+ "http://identifiers.org/biocyc/ADP-GROUP",
+ "http://identifiers.org/cas/58-64-0",
+ "http://identifiers.org/cas/58-64-0",
+ "http://identifiers.org/chebi/CHEBI:13222",
+ "http://identifiers.org/chebi/CHEBI:16761",
+ "http://identifiers.org/chebi/CHEBI:22244",
+ "http://identifiers.org/chebi/CHEBI:2342",
+ "http://identifiers.org/chebi/CHEBI:40553",
+ "http://identifiers.org/chebi/CHEBI:456216",
+ "http://identifiers.org/hmdb/HMDB01341",
+ "http://identifiers.org/kegg.compound/C00008",
+ "http://identifiers.org/kegg.glycan/G11113",
+ "http://identifiers.org/pubchem.substance/3310",
+ "http://identifiers.org/reactome/REACT_113581",
+ "http://identifiers.org/reactome/REACT_113582",
+ "http://identifiers.org/reactome/REACT_114564",
+ "http://identifiers.org/reactome/REACT_114565",
+ "http://identifiers.org/reactome/REACT_190072",
+ "http://identifiers.org/reactome/REACT_196180",
+ "http://identifiers.org/reactome/REACT_211606",
+ "http://identifiers.org/reactome/REACT_29370",
+ "http://identifiers.org/reactome/REACT_429153",
+ "http://identifiers.org/reactome/REACT_429160",
+ "http://identifiers.org/reactome/REACT_481002",
+ "http://identifiers.org/seed.compound/cpd00008",
+ "http://identifiers.org/unipathway.compound/UPC00008"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -3,
+ "compartment": "c",
+ "formula": "C10H12N5O10P2",
+ "id": "M_adp_c",
+ "name": "ADP"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/atp",
+ "http://identifiers.org/biocyc/ATP",
+ "http://identifiers.org/cas/56-65-5",
+ "http://identifiers.org/cas/56-65-5",
+ "http://identifiers.org/chebi/CHEBI:10789",
+ "http://identifiers.org/chebi/CHEBI:10841",
+ "http://identifiers.org/chebi/CHEBI:13236",
+ "http://identifiers.org/chebi/CHEBI:15422",
+ "http://identifiers.org/chebi/CHEBI:22249",
+ "http://identifiers.org/chebi/CHEBI:2359",
+ "http://identifiers.org/chebi/CHEBI:30616",
+ "http://identifiers.org/chebi/CHEBI:40938",
+ "http://identifiers.org/chebi/CHEBI:57299",
+ "http://identifiers.org/hmdb/HMDB00538",
+ "http://identifiers.org/kegg.compound/C00002",
+ "http://identifiers.org/kegg.drug/D08646",
+ "http://identifiers.org/pubchem.substance/3304",
+ "http://identifiers.org/reactome/REACT_113592",
+ "http://identifiers.org/reactome/REACT_113593",
+ "http://identifiers.org/reactome/REACT_114570",
+ "http://identifiers.org/reactome/REACT_139836",
+ "http://identifiers.org/reactome/REACT_190078",
+ "http://identifiers.org/reactome/REACT_211579",
+ "http://identifiers.org/reactome/REACT_29358",
+ "http://identifiers.org/reactome/REACT_389573",
+ "http://identifiers.org/seed.compound/cpd00002",
+ "http://identifiers.org/unipathway.compound/UPC00002"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -4,
+ "compartment": "c",
+ "formula": "C10H12N5O13P3",
+ "id": "M_atp_c",
+ "name": "ATP"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/dhap",
+ "http://identifiers.org/biocyc/DIHYDROXY-ACETONE-PHOSPHATE",
+ "http://identifiers.org/cas/57-04-5",
+ "http://identifiers.org/cas/57-04-5",
+ "http://identifiers.org/chebi/CHEBI:14341",
+ "http://identifiers.org/chebi/CHEBI:14342",
+ "http://identifiers.org/chebi/CHEBI:16108",
+ "http://identifiers.org/chebi/CHEBI:24355",
+ "http://identifiers.org/chebi/CHEBI:39571",
+ "http://identifiers.org/chebi/CHEBI:5454",
+ "http://identifiers.org/chebi/CHEBI:57642",
+ "http://identifiers.org/hmdb/HMDB01473",
+ "http://identifiers.org/hmdb/HMDB11735",
+ "http://identifiers.org/kegg.compound/C00111",
+ "http://identifiers.org/pubchem.substance/3411",
+ "http://identifiers.org/reactome/REACT_188451",
+ "http://identifiers.org/reactome/REACT_390404",
+ "http://identifiers.org/reactome/REACT_75970",
+ "http://identifiers.org/seed.compound/cpd00095",
+ "http://identifiers.org/unipathway.compound/UPC00111"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -2,
+ "compartment": "c",
+ "formula": "C3H5O6P",
+ "id": "M_dhap_c",
+ "name": "Dihydroxyacetone phosphate"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/f6p",
+ "http://identifiers.org/biocyc/FRUCTOSE-6P",
+ "http://identifiers.org/cas/643-13-0",
+ "http://identifiers.org/cas/643-13-0",
+ "http://identifiers.org/chebi/CHEBI:10375",
+ "http://identifiers.org/chebi/CHEBI:12352",
+ "http://identifiers.org/chebi/CHEBI:16084",
+ "http://identifiers.org/chebi/CHEBI:22768",
+ "http://identifiers.org/chebi/CHEBI:42378",
+ "http://identifiers.org/chebi/CHEBI:45804",
+ "http://identifiers.org/chebi/CHEBI:57634",
+ "http://identifiers.org/chebi/CHEBI:61527",
+ "http://identifiers.org/chebi/CHEBI:61553",
+ "http://identifiers.org/hmdb/HMDB03971",
+ "http://identifiers.org/kegg.compound/C00085",
+ "http://identifiers.org/kegg.compound/C05345",
+ "http://identifiers.org/pubchem.substance/3385",
+ "http://identifiers.org/seed.compound/cpd00072",
+ "http://identifiers.org/unipathway.compound/UPC00085",
+ "http://identifiers.org/unipathway.compound/UPC05345"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -2,
+ "compartment": "c",
+ "formula": "C6H11O9P",
+ "id": "M_f6p_c",
+ "name": "D-Fructose 6-phosphate"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/fdp",
+ "http://identifiers.org/biocyc/FRUCTOSE-16-DIPHOSPHATE",
+ "http://identifiers.org/cas/488-69-7",
+ "http://identifiers.org/cas/488-69-7",
+ "http://identifiers.org/chebi/CHEBI:10374",
+ "http://identifiers.org/chebi/CHEBI:22767",
+ "http://identifiers.org/chebi/CHEBI:28013",
+ "http://identifiers.org/chebi/CHEBI:32966",
+ "http://identifiers.org/chebi/CHEBI:32967",
+ "http://identifiers.org/chebi/CHEBI:32968",
+ "http://identifiers.org/chebi/CHEBI:37736",
+ "http://identifiers.org/chebi/CHEBI:40591",
+ "http://identifiers.org/chebi/CHEBI:40595",
+ "http://identifiers.org/chebi/CHEBI:41014",
+ "http://identifiers.org/chebi/CHEBI:42553",
+ "http://identifiers.org/chebi/CHEBI:49299",
+ "http://identifiers.org/kegg.compound/C00354",
+ "http://identifiers.org/kegg.compound/C05378",
+ "http://identifiers.org/pubchem.substance/3647",
+ "http://identifiers.org/seed.compound/cpd00290",
+ "http://identifiers.org/unipathway.compound/UPC00354"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -4,
+ "compartment": "c",
+ "formula": "C6H10O12P2",
+ "id": "M_fdp_c",
+ "name": "D-Fructose 1,6-bisphosphate"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/g3p",
+ "http://identifiers.org/cas/142-10-9",
+ "http://identifiers.org/cas/142-10-9",
+ "http://identifiers.org/chebi/CHEBI:14333",
+ "http://identifiers.org/chebi/CHEBI:17138",
+ "http://identifiers.org/chebi/CHEBI:5446",
+ "http://identifiers.org/chebi/CHEBI:58027",
+ "http://identifiers.org/hmdb/HMDB01112",
+ "http://identifiers.org/kegg.compound/C00118",
+ "http://identifiers.org/kegg.compound/C00661",
+ "http://identifiers.org/pubchem.substance/3930",
+ "http://identifiers.org/seed.compound/cpd00102",
+ "http://identifiers.org/unipathway.compound/UPC00118",
+ "http://identifiers.org/unipathway.compound/UPC00661"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -2,
+ "compartment": "c",
+ "formula": "C3H5O6P",
+ "id": "M_g3p_c",
+ "name": "Glyceraldehyde 3-phosphate"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/g6p",
+ "http://identifiers.org/biocyc/D-glucose-6-phosphate",
+ "http://identifiers.org/biocyc/GLC-6-P",
+ "http://identifiers.org/cas/56-73-5",
+ "http://identifiers.org/cas/56-73-5",
+ "http://identifiers.org/chebi/CHEBI:10399",
+ "http://identifiers.org/chebi/CHEBI:12375",
+ "http://identifiers.org/chebi/CHEBI:17719",
+ "http://identifiers.org/chebi/CHEBI:22797",
+ "http://identifiers.org/chebi/CHEBI:41041",
+ "http://identifiers.org/chebi/CHEBI:4170",
+ "http://identifiers.org/chebi/CHEBI:58247",
+ "http://identifiers.org/chebi/CHEBI:61548",
+ "http://identifiers.org/hmdb/HMDB01401",
+ "http://identifiers.org/hmdb/HMDB01549",
+ "http://identifiers.org/hmdb/HMDB03498",
+ "http://identifiers.org/hmdb/HMDB06793",
+ "http://identifiers.org/kegg.compound/C00092",
+ "http://identifiers.org/kegg.compound/C01172",
+ "http://identifiers.org/pubchem.substance/3392",
+ "http://identifiers.org/reactome/REACT_1629756",
+ "http://identifiers.org/seed.compound/cpd00079",
+ "http://identifiers.org/unipathway.compound/UPC00092"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -2,
+ "compartment": "c",
+ "formula": "C6H11O9P",
+ "id": "M_g6p_c",
+ "name": "D-Glucose 6-phosphate"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/glc__D",
+ "http://identifiers.org/cas/50-99-7",
+ "http://identifiers.org/cas/50-99-7",
+ "http://identifiers.org/kegg.compound/C00031",
+ "http://identifiers.org/pubchem.substance/3333"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": 0,
+ "compartment": "e",
+ "formula": "C6H12O6",
+ "id": "M_glc__D_e",
+ "name": "D-Glucose"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/h2o",
+ "http://identifiers.org/biocyc/OH",
+ "http://identifiers.org/biocyc/OXONIUM",
+ "http://identifiers.org/biocyc/WATER",
+ "http://identifiers.org/cas/7732-18-5",
+ "http://identifiers.org/cas/7732-18-5",
+ "http://identifiers.org/chebi/CHEBI:10743",
+ "http://identifiers.org/chebi/CHEBI:13352",
+ "http://identifiers.org/chebi/CHEBI:13365",
+ "http://identifiers.org/chebi/CHEBI:13419",
+ "http://identifiers.org/chebi/CHEBI:15377",
+ "http://identifiers.org/chebi/CHEBI:16234",
+ "http://identifiers.org/chebi/CHEBI:27313",
+ "http://identifiers.org/chebi/CHEBI:29356",
+ "http://identifiers.org/chebi/CHEBI:29373",
+ "http://identifiers.org/chebi/CHEBI:29374",
+ "http://identifiers.org/chebi/CHEBI:29375",
+ "http://identifiers.org/chebi/CHEBI:29412",
+ "http://identifiers.org/chebi/CHEBI:33811",
+ "http://identifiers.org/chebi/CHEBI:33813",
+ "http://identifiers.org/chebi/CHEBI:35511",
+ "http://identifiers.org/chebi/CHEBI:36385",
+ "http://identifiers.org/chebi/CHEBI:41979",
+ "http://identifiers.org/chebi/CHEBI:41981",
+ "http://identifiers.org/chebi/CHEBI:42043",
+ "http://identifiers.org/chebi/CHEBI:42857",
+ "http://identifiers.org/chebi/CHEBI:43228",
+ "http://identifiers.org/chebi/CHEBI:44292",
+ "http://identifiers.org/chebi/CHEBI:44641",
+ "http://identifiers.org/chebi/CHEBI:44701",
+ "http://identifiers.org/chebi/CHEBI:44819",
+ "http://identifiers.org/chebi/CHEBI:53442",
+ "http://identifiers.org/chebi/CHEBI:5585",
+ "http://identifiers.org/chebi/CHEBI:5594",
+ "http://identifiers.org/hmdb/HMDB01039",
+ "http://identifiers.org/hmdb/HMDB02111",
+ "http://identifiers.org/kegg.compound/C00001",
+ "http://identifiers.org/kegg.compound/C01328",
+ "http://identifiers.org/kegg.compound/C18712",
+ "http://identifiers.org/kegg.compound/C18714",
+ "http://identifiers.org/kegg.drug/D00001",
+ "http://identifiers.org/kegg.drug/D03703",
+ "http://identifiers.org/kegg.drug/D06322",
+ "http://identifiers.org/pubchem.substance/3303",
+ "http://identifiers.org/reactome/REACT_109276",
+ "http://identifiers.org/reactome/REACT_113518",
+ "http://identifiers.org/reactome/REACT_113519",
+ "http://identifiers.org/reactome/REACT_113521",
+ "http://identifiers.org/reactome/REACT_141343",
+ "http://identifiers.org/reactome/REACT_1605715",
+ "http://identifiers.org/reactome/REACT_189422",
+ "http://identifiers.org/reactome/REACT_2022884",
+ "http://identifiers.org/reactome/REACT_29356",
+ "http://identifiers.org/reactome/REACT_351603",
+ "http://identifiers.org/reactome/REACT_947593",
+ "http://identifiers.org/seed.compound/cpd00001",
+ "http://identifiers.org/seed.compound/cpd15275",
+ "http://identifiers.org/unipathway.compound/UPC00001",
+ "http://identifiers.org/unipathway.compound/UPC01328"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": 0,
+ "compartment": "c",
+ "formula": "H2O",
+ "id": "M_h2o_c",
+ "name": "H2O"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/h2o",
+ "http://identifiers.org/biocyc/OH",
+ "http://identifiers.org/biocyc/OXONIUM",
+ "http://identifiers.org/biocyc/WATER",
+ "http://identifiers.org/cas/7732-18-5",
+ "http://identifiers.org/cas/7732-18-5",
+ "http://identifiers.org/chebi/CHEBI:10743",
+ "http://identifiers.org/chebi/CHEBI:13352",
+ "http://identifiers.org/chebi/CHEBI:13365",
+ "http://identifiers.org/chebi/CHEBI:13419",
+ "http://identifiers.org/chebi/CHEBI:15377",
+ "http://identifiers.org/chebi/CHEBI:16234",
+ "http://identifiers.org/chebi/CHEBI:27313",
+ "http://identifiers.org/chebi/CHEBI:29356",
+ "http://identifiers.org/chebi/CHEBI:29373",
+ "http://identifiers.org/chebi/CHEBI:29374",
+ "http://identifiers.org/chebi/CHEBI:29375",
+ "http://identifiers.org/chebi/CHEBI:29412",
+ "http://identifiers.org/chebi/CHEBI:33811",
+ "http://identifiers.org/chebi/CHEBI:33813",
+ "http://identifiers.org/chebi/CHEBI:35511",
+ "http://identifiers.org/chebi/CHEBI:36385",
+ "http://identifiers.org/chebi/CHEBI:41979",
+ "http://identifiers.org/chebi/CHEBI:41981",
+ "http://identifiers.org/chebi/CHEBI:42043",
+ "http://identifiers.org/chebi/CHEBI:42857",
+ "http://identifiers.org/chebi/CHEBI:43228",
+ "http://identifiers.org/chebi/CHEBI:44292",
+ "http://identifiers.org/chebi/CHEBI:44641",
+ "http://identifiers.org/chebi/CHEBI:44701",
+ "http://identifiers.org/chebi/CHEBI:44819",
+ "http://identifiers.org/chebi/CHEBI:53442",
+ "http://identifiers.org/chebi/CHEBI:5585",
+ "http://identifiers.org/chebi/CHEBI:5594",
+ "http://identifiers.org/hmdb/HMDB01039",
+ "http://identifiers.org/hmdb/HMDB02111",
+ "http://identifiers.org/kegg.compound/C00001",
+ "http://identifiers.org/kegg.compound/C01328",
+ "http://identifiers.org/kegg.compound/C18712",
+ "http://identifiers.org/kegg.compound/C18714",
+ "http://identifiers.org/kegg.drug/D00001",
+ "http://identifiers.org/kegg.drug/D03703",
+ "http://identifiers.org/kegg.drug/D06322",
+ "http://identifiers.org/pubchem.substance/3303",
+ "http://identifiers.org/reactome/REACT_109276",
+ "http://identifiers.org/reactome/REACT_113518",
+ "http://identifiers.org/reactome/REACT_113519",
+ "http://identifiers.org/reactome/REACT_113521",
+ "http://identifiers.org/reactome/REACT_141343",
+ "http://identifiers.org/reactome/REACT_1605715",
+ "http://identifiers.org/reactome/REACT_189422",
+ "http://identifiers.org/reactome/REACT_2022884",
+ "http://identifiers.org/reactome/REACT_29356",
+ "http://identifiers.org/reactome/REACT_351603",
+ "http://identifiers.org/reactome/REACT_947593",
+ "http://identifiers.org/seed.compound/cpd00001",
+ "http://identifiers.org/seed.compound/cpd15275",
+ "http://identifiers.org/unipathway.compound/UPC00001",
+ "http://identifiers.org/unipathway.compound/UPC01328"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": 0,
+ "compartment": "e",
+ "formula": "H2O",
+ "id": "M_h2o_e",
+ "name": "H2O"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/h",
+ "http://identifiers.org/biocyc/PROTON",
+ "http://identifiers.org/cas/12408-02-5",
+ "http://identifiers.org/cas/12408-02-5",
+ "http://identifiers.org/chebi/CHEBI:10744",
+ "http://identifiers.org/chebi/CHEBI:13357",
+ "http://identifiers.org/chebi/CHEBI:15378",
+ "http://identifiers.org/chebi/CHEBI:24636",
+ "http://identifiers.org/chebi/CHEBI:5584",
+ "http://identifiers.org/kegg.compound/C00080",
+ "http://identifiers.org/pubchem.substance/3380",
+ "http://identifiers.org/reactome/REACT_113529",
+ "http://identifiers.org/reactome/REACT_1470067",
+ "http://identifiers.org/reactome/REACT_156540",
+ "http://identifiers.org/reactome/REACT_1614597",
+ "http://identifiers.org/reactome/REACT_163953",
+ "http://identifiers.org/reactome/REACT_193465",
+ "http://identifiers.org/reactome/REACT_194688",
+ "http://identifiers.org/reactome/REACT_2000349",
+ "http://identifiers.org/reactome/REACT_351626",
+ "http://identifiers.org/reactome/REACT_372511",
+ "http://identifiers.org/reactome/REACT_374900",
+ "http://identifiers.org/reactome/REACT_425969",
+ "http://identifiers.org/reactome/REACT_425978",
+ "http://identifiers.org/reactome/REACT_425999",
+ "http://identifiers.org/reactome/REACT_427899",
+ "http://identifiers.org/reactome/REACT_428040",
+ "http://identifiers.org/reactome/REACT_428548",
+ "http://identifiers.org/reactome/REACT_70106",
+ "http://identifiers.org/reactome/REACT_74722",
+ "http://identifiers.org/seed.compound/cpd00067",
+ "http://identifiers.org/unipathway.compound/UPC00080"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": 1,
+ "compartment": "c",
+ "formula": "H",
+ "id": "M_h_c",
+ "name": "H+"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/h",
+ "http://identifiers.org/biocyc/PROTON",
+ "http://identifiers.org/cas/12408-02-5",
+ "http://identifiers.org/cas/12408-02-5",
+ "http://identifiers.org/chebi/CHEBI:10744",
+ "http://identifiers.org/chebi/CHEBI:13357",
+ "http://identifiers.org/chebi/CHEBI:15378",
+ "http://identifiers.org/chebi/CHEBI:24636",
+ "http://identifiers.org/chebi/CHEBI:5584",
+ "http://identifiers.org/kegg.compound/C00080",
+ "http://identifiers.org/pubchem.substance/3380",
+ "http://identifiers.org/reactome/REACT_113529",
+ "http://identifiers.org/reactome/REACT_1470067",
+ "http://identifiers.org/reactome/REACT_156540",
+ "http://identifiers.org/reactome/REACT_1614597",
+ "http://identifiers.org/reactome/REACT_163953",
+ "http://identifiers.org/reactome/REACT_193465",
+ "http://identifiers.org/reactome/REACT_194688",
+ "http://identifiers.org/reactome/REACT_2000349",
+ "http://identifiers.org/reactome/REACT_351626",
+ "http://identifiers.org/reactome/REACT_372511",
+ "http://identifiers.org/reactome/REACT_374900",
+ "http://identifiers.org/reactome/REACT_425969",
+ "http://identifiers.org/reactome/REACT_425978",
+ "http://identifiers.org/reactome/REACT_425999",
+ "http://identifiers.org/reactome/REACT_427899",
+ "http://identifiers.org/reactome/REACT_428040",
+ "http://identifiers.org/reactome/REACT_428548",
+ "http://identifiers.org/reactome/REACT_70106",
+ "http://identifiers.org/reactome/REACT_74722",
+ "http://identifiers.org/seed.compound/cpd00067",
+ "http://identifiers.org/unipathway.compound/UPC00080"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": 1,
+ "compartment": "e",
+ "formula": "H",
+ "id": "M_h_e",
+ "name": "H+"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/lac__D",
+ "http://identifiers.org/biocyc/META:D-LACTATE",
+ "http://identifiers.org/chebi/CHEBI:11001",
+ "http://identifiers.org/chebi/CHEBI:16004",
+ "http://identifiers.org/chebi/CHEBI:18684",
+ "http://identifiers.org/chebi/CHEBI:341",
+ "http://identifiers.org/chebi/CHEBI:42105",
+ "http://identifiers.org/chebi/CHEBI:42111",
+ "http://identifiers.org/chebi/CHEBI:43701",
+ "http://identifiers.org/hmdb/HMDB00171",
+ "http://identifiers.org/hmdb/HMDB01311",
+ "http://identifiers.org/kegg.compound/C00256",
+ "http://identifiers.org/metanetx.chemical/MNXM285",
+ "http://identifiers.org/seed.compound/cpd00221"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -1,
+ "compartment": "c",
+ "formula": "C3H5O3",
+ "id": "M_lac__D_c",
+ "name": "D-Lactate"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/lac__D",
+ "http://identifiers.org/biocyc/META:D-LACTATE",
+ "http://identifiers.org/chebi/CHEBI:11001",
+ "http://identifiers.org/chebi/CHEBI:16004",
+ "http://identifiers.org/chebi/CHEBI:18684",
+ "http://identifiers.org/chebi/CHEBI:341",
+ "http://identifiers.org/chebi/CHEBI:42105",
+ "http://identifiers.org/chebi/CHEBI:42111",
+ "http://identifiers.org/chebi/CHEBI:43701",
+ "http://identifiers.org/hmdb/HMDB00171",
+ "http://identifiers.org/hmdb/HMDB01311",
+ "http://identifiers.org/kegg.compound/C00256",
+ "http://identifiers.org/metanetx.chemical/MNXM285",
+ "http://identifiers.org/seed.compound/cpd00221"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -1,
+ "compartment": "e",
+ "formula": "C3H5O3",
+ "id": "M_lac__D_e",
+ "name": "D-Lactate"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/nad",
+ "http://identifiers.org/biocyc/NAD",
+ "http://identifiers.org/cas/53-84-9",
+ "http://identifiers.org/cas/53-84-9",
+ "http://identifiers.org/chebi/CHEBI:13389",
+ "http://identifiers.org/chebi/CHEBI:13393",
+ "http://identifiers.org/chebi/CHEBI:13394",
+ "http://identifiers.org/chebi/CHEBI:15846",
+ "http://identifiers.org/chebi/CHEBI:21901",
+ "http://identifiers.org/chebi/CHEBI:44214",
+ "http://identifiers.org/chebi/CHEBI:44215",
+ "http://identifiers.org/chebi/CHEBI:44281",
+ "http://identifiers.org/chebi/CHEBI:57540",
+ "http://identifiers.org/chebi/CHEBI:7422",
+ "http://identifiers.org/hmdb/HMDB00902",
+ "http://identifiers.org/kegg.compound/C00003",
+ "http://identifiers.org/kegg.drug/D00002",
+ "http://identifiers.org/pubchem.substance/3305",
+ "http://identifiers.org/reactome/REACT_113526",
+ "http://identifiers.org/reactome/REACT_192307",
+ "http://identifiers.org/reactome/REACT_194653",
+ "http://identifiers.org/reactome/REACT_29360",
+ "http://identifiers.org/reactome/REACT_427523",
+ "http://identifiers.org/seed.compound/cpd00003",
+ "http://identifiers.org/unipathway.compound/UPC00003"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -1,
+ "compartment": "c",
+ "formula": "C21H26N7O14P2",
+ "id": "M_nad_c",
+ "name": "Nicotinamide adenine dinucleotide"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/nadh",
+ "http://identifiers.org/biocyc/NADH",
+ "http://identifiers.org/cas/58-68-4",
+ "http://identifiers.org/cas/58-68-4",
+ "http://identifiers.org/chebi/CHEBI:13395",
+ "http://identifiers.org/chebi/CHEBI:13396",
+ "http://identifiers.org/chebi/CHEBI:16908",
+ "http://identifiers.org/chebi/CHEBI:21902",
+ "http://identifiers.org/chebi/CHEBI:44216",
+ "http://identifiers.org/chebi/CHEBI:57945",
+ "http://identifiers.org/chebi/CHEBI:7423",
+ "http://identifiers.org/hmdb/HMDB01487",
+ "http://identifiers.org/kegg.compound/C00004",
+ "http://identifiers.org/pubchem.substance/3306",
+ "http://identifiers.org/reactome/REACT_192305",
+ "http://identifiers.org/reactome/REACT_194697",
+ "http://identifiers.org/reactome/REACT_29362",
+ "http://identifiers.org/reactome/REACT_73473",
+ "http://identifiers.org/seed.compound/cpd00004",
+ "http://identifiers.org/unipathway.compound/UPC00004"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -2,
+ "compartment": "c",
+ "formula": "C21H27N7O14P2",
+ "id": "M_nadh_c",
+ "name": "Nicotinamide adenine dinucleotide - reduced"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/pep",
+ "http://identifiers.org/biocyc/PHOSPHO-ENOL-PYRUVATE",
+ "http://identifiers.org/cas/138-08-9",
+ "http://identifiers.org/cas/138-08-9",
+ "http://identifiers.org/chebi/CHEBI:14812",
+ "http://identifiers.org/chebi/CHEBI:18021",
+ "http://identifiers.org/chebi/CHEBI:26054",
+ "http://identifiers.org/chebi/CHEBI:26055",
+ "http://identifiers.org/chebi/CHEBI:44894",
+ "http://identifiers.org/chebi/CHEBI:44897",
+ "http://identifiers.org/chebi/CHEBI:58702",
+ "http://identifiers.org/chebi/CHEBI:8147",
+ "http://identifiers.org/hmdb/HMDB00263",
+ "http://identifiers.org/kegg.compound/C00074",
+ "http://identifiers.org/pubchem.substance/3374",
+ "http://identifiers.org/reactome/REACT_29492",
+ "http://identifiers.org/reactome/REACT_372364",
+ "http://identifiers.org/seed.compound/cpd00061",
+ "http://identifiers.org/unipathway.compound/UPC00074"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -3,
+ "compartment": "c",
+ "formula": "C3H2O6P",
+ "id": "M_pep_c",
+ "name": "Phosphoenolpyruvate"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/pi",
+ "http://identifiers.org/biocyc/CPD0-1421",
+ "http://identifiers.org/biocyc/PHOSPHATE-GROUP",
+ "http://identifiers.org/biocyc/Pi",
+ "http://identifiers.org/cas/14265-44-2",
+ "http://identifiers.org/cas/14265-44-2",
+ "http://identifiers.org/chebi/CHEBI:14791",
+ "http://identifiers.org/chebi/CHEBI:18367",
+ "http://identifiers.org/chebi/CHEBI:24838",
+ "http://identifiers.org/chebi/CHEBI:26020",
+ "http://identifiers.org/chebi/CHEBI:26078",
+ "http://identifiers.org/chebi/CHEBI:29137",
+ "http://identifiers.org/chebi/CHEBI:29139",
+ "http://identifiers.org/chebi/CHEBI:32596",
+ "http://identifiers.org/chebi/CHEBI:32597",
+ "http://identifiers.org/chebi/CHEBI:34683",
+ "http://identifiers.org/chebi/CHEBI:34855",
+ "http://identifiers.org/chebi/CHEBI:35433",
+ "http://identifiers.org/chebi/CHEBI:37583",
+ "http://identifiers.org/chebi/CHEBI:37585",
+ "http://identifiers.org/chebi/CHEBI:39739",
+ "http://identifiers.org/chebi/CHEBI:39745",
+ "http://identifiers.org/chebi/CHEBI:43470",
+ "http://identifiers.org/chebi/CHEBI:43474",
+ "http://identifiers.org/chebi/CHEBI:4496",
+ "http://identifiers.org/chebi/CHEBI:45024",
+ "http://identifiers.org/chebi/CHEBI:63036",
+ "http://identifiers.org/chebi/CHEBI:63051",
+ "http://identifiers.org/chebi/CHEBI:7793",
+ "http://identifiers.org/chebi/CHEBI:9679",
+ "http://identifiers.org/hmdb/HMDB02142",
+ "http://identifiers.org/kegg.compound/C00009",
+ "http://identifiers.org/kegg.compound/C13556",
+ "http://identifiers.org/kegg.compound/C13558",
+ "http://identifiers.org/kegg.drug/D05467",
+ "http://identifiers.org/pubchem.substance/3311",
+ "http://identifiers.org/reactome/REACT_109277",
+ "http://identifiers.org/reactome/REACT_113548",
+ "http://identifiers.org/reactome/REACT_113550",
+ "http://identifiers.org/reactome/REACT_113551",
+ "http://identifiers.org/reactome/REACT_2255331",
+ "http://identifiers.org/reactome/REACT_29372",
+ "http://identifiers.org/reactome/REACT_947590",
+ "http://identifiers.org/seed.compound/cpd00009",
+ "http://identifiers.org/seed.compound/cpd09463",
+ "http://identifiers.org/seed.compound/cpd09464",
+ "http://identifiers.org/unipathway.compound/UPC00009"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -2,
+ "compartment": "c",
+ "formula": "HO4P",
+ "id": "M_pi_c",
+ "name": "Phosphate"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/pi",
+ "http://identifiers.org/biocyc/CPD0-1421",
+ "http://identifiers.org/biocyc/PHOSPHATE-GROUP",
+ "http://identifiers.org/biocyc/Pi",
+ "http://identifiers.org/cas/14265-44-2",
+ "http://identifiers.org/cas/14265-44-2",
+ "http://identifiers.org/chebi/CHEBI:14791",
+ "http://identifiers.org/chebi/CHEBI:18367",
+ "http://identifiers.org/chebi/CHEBI:24838",
+ "http://identifiers.org/chebi/CHEBI:26020",
+ "http://identifiers.org/chebi/CHEBI:26078",
+ "http://identifiers.org/chebi/CHEBI:29137",
+ "http://identifiers.org/chebi/CHEBI:29139",
+ "http://identifiers.org/chebi/CHEBI:32596",
+ "http://identifiers.org/chebi/CHEBI:32597",
+ "http://identifiers.org/chebi/CHEBI:34683",
+ "http://identifiers.org/chebi/CHEBI:34855",
+ "http://identifiers.org/chebi/CHEBI:35433",
+ "http://identifiers.org/chebi/CHEBI:37583",
+ "http://identifiers.org/chebi/CHEBI:37585",
+ "http://identifiers.org/chebi/CHEBI:39739",
+ "http://identifiers.org/chebi/CHEBI:39745",
+ "http://identifiers.org/chebi/CHEBI:43470",
+ "http://identifiers.org/chebi/CHEBI:43474",
+ "http://identifiers.org/chebi/CHEBI:4496",
+ "http://identifiers.org/chebi/CHEBI:45024",
+ "http://identifiers.org/chebi/CHEBI:63036",
+ "http://identifiers.org/chebi/CHEBI:63051",
+ "http://identifiers.org/chebi/CHEBI:7793",
+ "http://identifiers.org/chebi/CHEBI:9679",
+ "http://identifiers.org/hmdb/HMDB02142",
+ "http://identifiers.org/kegg.compound/C00009",
+ "http://identifiers.org/kegg.compound/C13556",
+ "http://identifiers.org/kegg.compound/C13558",
+ "http://identifiers.org/kegg.drug/D05467",
+ "http://identifiers.org/pubchem.substance/3311",
+ "http://identifiers.org/reactome/REACT_109277",
+ "http://identifiers.org/reactome/REACT_113548",
+ "http://identifiers.org/reactome/REACT_113550",
+ "http://identifiers.org/reactome/REACT_113551",
+ "http://identifiers.org/reactome/REACT_2255331",
+ "http://identifiers.org/reactome/REACT_29372",
+ "http://identifiers.org/reactome/REACT_947590",
+ "http://identifiers.org/seed.compound/cpd00009",
+ "http://identifiers.org/seed.compound/cpd09463",
+ "http://identifiers.org/seed.compound/cpd09464",
+ "http://identifiers.org/unipathway.compound/UPC00009"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -2,
+ "compartment": "e",
+ "formula": "HO4P",
+ "id": "M_pi_e",
+ "name": "Phosphate"
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/pyr",
+ "http://identifiers.org/biocyc/PYRUVATE",
+ "http://identifiers.org/cas/127-17-3",
+ "http://identifiers.org/cas/127-17-3",
+ "http://identifiers.org/chebi/CHEBI:14987",
+ "http://identifiers.org/chebi/CHEBI:15361",
+ "http://identifiers.org/chebi/CHEBI:26462",
+ "http://identifiers.org/chebi/CHEBI:26466",
+ "http://identifiers.org/chebi/CHEBI:32816",
+ "http://identifiers.org/chebi/CHEBI:45253",
+ "http://identifiers.org/chebi/CHEBI:8685",
+ "http://identifiers.org/hmdb/HMDB00243",
+ "http://identifiers.org/kegg.compound/C00022",
+ "http://identifiers.org/lipidmaps/LMFA01060077",
+ "http://identifiers.org/pubchem.substance/3324",
+ "http://identifiers.org/reactome/REACT_113557",
+ "http://identifiers.org/reactome/REACT_29398",
+ "http://identifiers.org/reactome/REACT_389680",
+ "http://identifiers.org/seed.compound/cpd00020",
+ "http://identifiers.org/unipathway.compound/UPC00022"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "charge": -1,
+ "compartment": "c",
+ "formula": "C3H3O3",
+ "id": "M_pyr_c",
+ "name": "Pyruvate"
+ }
+ ],
+ "reactions": [
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/ATPM"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "",
+ "id": "R_ATPM",
+ "lower_bound": 8.39,
+ "metabolites": {
+ "M_adp_c": 1.0,
+ "M_atp_c": -1.0,
+ "M_h2o_c": -1.0,
+ "M_h_c": 1.0,
+ "M_pi_c": 1.0
+ },
+ "name": "ATP maintenance requirement",
+ "objective_coefficient": 1.0,
+ "upper_bound": 1000.0
+ },
+ {
+ "gene_reaction_rule": "",
+ "id": "R_D_LACt2",
+ "lower_bound": -1000.0,
+ "metabolites": {},
+ "name": "",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/ENO"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "b2779",
+ "id": "R_ENO",
+ "lower_bound": -1000.0,
+ "metabolites": {
+ "M_2pg_c": -1.0,
+ "M_h2o_c": 1.0,
+ "M_pep_c": 1.0
+ },
+ "name": "enolase",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "sbo": "SBO:0000627",
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/glc"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "",
+ "id": "R_EX_glc__D_e",
+ "lower_bound": -10.0,
+ "metabolites": {
+ "M_glc__D_e": -1.0
+ },
+ "name": "D-Glucose exchange",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "sbo": "SBO:0000627",
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/h"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "",
+ "id": "R_EX_h_e",
+ "lower_bound": -1000.0,
+ "metabolites": {
+ "M_h_e": -1.0
+ },
+ "name": "H+ exchange",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "sbo": "SBO:0000627",
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/lac__D"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "",
+ "id": "R_EX_lac__D_e",
+ "lower_bound": 0.0,
+ "metabolites": {
+ "M_lac__D_e": -1.0
+ },
+ "name": "D-lactate exchange",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/FBA"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "b1773 or b2097 or b2925",
+ "id": "R_FBA",
+ "lower_bound": -1000.0,
+ "metabolites": {
+ "M_dhap_c": 1.0,
+ "M_fdp_c": -1.0,
+ "M_g3p_c": 1.0
+ },
+ "name": "fructose-bisphosphate aldolase",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/GAPD"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "b1779",
+ "id": "R_GAPD",
+ "lower_bound": -1000.0,
+ "metabolites": {
+ "M_13dpg_c": 1.0,
+ "M_g3p_c": -1.0,
+ "M_h_c": 1.0,
+ "M_nad_c": -1.0,
+ "M_nadh_c": 1.0,
+ "M_pi_c": -1.0
+ },
+ "name": "glyceraldehyde-3-phosphate dehydrogenase",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/GLCpts"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "(b2415 and b2417 and b1101 and b2416) or (b2415 and b2417 and b1621 and b2416) or (b2415 and b1818 and b1817 and b1819 and b2416)",
+ "id": "R_GLCpts",
+ "lower_bound": 0.0,
+ "metabolites": {
+ "M_g6p_c": 1.0,
+ "M_glc__D_e": -1.0,
+ "M_pep_c": -1.0,
+ "M_pyr_c": 1.0
+ },
+ "name": "D-glucose transport via PEP:Pyr PTS",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/H2Ot"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "b0875 or s0001",
+ "id": "R_H2Ot",
+ "lower_bound": -1000.0,
+ "metabolites": {
+ "M_h2o_c": 1.0,
+ "M_h2o_e": -1.0
+ },
+ "name": "R H2O transport via - diffusion",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "sbo": "SBO:0000375",
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/LDH_D",
+ "http://identifiers.org/biocyc/META:DLACTDEHYDROGNAD-RXN",
+ "http://identifiers.org/ec-code/1.1.1.28",
+ "http://identifiers.org/kegg.reaction/R00704",
+ "http://identifiers.org/metanetx.reaction/MNXR101037",
+ "http://identifiers.org/rhea/16369",
+ "http://identifiers.org/rhea/16370",
+ "http://identifiers.org/rhea/16371",
+ "http://identifiers.org/rhea/16372"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "b2133 or b1380",
+ "id": "R_LDH_D",
+ "lower_bound": -1000.0,
+ "metabolites": {
+ "M_h_c": 1.0,
+ "M_lac__D_c": -1.0,
+ "M_nad_c": -1.0,
+ "M_nadh_c": 1.0,
+ "M_pyr_c": 1.0
+ },
+ "name": "D-lactate dehydrogenase",
+ "subsystem": "Pyruvate Metabolism",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PFK"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "b3916 or b1723",
+ "id": "R_PFK",
+ "lower_bound": 0.0,
+ "metabolites": {
+ "M_adp_c": 1.0,
+ "M_atp_c": -1.0,
+ "M_f6p_c": -1.0,
+ "M_fdp_c": 1.0,
+ "M_h_c": 1.0
+ },
+ "name": "phosphofructokinase",
+ "objective_coefficient": 1.0,
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PGI"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "b4025",
+ "id": "R_PGI",
+ "lower_bound": -1000.0,
+ "metabolites": {
+ "M_f6p_c": 1.0,
+ "M_g6p_c": -1.0
+ },
+ "name": "glucose-6-phosphate isomerase",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PGK"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "b2926",
+ "id": "R_PGK",
+ "lower_bound": -1000.0,
+ "metabolites": {
+ "M_13dpg_c": 1.0,
+ "M_3pg_c": -1.0,
+ "M_adp_c": 1.0,
+ "M_atp_c": -1.0
+ },
+ "name": "phosphoglycerate kinase",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PGM"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "b4395 or b3612 or b0755",
+ "id": "R_PGM",
+ "lower_bound": -1000.0,
+ "metabolites": {
+ "M_2pg_c": -1.0,
+ "M_3pg_c": 1.0
+ },
+ "name": "phosphoglycerate mutase",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PIt2r"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "b2987 or b3493",
+ "id": "R_PIt2r",
+ "lower_bound": -1000.0,
+ "metabolites": {
+ "M_h_c": 1.0,
+ "M_h_e": -1.0,
+ "M_pi_c": 1.0,
+ "M_pi_e": -1.0
+ },
+ "name": "R phosphate reversible transport via - symport",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PYK"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "b1854 or b1676",
+ "id": "R_PYK",
+ "lower_bound": 0.0,
+ "metabolites": {
+ "M_adp_c": -1.0,
+ "M_atp_c": 1.0,
+ "M_h_c": -1.0,
+ "M_pep_c": -1.0,
+ "M_pyr_c": 1.0
+ },
+ "name": "pyruvate kinase",
+ "upper_bound": 1000.0
+ },
+ {
+ "annotation": {
+ "standardized": [
+ {
+ "external_resources": {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/TPI"
+ ]
+ },
+ "qualifier": "bqb_is"
+ }
+ ]
+ },
+ "gene_reaction_rule": "b3919",
+ "id": "R_TPI",
+ "lower_bound": -1000.0,
+ "metabolites": {
+ "M_dhap_c": -1.0,
+ "M_g3p_c": 1.0
+ },
+ "name": "triose-phosphate isomerase",
+ "upper_bound": 1000.0
+ }
+ ],
+ "version": "1"
+}
diff --git a/tests/data/mini.pickle b/tests/data/mini.pickle
index b0e0f1f40..4f0b9355e 100644
Binary files a/tests/data/mini.pickle and b/tests/data/mini.pickle differ
diff --git a/tests/data/mini_cobra.xml b/tests/data/mini_cobra.xml
index bc0d31f38..fea4da98b 100644
--- a/tests/data/mini_cobra.xml
+++ b/tests/data/mini_cobra.xml
@@ -21,19 +21,19 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -46,23 +46,23 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -75,29 +75,29 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -110,33 +110,33 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -149,32 +149,32 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -187,25 +187,25 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -218,25 +218,25 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -249,26 +249,26 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -281,19 +281,19 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -306,28 +306,28 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -340,10 +340,10 @@
-
-
-
-
+
+
+
+
@@ -356,64 +356,64 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -426,64 +426,64 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -496,37 +496,37 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -539,37 +539,37 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -582,20 +582,20 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -608,20 +608,20 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -634,30 +634,30 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -670,25 +670,25 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -701,24 +701,24 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -731,52 +731,52 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -789,52 +789,52 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -847,25 +847,25 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -889,7 +889,7 @@
-
+
@@ -905,14 +905,14 @@
-
+
-
+
@@ -935,7 +935,7 @@
-
+
@@ -951,7 +951,7 @@
-
+
@@ -967,7 +967,7 @@
-
+
@@ -983,7 +983,7 @@
-
+
@@ -1010,7 +1010,7 @@
-
+
@@ -1036,7 +1036,7 @@
-
+
@@ -1080,7 +1080,7 @@
-
+
@@ -1105,15 +1105,15 @@
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
@@ -1141,7 +1141,7 @@
-
+
@@ -1169,7 +1169,7 @@
-
+
@@ -1191,7 +1191,7 @@
-
+
@@ -1215,7 +1215,7 @@
-
+
@@ -1241,7 +1241,7 @@
-
+
@@ -1268,7 +1268,7 @@
-
+
@@ -1296,7 +1296,7 @@
-
+
@@ -1322,97 +1322,97 @@
-
-
-
-
-
+
+
+
+
+
-
-
+
+
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
-
+
-
+
-
+
-
-
-
+
+
+
-
-
+
+
-
+
-
+
-
-
+
+
diff --git a/tests/data/mini_fbc2.xml b/tests/data/mini_fbc2.xml
index bc0d31f38..fea4da98b 100644
--- a/tests/data/mini_fbc2.xml
+++ b/tests/data/mini_fbc2.xml
@@ -21,19 +21,19 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -46,23 +46,23 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -75,29 +75,29 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -110,33 +110,33 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -149,32 +149,32 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -187,25 +187,25 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -218,25 +218,25 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -249,26 +249,26 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -281,19 +281,19 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -306,28 +306,28 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -340,10 +340,10 @@
-
-
-
-
+
+
+
+
@@ -356,64 +356,64 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -426,64 +426,64 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -496,37 +496,37 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -539,37 +539,37 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -582,20 +582,20 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -608,20 +608,20 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -634,30 +634,30 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -670,25 +670,25 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -701,24 +701,24 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -731,52 +731,52 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -789,52 +789,52 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -847,25 +847,25 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -889,7 +889,7 @@
-
+
@@ -905,14 +905,14 @@
-
+
-
+
@@ -935,7 +935,7 @@
-
+
@@ -951,7 +951,7 @@
-
+
@@ -967,7 +967,7 @@
-
+
@@ -983,7 +983,7 @@
-
+
@@ -1010,7 +1010,7 @@
-
+
@@ -1036,7 +1036,7 @@
-
+
@@ -1080,7 +1080,7 @@
-
+
@@ -1105,15 +1105,15 @@
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
@@ -1141,7 +1141,7 @@
-
+
@@ -1169,7 +1169,7 @@
-
+
@@ -1191,7 +1191,7 @@
-
+
@@ -1215,7 +1215,7 @@
-
+
@@ -1241,7 +1241,7 @@
-
+
@@ -1268,7 +1268,7 @@
-
+
@@ -1296,7 +1296,7 @@
-
+
@@ -1322,97 +1322,97 @@
-
-
-
-
-
+
+
+
+
+
-
-
+
+
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
-
+
-
+
-
+
-
-
-
+
+
+
-
-
+
+
-
+
-
+
-
-
+
+
diff --git a/tests/data/mini_fbc2.xml.bz2 b/tests/data/mini_fbc2.xml.bz2
index 73cc7b9e0..ac2b19cf1 100644
Binary files a/tests/data/mini_fbc2.xml.bz2 and b/tests/data/mini_fbc2.xml.bz2 differ
diff --git a/tests/data/mini_fbc2.xml.gz b/tests/data/mini_fbc2.xml.gz
index 569cd4ffe..651a743f0 100644
Binary files a/tests/data/mini_fbc2.xml.gz and b/tests/data/mini_fbc2.xml.gz differ
diff --git a/tests/data/mini_fbc3.xml b/tests/data/mini_fbc3.xml
new file mode 100644
index 000000000..0cbf9dfed
--- /dev/null
+++ b/tests/data/mini_fbc3.xml
@@ -0,0 +1,1436 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/tests/data/mini_fbc3.xml.bz2 b/tests/data/mini_fbc3.xml.bz2
new file mode 100644
index 000000000..7cf72b0b4
Binary files /dev/null and b/tests/data/mini_fbc3.xml.bz2 differ
diff --git a/tests/data/mini_fbc3.xml.gz b/tests/data/mini_fbc3.xml.gz
new file mode 100644
index 000000000..fa678321c
Binary files /dev/null and b/tests/data/mini_fbc3.xml.gz differ
diff --git a/tests/data/mini_wrong_key_caps.mat b/tests/data/mini_wrong_key_caps.mat
index 017c0c53c..49177ea78 100644
Binary files a/tests/data/mini_wrong_key_caps.mat and b/tests/data/mini_wrong_key_caps.mat differ
diff --git a/tests/data/raven.pickle b/tests/data/raven.pickle
index 8d4b59859..264c3a1fa 100644
Binary files a/tests/data/raven.pickle and b/tests/data/raven.pickle differ
diff --git a/tests/data/salmonella.pickle b/tests/data/salmonella.pickle
index 1f355d41c..c1fda9792 100644
Binary files a/tests/data/salmonella.pickle and b/tests/data/salmonella.pickle differ
diff --git a/tests/data/salmonella_old.pickle b/tests/data/salmonella_old.pickle
new file mode 100644
index 000000000..33b1e8f7a
Binary files /dev/null and b/tests/data/salmonella_old.pickle differ
diff --git a/tests/data/textbook_fva.json b/tests/data/textbook_fva.json
index 84f685f75..5c5dc7fe7 100644
--- a/tests/data/textbook_fva.json
+++ b/tests/data/textbook_fva.json
@@ -1 +1 @@
-{"maximum": {"ACALD": 0.0, "ACALDt": 0.0, "ACKr": 0.0, "ACONTa": 6.00725, "ACONTb": 6.00725, "ACt2r": 0.0, "ADK1": -0.0, "AKGDH": 5.06438, "AKGt2r": 0.0, "ALCD2x": 0.0, "ATPM": 8.39, "ATPS4r": 45.51401, "Biomass_Ecoli_core": 0.87392, "CO2t": -22.80983, "CS": 6.00725, "CYTBD": 43.59899, "D_LACt2": 0.0, "ENO": 14.71614, "ETOHt2r": 0.0, "EX_ac_e": -0.0, "EX_acald_e": -0.0, "EX_akg_e": -0.0, "EX_co2_e": 22.80983, "EX_etoh_e": -0.0, "EX_for_e": -0.0, "EX_fru_e": -0.0, "EX_fum_e": 0.0, "EX_glc__D_e": -10.0, "EX_gln__L_e": 0.0, "EX_glu__L_e": -0.0, "EX_h_e": 17.53087, "EX_h2o_e": 29.17583, "EX_lac__D_e": -0.0, "EX_mal__L_e": -0.0, "EX_nh4_e": -4.76532, "EX_o2_e": -21.79949, "EX_pi_e": -3.2149, "EX_pyr_e": -0.0, "EX_succ_e": -0.0, "FBA": 7.47738, "FBP": -0.0, "FORt2": -0.0, "FORti": -0.0, "FRD7": 994.93562, "FRUpts2": 0.0, "FUM": 5.06438, "FUMt2_2": 0.0, "G6PDH2r": 4.95998, "GAPD": 16.02353, "GLCpts": 10.0, "GLNS": 0.22346, "GLNabc": 0.0, "GLUDy": -4.54186, "GLUN": -0.0, "GLUSy": -0.0, "GLUt2r": 0.0, "GND": 4.95998, "H2Ot": -29.17583, "ICDHyr": 6.00725, "ICL": -0.0, "LDH_D": 0.0, "MALS": -0.0, "MALt2_2": 0.0, "MDH": 5.06438, "ME1": -0.0, "ME2": -0.0, "NADH16": 38.53461, "NADTRHD": -0.0, "NH4t": 4.76532, "O2t": 21.79949, "PDH": 9.28253, "PFK": 7.47738, "PFL": -0.0, "PGI": 4.86086, "PGK": -16.02353, "PGL": 4.95998, "PGM": -14.71614, "PIt2r": 3.2149, "PPC": 2.50431, "PPCK": -0.0, "PPS": -0.0, "PTAr": -0.0, "PYK": 1.75818, "PYRt2": 0.0, "RPE": 2.67848, "RPI": -2.2815, "SUCCt2_2": -0.0, "SUCCt3": -0.0, "SUCDi": 1000.0, "SUCOAS": -5.06438, "TALA": 1.49698, "THD2": -0.0, "TKT1": 1.49698, "TKT2": 1.1815, "TPI": 7.47738}, "minimum": {"ACALD": 0.0, "ACALDt": 0.0, "ACKr": 0.0, "ACONTa": 6.00725, "ACONTb": 6.00725, "ACt2r": 0.0, "ADK1": 0.0, "AKGDH": 5.06438, "AKGt2r": 0.0, "ALCD2x": 0.0, "ATPM": 8.39, "ATPS4r": 45.51401, "Biomass_Ecoli_core": 0.87392, "CO2t": -22.80983, "CS": 6.00725, "CYTBD": 43.59899, "D_LACt2": 0.0, "ENO": 14.71614, "ETOHt2r": 0.0, "EX_ac_e": 0.0, "EX_acald_e": 0.0, "EX_akg_e": 0.0, "EX_co2_e": 22.80983, "EX_etoh_e": 0.0, "EX_for_e": 0.0, "EX_fru_e": 0.0, "EX_fum_e": 0.0, "EX_glc__D_e": -10.0, "EX_gln__L_e": 0.0, "EX_glu__L_e": 0.0, "EX_h_e": 17.53087, "EX_h2o_e": 29.17583, "EX_lac__D_e": 0.0, "EX_mal__L_e": 0.0, "EX_nh4_e": -4.76532, "EX_o2_e": -21.79949, "EX_pi_e": -3.2149, "EX_pyr_e": 0.0, "EX_succ_e": 0.0, "FBA": 7.47738, "FBP": 0.0, "FORt2": 0.0, "FORti": 0.0, "FRD7": 0.0, "FRUpts2": 0.0, "FUM": 5.06438, "FUMt2_2": 0.0, "G6PDH2r": 4.95998, "GAPD": 16.02353, "GLCpts": 10.0, "GLNS": 0.22346, "GLNabc": 0.0, "GLUDy": -4.54186, "GLUN": 0.0, "GLUSy": 0.0, "GLUt2r": 0.0, "GND": 4.95998, "H2Ot": -29.17583, "ICDHyr": 6.00725, "ICL": 0.0, "LDH_D": 0.0, "MALS": 0.0, "MALt2_2": 0.0, "MDH": 5.06438, "ME1": 0.0, "ME2": 0.0, "NADH16": 38.53461, "NADTRHD": 0.0, "NH4t": 4.76532, "O2t": 21.79949, "PDH": 9.28253, "PFK": 7.47738, "PFL": 0.0, "PGI": 4.86086, "PGK": -16.02353, "PGL": 4.95998, "PGM": -14.71614, "PIt2r": 3.2149, "PPC": 2.50431, "PPCK": 0.0, "PPS": 0.0, "PTAr": 0.0, "PYK": 1.75818, "PYRt2": 0.0, "RPE": 2.67848, "RPI": -2.2815, "SUCCt2_2": 0.0, "SUCCt3": 0.0, "SUCDi": 5.06438, "SUCOAS": -5.06438, "TALA": 1.49698, "THD2": 0.0, "TKT1": 1.49698, "TKT2": 1.1815, "TPI": 7.47738}}
\ No newline at end of file
+{"maximum": {"ACALD": 0.0, "ACALDt": 0.0, "ACKr": 0.0, "ACONTa": 6.00725, "ACONTb": 6.00725, "ACt2r": 0.0, "ADK1": 0.0, "AKGDH": 5.06438, "AKGt2r": 0.0, "ALCD2x": 0.0, "ATPM": 8.39, "ATPS4r": 45.51401, "Biomass_Ecoli_core": 0.87392, "CO2t": -22.80983, "CS": 6.00725, "CYTBD": 43.59899, "D_LACt2": 0.0, "ENO": 14.71614, "ETOHt2r": 0.0, "EX_ac_e": 0.0, "EX_acald_e": 0.0, "EX_akg_e": 0.0, "EX_co2_e": 22.80983, "EX_etoh_e": 0.0, "EX_for_e": 0.0, "EX_fru_e": 0.0, "EX_fum_e": 0.0, "EX_glc__D_e": -10.0, "EX_gln__L_e": 0.0, "EX_glu__L_e": 0.0, "EX_h_e": 17.53087, "EX_h2o_e": 29.17583, "EX_lac__D_e": 0.0, "EX_mal__L_e": 0.0, "EX_nh4_e": -4.76532, "EX_o2_e": -21.79949, "EX_pi_e": -3.2149, "EX_pyr_e": 0.0, "EX_succ_e": 0.0, "FBA": 7.47738, "FBP": 0.0, "FORt2": 0.0, "FORti": 0.0, "FRD7": 994.93562, "FRUpts2": 0.0, "FUM": 5.06438, "FUMt2_2": 0.0, "G6PDH2r": 4.95998, "GAPD": 16.02353, "GLCpts": 10.0, "GLNS": 0.22346, "GLNabc": 0.0, "GLUDy": -4.54186, "GLUN": 0.0, "GLUSy": 0.0, "GLUt2r": 0.0, "GND": 4.95998, "H2Ot": -29.17583, "ICDHyr": 6.00725, "ICL": 0.0, "LDH_D": 0.0, "MALS": 0.0, "MALt2_2": 0.0, "MDH": 5.06438, "ME1": 0.0, "ME2": 0.0, "NADH16": 38.53461, "NADTRHD": 0.0, "NH4t": 4.76532, "O2t": 21.79949, "PDH": 9.28253, "PFK": 7.47738, "PFL": 0.0, "PGI": 4.86086, "PGK": -16.02353, "PGL": 4.95998, "PGM": -14.71614, "PIt2r": 3.2149, "PPC": 2.50431, "PPCK": 0.0, "PPS": 0.0, "PTAr": 0.0, "PYK": 1.75818, "PYRt2": 0.0, "RPE": 2.67848, "RPI": -2.2815, "SUCCt2_2": 0.0, "SUCCt3": 0.0, "SUCDi": 1000.0, "SUCOAS": -5.06438, "TALA": 1.49698, "THD2": 0.0, "TKT1": 1.49698, "TKT2": 1.1815, "TPI": 7.47738}, "minimum": {"ACALD": -0.0, "ACALDt": -0.0, "ACKr": -0.0, "ACONTa": 6.00725, "ACONTb": 6.00725, "ACt2r": -0.0, "ADK1": 0.0, "AKGDH": 5.06438, "AKGt2r": -0.0, "ALCD2x": -0.0, "ATPM": 8.39, "ATPS4r": 45.51401, "Biomass_Ecoli_core": 0.87392, "CO2t": -22.80983, "CS": 6.00725, "CYTBD": 43.59899, "D_LACt2": -0.0, "ENO": 14.71614, "ETOHt2r": -0.0, "EX_ac_e": 0.0, "EX_acald_e": 0.0, "EX_akg_e": 0.0, "EX_co2_e": 22.80983, "EX_etoh_e": 0.0, "EX_for_e": 0.0, "EX_fru_e": 0.0, "EX_fum_e": 0.0, "EX_glc__D_e": -10.0, "EX_gln__L_e": 0.0, "EX_glu__L_e": 0.0, "EX_h_e": 17.53087, "EX_h2o_e": 29.17583, "EX_lac__D_e": 0.0, "EX_mal__L_e": 0.0, "EX_nh4_e": -4.76532, "EX_o2_e": -21.79949, "EX_pi_e": -3.2149, "EX_pyr_e": 0.0, "EX_succ_e": 0.0, "FBA": 7.47738, "FBP": 0.0, "FORt2": 0.0, "FORti": 0.0, "FRD7": 0.0, "FRUpts2": -0.0, "FUM": 5.06438, "FUMt2_2": -0.0, "G6PDH2r": 4.95998, "GAPD": 16.02353, "GLCpts": 10.0, "GLNS": 0.22346, "GLNabc": -0.0, "GLUDy": -4.54186, "GLUN": 0.0, "GLUSy": 0.0, "GLUt2r": -0.0, "GND": 4.95998, "H2Ot": -29.17583, "ICDHyr": 6.00725, "ICL": 0.0, "LDH_D": -0.0, "MALS": 0.0, "MALt2_2": 0.0, "MDH": 5.06438, "ME1": 0.0, "ME2": 0.0, "NADH16": 38.53461, "NADTRHD": 0.0, "NH4t": 4.76532, "O2t": 21.79949, "PDH": 9.28253, "PFK": 7.47738, "PFL": 0.0, "PGI": 4.86086, "PGK": -16.02353, "PGL": 4.95998, "PGM": -14.71614, "PIt2r": 3.2149, "PPC": 2.50431, "PPCK": 0.0, "PPS": 0.0, "PTAr": 0.0, "PYK": 1.75818, "PYRt2": -0.0, "RPE": 2.67848, "RPI": -2.2815, "SUCCt2_2": -0.0, "SUCCt3": 0.0, "SUCDi": 5.06438, "SUCOAS": -5.06438, "TALA": 1.49698, "THD2": 0.0, "TKT1": 1.49698, "TKT2": 1.1815, "TPI": 7.47738}}
\ No newline at end of file
diff --git a/tests/data/textbook_pfba_fva.json b/tests/data/textbook_pfba_fva.json
index 09633dd87..5eeaff2ae 100644
--- a/tests/data/textbook_pfba_fva.json
+++ b/tests/data/textbook_pfba_fva.json
@@ -1 +1 @@
-{"maximum": {"ACALD": 0.0, "ACALDt": 0.0, "ACKr": 0.0, "ACONTa": 6.00725, "ACONTb": 6.00725, "ACt2r": 0.0, "ADK1": 0.0, "AKGDH": 5.06438, "AKGt2r": 0.0, "ALCD2x": 0.0, "ATPM": 8.39, "ATPS4r": 45.51401, "Biomass_Ecoli_core": 0.87392, "CO2t": -22.80983, "CS": 6.00725, "CYTBD": 43.59899, "D_LACt2": 0.0, "ENO": 14.71614, "ETOHt2r": 0.0, "EX_ac_e": 0.0, "EX_acald_e": 0.0, "EX_akg_e": 0.0, "EX_co2_e": 22.80983, "EX_etoh_e": 0.0, "EX_for_e": 0.0, "EX_fru_e": 0.0, "EX_fum_e": 0.0, "EX_glc__D_e": -10.0, "EX_gln__L_e": 0.0, "EX_glu__L_e": 0.0, "EX_h_e": 17.53087, "EX_h2o_e": 29.17583, "EX_lac__D_e": 0.0, "EX_mal__L_e": 0.0, "EX_nh4_e": -4.76532, "EX_o2_e": -21.79949, "EX_pi_e": -3.2149, "EX_pyr_e": 0.0, "EX_succ_e": 0.0, "FBA": 7.47738, "FBP": 0.0, "FORt2": 0.0, "FORti": 0.0, "FRD7": 25.9211, "FRUpts2": 0.0, "FUM": 5.06438, "FUMt2_2": 0.0, "G6PDH2r": 4.95998, "GAPD": 16.02353, "GLCpts": 10.0, "GLNS": 0.22346, "GLNabc": 0.0, "GLUDy": -4.54186, "GLUN": 0.0, "GLUSy": 0.0, "GLUt2r": 0.0, "GND": 4.95998, "H2Ot": -29.17583, "ICDHyr": 6.00725, "ICL": 0.0, "LDH_D": 0.0, "MALS": 0.0, "MALt2_2": 0.0, "MDH": 5.06438, "ME1": 0.0, "ME2": 0.0, "NADH16": 38.53461, "NADTRHD": 0.0, "NH4t": 4.76532, "O2t": 21.79949, "PDH": 9.28253, "PFK": 7.47738, "PFL": 0.0, "PGI": 4.86086, "PGK": -16.02353, "PGL": 4.95998, "PGM": -14.71614, "PIt2r": 3.2149, "PPC": 2.50431, "PPCK": 0.0, "PPS": 0.0, "PTAr": 0.0, "PYK": 1.75818, "PYRt2": 0.0, "RPE": 2.67848, "RPI": -2.2815, "SUCCt2_2": 0.0, "SUCCt3": 0.0, "SUCDi": 30.98548, "SUCOAS": -5.06438, "TALA": 1.49698, "THD2": 0.0, "TKT1": 1.49698, "TKT2": 1.1815, "TPI": 7.47738}, "minimum": {"ACALD": 0.0, "ACALDt": 0.0, "ACKr": 0.0, "ACONTa": 6.00725, "ACONTb": 6.00725, "ACt2r": 0.0, "ADK1": 0.0, "AKGDH": 5.06438, "AKGt2r": 0.0, "ALCD2x": 0.0, "ATPM": 8.39, "ATPS4r": 45.51401, "Biomass_Ecoli_core": 0.87392, "CO2t": -22.80983, "CS": 6.00725, "CYTBD": 43.59899, "D_LACt2": 0.0, "ENO": 14.71614, "ETOHt2r": 0.0, "EX_ac_e": 0.0, "EX_acald_e": 0.0, "EX_akg_e": 0.0, "EX_co2_e": 22.80983, "EX_etoh_e": 0.0, "EX_for_e": 0.0, "EX_fru_e": 0.0, "EX_fum_e": 0.0, "EX_glc__D_e": -10.0, "EX_gln__L_e": 0.0, "EX_glu__L_e": 0.0, "EX_h_e": 17.53087, "EX_h2o_e": 29.17583, "EX_lac__D_e": 0.0, "EX_mal__L_e": 0.0, "EX_nh4_e": -4.76532, "EX_o2_e": -21.79949, "EX_pi_e": -3.2149, "EX_pyr_e": 0.0, "EX_succ_e": 0.0, "FBA": 7.47738, "FBP": 0.0, "FORt2": 0.0, "FORti": 0.0, "FRD7": 0.0, "FRUpts2": 0.0, "FUM": 5.06438, "FUMt2_2": 0.0, "G6PDH2r": 4.95998, "GAPD": 16.02353, "GLCpts": 10.0, "GLNS": 0.22346, "GLNabc": 0.0, "GLUDy": -4.54186, "GLUN": 0.0, "GLUSy": 0.0, "GLUt2r": 0.0, "GND": 4.95998, "H2Ot": -29.17583, "ICDHyr": 6.00725, "ICL": 0.0, "LDH_D": 0.0, "MALS": 0.0, "MALt2_2": 0.0, "MDH": 5.06438, "ME1": 0.0, "ME2": 0.0, "NADH16": 38.53461, "NADTRHD": 0.0, "NH4t": 4.76532, "O2t": 21.79949, "PDH": 9.28253, "PFK": 7.47738, "PFL": 0.0, "PGI": 4.86086, "PGK": -16.02353, "PGL": 4.95998, "PGM": -14.71614, "PIt2r": 3.2149, "PPC": 2.50431, "PPCK": 0.0, "PPS": 0.0, "PTAr": 0.0, "PYK": 1.75818, "PYRt2": 0.0, "RPE": 2.67848, "RPI": -2.2815, "SUCCt2_2": 0.0, "SUCCt3": 0.0, "SUCDi": 5.06438, "SUCOAS": -5.06438, "TALA": 1.49698, "THD2": 0.0, "TKT1": 1.49698, "TKT2": 1.1815, "TPI": 7.47738}}
\ No newline at end of file
+{"maximum": {"ACALD": 0.0, "ACALDt": 0.0, "ACKr": 0.0, "ACONTa": 6.00725, "ACONTb": 6.00725, "ACt2r": 0.0, "ADK1": -0.0, "AKGDH": 5.06438, "AKGt2r": 0.0, "ALCD2x": 0.0, "ATPM": 8.39, "ATPS4r": 45.51401, "Biomass_Ecoli_core": 0.87392, "CO2t": -22.80983, "CS": 6.00725, "CYTBD": 43.59899, "D_LACt2": 0.0, "ENO": 14.71614, "ETOHt2r": 0.0, "EX_ac_e": -0.0, "EX_acald_e": -0.0, "EX_akg_e": -0.0, "EX_co2_e": 22.80983, "EX_etoh_e": -0.0, "EX_for_e": -0.0, "EX_fru_e": 0.0, "EX_fum_e": -0.0, "EX_glc__D_e": -10.0, "EX_gln__L_e": -0.0, "EX_glu__L_e": 0.0, "EX_h_e": 17.53087, "EX_h2o_e": 29.17583, "EX_lac__D_e": -0.0, "EX_mal__L_e": 0.0, "EX_nh4_e": -4.76532, "EX_o2_e": -21.79949, "EX_pi_e": -3.2149, "EX_pyr_e": -0.0, "EX_succ_e": 0.0, "FBA": 7.47738, "FBP": -0.0, "FORt2": -0.0, "FORti": -0.0, "FRD7": 25.9211, "FRUpts2": 0.0, "FUM": 5.06438, "FUMt2_2": 0.0, "G6PDH2r": 4.95998, "GAPD": 16.02353, "GLCpts": 10.0, "GLNS": 0.22346, "GLNabc": 0.0, "GLUDy": -4.54186, "GLUN": -0.0, "GLUSy": -0.0, "GLUt2r": 0.0, "GND": 4.95998, "H2Ot": -29.17583, "ICDHyr": 6.00725, "ICL": -0.0, "LDH_D": 0.0, "MALS": 0.0, "MALt2_2": 0.0, "MDH": 5.06438, "ME1": -0.0, "ME2": -0.0, "NADH16": 38.53461, "NADTRHD": -0.0, "NH4t": 4.76532, "O2t": 21.79949, "PDH": 9.28253, "PFK": 7.47738, "PFL": -0.0, "PGI": 4.86086, "PGK": -16.02353, "PGL": 4.95998, "PGM": -14.71614, "PIt2r": 3.2149, "PPC": 2.50431, "PPCK": -0.0, "PPS": -0.0, "PTAr": -0.0, "PYK": 1.75818, "PYRt2": 0.0, "RPE": 2.67848, "RPI": -2.2815, "SUCCt2_2": -0.0, "SUCCt3": -0.0, "SUCDi": 30.98548, "SUCOAS": -5.06438, "TALA": 1.49698, "THD2": -0.0, "TKT1": 1.49698, "TKT2": 1.1815, "TPI": 7.47738}, "minimum": {"ACALD": 0.0, "ACALDt": 0.0, "ACKr": 0.0, "ACONTa": 6.00725, "ACONTb": 6.00725, "ACt2r": 0.0, "ADK1": 0.0, "AKGDH": 5.06438, "AKGt2r": 0.0, "ALCD2x": 0.0, "ATPM": 8.39, "ATPS4r": 45.51401, "Biomass_Ecoli_core": 0.87392, "CO2t": -22.80983, "CS": 6.00725, "CYTBD": 43.59899, "D_LACt2": 0.0, "ENO": 14.71614, "ETOHt2r": 0.0, "EX_ac_e": 0.0, "EX_acald_e": 0.0, "EX_akg_e": 0.0, "EX_co2_e": 22.80983, "EX_etoh_e": 0.0, "EX_for_e": 0.0, "EX_fru_e": 0.0, "EX_fum_e": 0.0, "EX_glc__D_e": -10.0, "EX_gln__L_e": 0.0, "EX_glu__L_e": 0.0, "EX_h_e": 17.53087, "EX_h2o_e": 29.17583, "EX_lac__D_e": 0.0, "EX_mal__L_e": 0.0, "EX_nh4_e": -4.76532, "EX_o2_e": -21.79949, "EX_pi_e": -3.2149, "EX_pyr_e": 0.0, "EX_succ_e": 0.0, "FBA": 7.47738, "FBP": 0.0, "FORt2": 0.0, "FORti": 0.0, "FRD7": 0.0, "FRUpts2": 0.0, "FUM": 5.06438, "FUMt2_2": 0.0, "G6PDH2r": 4.95998, "GAPD": 16.02353, "GLCpts": 10.0, "GLNS": 0.22346, "GLNabc": 0.0, "GLUDy": -4.54186, "GLUN": 0.0, "GLUSy": 0.0, "GLUt2r": 0.0, "GND": 4.95998, "H2Ot": -29.17583, "ICDHyr": 6.00725, "ICL": 0.0, "LDH_D": 0.0, "MALS": 0.0, "MALt2_2": 0.0, "MDH": 5.06438, "ME1": 0.0, "ME2": 0.0, "NADH16": 38.53461, "NADTRHD": 0.0, "NH4t": 4.76532, "O2t": 21.79949, "PDH": 9.28253, "PFK": 7.47738, "PFL": 0.0, "PGI": 4.86086, "PGK": -16.02353, "PGL": 4.95998, "PGM": -14.71614, "PIt2r": 3.2149, "PPC": 2.50431, "PPCK": 0.0, "PPS": 0.0, "PTAr": 0.0, "PYK": 1.75818, "PYRt2": 0.0, "RPE": 2.67848, "RPI": -2.2815, "SUCCt2_2": 0.0, "SUCCt3": 0.0, "SUCDi": 5.06438, "SUCOAS": -5.06438, "TALA": 1.49698, "THD2": 0.0, "TKT1": 1.49698, "TKT2": 1.1815, "TPI": 7.47738}}
\ No newline at end of file
diff --git a/tests/data/textbook_solution.pickle b/tests/data/textbook_solution.pickle
index 455a93840..d008b728e 100644
Binary files a/tests/data/textbook_solution.pickle and b/tests/data/textbook_solution.pickle differ
diff --git a/tests/data/update_pickles.py b/tests/data/update_pickles.py
index f26ce2caf..d1e1320e3 100755
--- a/tests/data/update_pickles.py
+++ b/tests/data/update_pickles.py
@@ -67,15 +67,19 @@
"ATPM",
"PIt2r",
):
- mini.add_reaction(r.copy())
+ mini.add_reactions([r.copy()])
mini.reactions.ATPM.upper_bound = mini.reactions.PGI.upper_bound
mini.objective = ["PFK", "ATPM"] # No biomass, 2 reactions
# add in some information from iJO1366
- mini.add_reaction(ecoli_model.reactions.LDH_D.copy())
- mini.add_reaction(ecoli_model.reactions.EX_lac__D_e.copy())
r = cobra.Reaction("D_LACt2")
- mini.add_reaction(r)
+ mini.add_reactions(
+ [
+ ecoli_model.reactions.LDH_D.copy(),
+ ecoli_model.reactions.EX_lac__D_e.copy(),
+ r,
+ ]
+ )
mini.reactions.GLCpts.gene_reaction_rule = (
ecoli_model.reactions.GLCptspp.gene_reaction_rule
)
@@ -104,9 +108,9 @@
mini, importlib_resources.files(cobra.data).joinpath("mini.json"), pretty=True
)
save_yaml_model(mini, importlib_resources.files(cobra.data).joinpath("mini.yml"))
- write_sbml_model(mini, "mini_fbc2.xml")
- write_sbml_model(mini, "mini_fbc2.xml.bz2")
- write_sbml_model(mini, "mini_fbc2.xml.gz")
+ write_sbml_model(mini, "mini_fbc3.xml")
+ write_sbml_model(mini, "mini_fbc3.xml.bz2")
+ write_sbml_model(mini, "mini_fbc3.xml.gz")
write_sbml_model(
mini, importlib_resources.files(cobra.data).joinpath("mini_cobra.xml")
)
diff --git a/tests/data/valid_annotation_format.json b/tests/data/valid_annotation_format.json
index 8bbb6a38c..38be556a7 100644
--- a/tests/data/valid_annotation_format.json
+++ b/tests/data/valid_annotation_format.json
@@ -5,9 +5,9 @@
"name":"",
"compartment":"c",
"annotation": {
- "bigg.reaction": [["is", "PFK26"]],
- "kegg.reaction": [["is", "R02732"]],
- "rhea": [["is", "15656"]]
+ "bigg.reaction": ["PFK26"],
+ "kegg.reaction": ["R02732"],
+ "rhea": ["15656"]
}
}
],
diff --git a/tests/test_core/test_group.py b/tests/test_core/test_group.py
index a5ed210e1..9f4d390a5 100644
--- a/tests/test_core/test_group.py
+++ b/tests/test_core/test_group.py
@@ -1,9 +1,12 @@
"""Test functions of group via model.py."""
+from os.path import join
+
import pytest
from cobra import Model
from cobra.core import Group
+from cobra.io import load_json_model, read_sbml_model, save_json_model
def test_group_add_elements(model: Model) -> None:
@@ -33,3 +36,18 @@ def test_group_kind() -> None:
group.kind = "collection"
assert group.kind == "collection"
+
+
+def test_read_write_json(data_directory, tmp_path):
+ """Test reading and writing groups to json."""
+ model = read_sbml_model(join(data_directory, "e_coli_core.xml"))
+ assert model.groups is not None
+ assert len(model.groups) == 10
+ assert len(model.groups[0].members) == 6
+
+ path_to_file = join(tmp_path, "group_ecoli.json")
+ save_json_model(model, path_to_file)
+ model_from_json = load_json_model(path_to_file)
+ assert model_from_json.groups is not None
+ assert len(model_from_json.groups) == 10
+ assert len(model_from_json.groups[0].members) == 6
diff --git a/tests/test_core/test_metadata/test_customannotations.py b/tests/test_core/test_metadata/test_customannotations.py
new file mode 100644
index 000000000..11b0b6009
--- /dev/null
+++ b/tests/test_core/test_metadata/test_customannotations.py
@@ -0,0 +1,283 @@
+"""Test functions of custom.py."""
+
+import sys
+from pathlib import Path
+
+import pytest
+
+from cobra.core import Model, Species
+from cobra.core.metadata.custom import CustomAnnotation, CustomAnnotationStore
+from cobra.core.metadata.resource import Qualifier
+from cobra.io import (
+ load_json_model,
+ load_yaml_model,
+ read_sbml_model,
+ save_json_model,
+ save_yaml_model,
+ write_sbml_model,
+)
+
+
+def test_customannotation():
+ """Test creating and manipulating a single CustomAnnotation."""
+ ann = CustomAnnotation.from_data(
+ {
+ "id": "KV_id",
+ "name": "abc_xyz",
+ "key": "keyX",
+ "value": "45",
+ "uri": "https://cobrapy.readthedocs.io/",
+ }
+ )
+ assert isinstance(ann, CustomAnnotation)
+ assert ann.id == "KV_id"
+ assert ann.name == "abc_xyz"
+ assert ann.key == "keyX"
+ assert ann.value == "45"
+ assert ann.uri == "https://cobrapy.readthedocs.io/"
+
+ with pytest.raises(ValueError):
+ ann.remove_from_parent()
+
+ with pytest.raises(AttributeError):
+ ann.key = "new_key"
+ ann.value = "42"
+ assert ann.value == "42"
+ ann.uri = "https://opencobra.github.io/"
+ assert ann.uri == "https://opencobra.github.io/"
+
+ with pytest.raises(TypeError):
+ ann = CustomAnnotation.from_data("key:value")
+ ann = CustomAnnotation.from_data(
+ {
+ "key": "keyX",
+ "value": "45",
+ "uri": "https://cobrapy.readthedocs.io/",
+ }
+ )
+ assert isinstance(ann.__str__(), str)
+ assert isinstance(ann.__repr__(), str)
+
+
+def test_customannotationstore():
+ """Test creating and manipulating a CustomAnnotationStore object."""
+ entry1 = {
+ "key": "key1",
+ "value": "45",
+ "uri": "https://cobrapy.readthedocs.io/",
+ }
+ entry2 = CustomAnnotation.from_data(
+ {
+ "key": "key2",
+ "value": "48",
+ "uri": "https://tinyurl2.com/ybyr7b62",
+ }
+ )
+ entry3 = CustomAnnotation(key="key3", value="50")
+
+ kvp = CustomAnnotationStore(entries=[entry1, entry2, entry3])
+
+ assert len(kvp) == 3
+ for key in ["key1", "key2", "key3"]:
+ assert key in kvp
+ assert kvp["key2"] == entry2
+
+ kvp["key1"] = {"key": "key1", "value": "test"}
+ assert kvp["key1"].value == "test"
+ with pytest.raises(ValueError):
+ kvp["key1"] = {"key": "key4", "value": "test"}
+
+ kvp2 = CustomAnnotation(key="key2", value="test")
+ kvp["key2"] = kvp2
+ assert kvp["key2"].value == "test"
+ with pytest.raises(ValueError):
+ kvp["key2"] = CustomAnnotation(key="key4", value="test")
+
+ with pytest.raises(ValueError):
+ other_store = CustomAnnotationStore(entries=[kvp2])
+ other_store = CustomAnnotationStore()
+ with pytest.raises(ValueError):
+ other_store.add(kvp2)
+ with pytest.raises(ValueError):
+ other_store[kvp2.key] = kvp2
+ with pytest.raises(ValueError):
+ kvp[kvp2.key] = kvp2
+
+ kvp["key3"] = "test"
+ assert kvp["key3"].value == "test"
+ with pytest.raises(TypeError):
+ kvp["key1"] = 10
+
+ kvp.add(dict(key="key4", value="value4"))
+ assert kvp["key4"].value == "value4"
+
+ with pytest.raises(IndexError):
+ kvp.add([dict(key="key4", value="other_value")])
+
+ assert len(kvp) == 4
+ kvp.remove(kvp2)
+ assert len(kvp) == 3
+ with pytest.raises(ValueError):
+ kvp.remove("key5")
+ with pytest.raises(ValueError):
+ kvp.remove(CustomAnnotation(key="key1", value="different"))
+ with pytest.raises(ValueError):
+ kvp.remove(CustomAnnotation(key="key5", value="different"))
+
+ kvp.remove("key1")
+ assert len(kvp) == 2
+
+ kvp["key3"].remove_from_parent()
+
+ assert isinstance(kvp.__repr__(), str)
+ assert isinstance(kvp._repr_html_(), str)
+
+
+def test_customannotation_for_object() -> None:
+ """Test accessing custom annotations of a cobrapy object."""
+ s = Species()
+ s.metadata.custom["key1"] = "value1"
+ assert s.metadata.custom["key1"].value == "value1"
+ s.add_annotations(
+ CustomAnnotation(
+ key="key2", value="value2", uri="https://cobrapy.readthedocs.io/"
+ )
+ )
+ assert s.metadata.custom["key2"].value == "value2"
+ assert s.metadata.custom["key2"].uri == "https://cobrapy.readthedocs.io/"
+
+ assert s.metadata.to_dict()["custom"]["key2"]["value"] == "value2"
+
+
+@pytest.mark.parametrize("model_type", ["direct", "sbml", "json", "yaml"])
+def test_read_write_model(complex_model: Model, tmp_path: Path, model_type: str):
+ """Test annotation consistency when writing and reading an SBML file."""
+ model = None
+ if model_type == "sbml":
+ out_path = tmp_path / "complex_model_writing.sbml"
+ assert write_sbml_model(complex_model, str(out_path)) is None
+
+ model = read_sbml_model(str(out_path))
+ elif model_type == "json":
+ out_path = tmp_path / "complex_model_writing.json"
+ assert save_json_model(complex_model, str(out_path)) is None
+
+ model = load_json_model(str(out_path))
+ elif model_type == "yaml":
+ out_path = tmp_path / "complex_model_writing.yaml"
+ assert save_yaml_model(complex_model, str(out_path)) is None
+
+ model = load_yaml_model(str(out_path))
+ else:
+ model = complex_model
+ assert model
+
+ assert (
+ model.metadata.standardized[Qualifier.Biological_hasTaxon][0]
+ .resources[0]
+ .identifier
+ == "511145"
+ )
+
+ assert model.metadata.custom
+ assert model.metadata.custom["trusted_source"].value == "42"
+
+ metabolite = model.metabolites.get_by_id("2pg_c")
+ assert metabolite.metadata.custom
+ assert metabolite.metadata.custom["toolset"].value == "expert"
+ assert (
+ metabolite.metadata.custom["toolset"].uri == "urn:awesometool.com:keyvaluepair"
+ )
+
+ assert metabolite.metadata.custom["nested"].value == "yes"
+
+
+@pytest.mark.parametrize(
+ "model_type",
+ [
+ "direct",
+ pytest.param(
+ "sbml", marks=pytest.mark.xfail(reason="not implemented in libsbml")
+ ),
+ "json",
+ "yaml",
+ ],
+)
+@pytest.mark.skipif(sys.version_info < (3, 9), reason="requires python 3.9 or higher")
+def test_read_write_cvterms_in_kvp_model(
+ complex_model: Model, tmp_path: Path, model_type: str
+):
+ """Test nested kvp annotation consistency when writing and reading an SBML file."""
+ model = None
+ if model_type == "sbml":
+ out_path = tmp_path / "complex_model_writing.sbml"
+ assert write_sbml_model(complex_model, str(out_path)) is None
+
+ model = read_sbml_model(str(out_path))
+ elif model_type == "json":
+ out_path = tmp_path / "complex_model_writing.json"
+ assert save_json_model(complex_model, str(out_path)) is None
+
+ model = load_json_model(str(out_path))
+ elif model_type == "yaml":
+ out_path = tmp_path / "complex_model_writing.yaml"
+ assert save_yaml_model(complex_model, str(out_path)) is None
+
+ model = load_yaml_model(str(out_path))
+ else:
+ model = complex_model
+ assert model
+
+ metabolite = model.metabolites.get_by_id("2pg_c")
+
+ assert (
+ metabolite.metadata.custom["nested"]
+ .metadata.standardized[Qualifier.Modelling_isDescribedBy][0]
+ .resources[0]
+ .identifier
+ == "e_coli_core"
+ )
+
+
+@pytest.mark.parametrize(
+ "model_type",
+ [
+ "direct",
+ pytest.param(
+ "sbml", marks=pytest.mark.xfail(reason="not implemented in libsbml")
+ ),
+ "json",
+ "yaml",
+ ],
+)
+@pytest.mark.skipif(sys.version_info < (3, 9), reason="requires python 3.9 or higher")
+def test_read_write_nested_kvp_model(
+ complex_model: Model, tmp_path: Path, model_type: str
+):
+ """Test nested kvp annotation consistency when writing and reading an SBML file."""
+ model = None
+ if model_type == "sbml":
+ out_path = tmp_path / "complex_model_writing.sbml"
+ assert write_sbml_model(complex_model, str(out_path)) is None
+
+ model = read_sbml_model(str(out_path))
+ elif model_type == "json":
+ out_path = tmp_path / "complex_model_writing.json"
+ assert save_json_model(complex_model, str(out_path)) is None
+
+ model = load_json_model(str(out_path))
+ elif model_type == "yaml":
+ out_path = tmp_path / "complex_model_writing.yaml"
+ assert save_yaml_model(complex_model, str(out_path)) is None
+
+ model = load_yaml_model(str(out_path))
+ else:
+ model = complex_model
+ assert model
+
+ metabolite = model.metabolites.get_by_id("2pg_c")
+
+ assert (
+ metabolite.metadata.custom["nested"].metadata.custom["nested_kvp"].value
+ == "not_recommended"
+ )
diff --git a/tests/test_core/test_metadata/test_history.py b/tests/test_core/test_metadata/test_history.py
new file mode 100644
index 000000000..402eb407f
--- /dev/null
+++ b/tests/test_core/test_metadata/test_history.py
@@ -0,0 +1,252 @@
+"""Test functions of history.py."""
+
+import os
+from datetime import datetime, timedelta, timezone
+
+import pytest
+
+from cobra.core import Species
+from cobra.core.metadata.history import Creator, History
+from cobra.io import read_sbml_model
+
+
+JUNE_26TH = "2020-06-26T12:34:11+00:00"
+JUNE_26TH_530 = "2020-06-26T00:34:11+05:30"
+TEST_COM = "test@test.com"
+
+
+def _read_ecoli_annotation_model(data_directory):
+ """Read model with history elements."""
+ test_xml = os.path.join(data_directory, "e_coli_core_for_annotation.xml")
+ model = read_sbml_model(test_xml)
+ return model
+
+
+def test_create_history():
+ """Create a history object and verify its contents."""
+ history = History(
+ creators=[
+ Creator(
+ given_name="Matthias",
+ family_name="Koenig",
+ organisation="HU",
+ email=TEST_COM,
+ ),
+ Creator(
+ name="Andreas Draeger",
+ organisation="University of Tübingen",
+ email="test2@test2.com",
+ ),
+ ],
+ created_date=JUNE_26TH_530,
+ modified_dates=[
+ JUNE_26TH,
+ JUNE_26TH_530,
+ ],
+ )
+ assert len(history.creators) == 2
+ assert history.created_date.isoformat() == JUNE_26TH_530
+ assert history.created_date == History.parse_datetime(JUNE_26TH_530)
+ assert history.creators[0].name == "Matthias Koenig"
+ assert history.creators[1].name == "Andreas Draeger"
+ assert len(history.modified_dates) == 2
+
+ with pytest.raises(TypeError):
+ _ = History.from_data(1)
+ assert history == History.from_data(history)
+
+ history = History()
+ assert history.is_empty()
+
+
+def test_history_from_ecoli_xml(data_directory):
+ """Test loading the history of an e_coli_core SBML file."""
+ model = _read_ecoli_annotation_model(data_directory)
+ history = History(
+ creators=[
+ Creator(
+ given_name="Matthias",
+ family_name="Koenig",
+ email="koenigmx@hu-berlin.de",
+ organisation="Humboldt-University Berlin, "
+ "Institute for Theoretical Biology",
+ ),
+ Creator(
+ given_name="Matthias",
+ family_name="Koenig",
+ email="koenigmx@hu-berlin.de",
+ ),
+ Creator(
+ given_name="Matthias",
+ family_name="Koenig",
+ organisation="Humboldt-University Berlin, "
+ "Institute for Theoretical Biology",
+ ),
+ Creator(
+ given_name="Matthias",
+ family_name="Koenig",
+ ),
+ ],
+ created_date="2019-03-06T14:40:55Z",
+ modified_dates=[
+ "2019-03-06T14:40:55Z",
+ "2019-03-06T14:41:55Z",
+ ],
+ )
+ print(history)
+ print(model.metadata.history)
+ assert model.metadata.history == history
+ model.metadata.history.created_date = None
+ assert model.metadata.history == History(
+ creators=[
+ Creator(
+ given_name="Matthias",
+ family_name="Koenig",
+ email="koenigmx@hu-berlin.de",
+ organisation="Humboldt-University Berlin, "
+ "Institute for Theoretical Biology",
+ ),
+ Creator(
+ given_name="Matthias",
+ family_name="Koenig",
+ email="koenigmx@hu-berlin.de",
+ ),
+ Creator(
+ given_name="Matthias",
+ family_name="Koenig",
+ organisation="Humboldt-University Berlin, "
+ "Institute for Theoretical Biology",
+ ),
+ Creator(
+ given_name="Matthias",
+ family_name="Koenig",
+ ),
+ ],
+ modified_dates=[
+ "2019-03-06T14:40:55Z",
+ "2019-03-06T14:41:55Z",
+ ],
+ )
+
+
+def test_create_creator():
+ """Test creating a Creator metadata object and verify its contents."""
+ creator = Creator(
+ name="Matthias König",
+ organisation="HU",
+ email=TEST_COM,
+ )
+ assert creator.name == "Matthias König"
+ assert creator.organisation == "HU"
+ assert creator.email == TEST_COM
+
+ creator = Creator(
+ given_name="Matthias",
+ family_name="König",
+ organisation="HU",
+ email=TEST_COM,
+ )
+ assert creator.name == "Matthias König"
+ assert creator.organisation == "HU"
+ assert creator.email == TEST_COM
+
+ creator = Creator(
+ given_name="Matthias",
+ organisation="HU",
+ email=TEST_COM,
+ )
+ assert creator.name == "Matthias"
+ assert creator.organisation == "HU"
+ assert creator.email == TEST_COM
+
+ creator = Creator(
+ **{
+ "given_name": "Matthias",
+ "family_name": "König",
+ "organisation": "HU",
+ "email": TEST_COM,
+ }
+ )
+
+ assert creator.name == "Matthias König"
+ assert creator.organisation == "HU"
+ assert creator.email == TEST_COM
+
+ creator = Creator(
+ **{
+ "given_name": "Matthias",
+ "organisation": "HU",
+ "email": TEST_COM,
+ }
+ )
+
+ assert creator.name == "Matthias"
+ assert creator.organisation == "HU"
+ assert creator.email == TEST_COM
+
+ creator = Creator().from_data(
+ {
+ "given_name": "Matthias",
+ "family_name": "König",
+ "organisation": "HU",
+ "email": TEST_COM,
+ }
+ )
+
+ assert creator.name == "Matthias König"
+ assert creator.organisation == "HU"
+ assert creator.email == TEST_COM
+
+ creator = Creator().from_data(
+ {
+ "given_name": "Matthias",
+ "organisation": "HU",
+ "email": TEST_COM,
+ }
+ )
+
+ assert creator.name == "Matthias"
+ assert creator.organisation == "HU"
+ assert creator.email == TEST_COM
+
+ with pytest.raises(ValueError):
+ creator = Creator(
+ name="Pascal A. Pieters", given_name="Pascal", family_name="Pieters"
+ )
+
+
+def test_historydatetime():
+ """Test the 'created_date' property of the History object."""
+ # valid date
+ dt_str1 = JUNE_26TH_530
+ datetime_obj = History(created_date=dt_str1)
+ assert datetime_obj.created_date.isoformat() == dt_str1
+
+ # valid date
+ datetime_obj = History(created_date=JUNE_26TH)
+ assert datetime_obj.created_date.isoformat() == JUNE_26TH
+ datetime_obj.created_date = None
+ assert datetime_obj.created_date is None
+
+ # create from python datetime
+ datetime_obj.created_date = datetime.now()
+ assert datetime_obj.created_date is not None
+
+ # incorrect format
+ with pytest.raises(ValueError):
+ datetime_obj.created_date = datetime.now(timezone(timedelta(hours=1))).strftime(
+ "%Y-%m-%dT%H:%M:%S%Z"
+ )
+
+ with pytest.raises(TypeError):
+ datetime_obj.created_date = {"date": "June 26th"}
+
+
+def test_object_history() -> None:
+ """Test history and creators for a cobrapy object."""
+ s = Species()
+ s.metadata.add_creators([Creator(name="Pascal A. Pieters")])
+ assert s.metadata.history.creators[0].name == "Pascal A. Pieters"
+
+ s.metadata.add_modification_dates(JUNE_26TH)
+ assert s.metadata.history.modified_dates[0].isoformat() == JUNE_26TH
diff --git a/tests/test_core/test_metadata/test_metadata.py b/tests/test_core/test_metadata/test_metadata.py
new file mode 100644
index 000000000..a4951f404
--- /dev/null
+++ b/tests/test_core/test_metadata/test_metadata.py
@@ -0,0 +1,1021 @@
+"""Tests for the metadata structures."""
+
+import json
+from pathlib import Path
+
+import pytest
+
+from cobra import Model
+from cobra.core.metadata import Metadata, Qualifier, StandardizedAnnotation
+from cobra.core.metadata.resource import QualifiersAlias, Resource
+from cobra.core.metadata.standardized import (
+ SimplifiedAnnotationInterface,
+ StandardizedAnnotationList,
+ StandardizedAnnotationStore,
+)
+from cobra.core.species import Species
+from cobra.io import load_json_model, read_sbml_model, save_json_model, write_sbml_model
+
+
+PUBMED_EXAMPLE = "https://identifiers.org/pubmed/1111111"
+ECO_EXAMPLE = "https://identifiers.org/eco/ECO:0000004"
+RESOURCE_LIST = [
+ "http://identifiers.org/bigg.metabolite/13dpg",
+ "http://identifiers.org/biocyc/DPG",
+ "http://identifiers.org/chebi/CHEBI:11881",
+ "http://identifiers.org/chebi/CHEBI:16001",
+ "http://identifiers.org/chebi/CHEBI:1658",
+ "http://identifiers.org/chebi/CHEBI:20189",
+ "http://identifiers.org/chebi/CHEBI:57604",
+ "http://identifiers.org/hmdb/HMDB01270",
+ "http://identifiers.org/kegg.compound/C00236",
+ "http://identifiers.org/pubchem.substance/3535",
+ "http://identifiers.org/reactome/REACT_29800",
+ "http://identifiers.org/seed.compound/cpd00203",
+ "http://identifiers.org/unipathway.compound/UPC00236",
+]
+ECOLI_MODEL_ANNOTATIONS = [
+ {
+ "qualifier": "bqb_hasTaxon",
+ "resources": ["http://identifiers.org/taxonomy/511145"],
+ },
+ {
+ "qualifier": "bqm_is",
+ "resources": ["http://identifiers.org/bigg.model/e_coli_core"],
+ "annotations": [
+ {
+ "qualifier": "bqb_isDescribedBy",
+ "resources": [PUBMED_EXAMPLE],
+ },
+ {
+ "qualifier": "bqb_isDescribedBy",
+ "resources": [ECO_EXAMPLE],
+ },
+ ],
+ },
+ {
+ "qualifier": "bqm_isDescribedBy",
+ "resources": ["http://identifiers.org/doi/10.1128/ecosalplus.10.2.1"],
+ },
+ {
+ "qualifier": "bqm_isDescribedBy",
+ "resources": ["http://identifiers.org/ncbiprotein/16128336"],
+ },
+]
+COBRA_URL = "https://cobrapy.readthedocs.io/"
+CHEBI_SET = {"CHEBI:43215", "CHEBI:11881"}
+
+
+def test_annotation() -> None:
+ """Test creating an annotation manually."""
+ # a cobra component
+ s = Species()
+ # assert s.metadata == {} # nothing set for annotation, so empty dict
+ assert s.metadata.standardized == StandardizedAnnotationStore()
+ # assert not s.annotation.keys()
+ # assert s.metadata.custom == {}
+ assert s.metadata.history.creators == []
+ assert s.metadata.history.modified_dates == []
+
+ # setting annotation via old annotation format
+ s.annotation["chebi"] = list(CHEBI_SET)
+
+ assert set(s.annotation["chebi"]) == CHEBI_SET
+ assert set(s.annotation["chebi"]) == CHEBI_SET
+ # assert set(s.metadata.standardized[Qualifier.Biological_is]["chebi"]) == CHEBI_SET
+
+ s.metadata.standardized = StandardizedAnnotationStore()
+
+ s.add_annotations(
+ [
+ "https://identifiers.org/chebi/CHEBI:43215",
+ "https://identifiers.org/chebi/CHEBI:11881",
+ ]
+ )
+ assert s.metadata.standardized == {
+ "https://identifiers.org/chebi/CHEBI:43215",
+ "https://identifiers.org/chebi/CHEBI:11881",
+ }
+
+ # checking old (fixed) annotation format
+ assert s.annotation == {"chebi": list(sorted(["CHEBI:43215", "CHEBI:11881"]))}
+
+ # checking new standardized
+ cvt = StandardizedAnnotationStore(
+ [
+ StandardizedAnnotation(
+ qualifier=Qualifier.Biological_is,
+ resources=[
+ "https://identifiers.org/chebi/CHEBI:43215",
+ "https://identifiers.org/chebi/CHEBI:11881",
+ ],
+ ),
+ ]
+ )
+
+ # The next assertion should probably not hold, because of how we add annotations
+ # with the same qualifier. Or we should change the behaviour of add_annotations
+ # etc. when only strings are supplied.
+ # assert s.metadata.standardized == cvt
+ s.metadata.standardized = []
+ assert s.metadata.standardized == StandardizedAnnotationStore()
+ assert s.metadata.standardized.resources == frozenset()
+ assert s.metadata.standardized == {}
+
+ s.metadata.standardized = cvt
+
+ assert s.metadata.standardized.resources == {
+ Resource("CHEBI:43215"),
+ Resource("CHEBI:11881"),
+ }
+
+ # checking old (fixed) annotation format
+ assert s.annotation == {"chebi": list(sorted(["CHEBI:43215", "CHEBI:11881"]))}
+
+ cvt[0].remove_from_parent()
+ assert s.metadata.standardized == []
+
+ # adding an SBO term
+ s.metadata.sbo = ["SBO:0000123"]
+ assert "sbo" in s.annotation
+ # assert s.annotation == {
+ # "chebi": ["CHEBI:43215", "CHEBI:11881"],
+ # "sbo": ["SBO:0000123"],
+ # }
+
+ cvt2 = StandardizedAnnotationStore(
+ [
+ StandardizedAnnotation(
+ qualifier="bqb_is",
+ resources=["https://identifiers.org/chebi/CHEBI:11881"],
+ ),
+ StandardizedAnnotation("https://identifiers.org/chebi/CHEBI:43215"),
+ ]
+ )
+
+ s.metadata.standardized = cvt2
+ assert s.metadata.standardized.uris == {
+ "https://identifiers.org/chebi/CHEBI:43215",
+ "https://identifiers.org/chebi/CHEBI:11881",
+ }
+
+ # print(s.annotation[Qualifier.Biological_is])
+ # print(s.annotation[0])
+ print(s.annotation["chebi"])
+
+ assert (
+ s.metadata.standardized[0].resources[0].uri
+ == "https://identifiers.org/chebi/CHEBI:11881"
+ )
+
+ assert set(s.metadata.standardized[Qualifier.Biological_is].uris) == {
+ "https://identifiers.org/chebi/CHEBI:43215",
+ "https://identifiers.org/chebi/CHEBI:11881",
+ }
+
+ # assert 0 == 1
+ # s.annotation.__delitem__("sbo")
+
+ # checking old (fixed) annotation format
+ # assert s.annotation == {"chebi": sorted(["CHEBI:43215", "CHEBI:11881"])}
+
+
+def test_standardized_annotation() -> None:
+ """Test creating and manipulating standardized annotations."""
+
+ s = Species()
+ s.metadata.add_standardized(ECOLI_MODEL_ANNOTATIONS)
+ assert s.metadata.standardized == ECOLI_MODEL_ANNOTATIONS
+
+ s_other = Species()
+ with pytest.raises(ValueError):
+ s_other.add_annotations(s.metadata.standardized[0])
+
+ ann = StandardizedAnnotation("https://identifiers.org/chebi/CHEBI:43215")
+ s_other.add_annotations([ann])
+
+ assert (
+ s_other.metadata.standardized.resources_for("chebi")[0].identifier
+ == "CHEBI:43215"
+ )
+
+ ann.remove_from_parent()
+ assert len(s_other.metadata.standardized.resources_for("chebi")) == 0
+ with pytest.raises(ValueError):
+ ann.remove_from_parent()
+
+ ann.qualifier = Qualifier.Biological_hasPart
+ assert ann.qualifier == Qualifier.Biological_hasPart
+ assert ann.qualifier in QualifiersAlias.Biological_any
+
+ ann.qualifier = "bqm_is"
+ assert ann.qualifier == Qualifier.Modelling_is
+ assert ann.qualifier not in QualifiersAlias.Biological_known
+
+ ann.resources = [
+ "https://identifiers.org/chebi/CHEBI:43215",
+ "https://identifiers.org/chebi/CHEBI:11881",
+ ]
+ assert next(iter(ann.resources)).identifier == "CHEBI:43215"
+
+ ann.annotations = [
+ StandardizedAnnotation(["http://identifiers.org/taxonomy/511145"])
+ ]
+ assert len(ann.uris) == 2
+ assert len(ann.all_uris) == 3
+
+ assert all(resource.namespace == "chebi" for resource in ann.resources)
+ assert all(namespace == "chebi" for (namespace, _) in ann.to_tuples())
+
+ records = ann.to_records()
+ assert len(records) == 3
+ main_group = next(x["annotation_group"] for x in records if x["parent_group"] == 0)
+ assert (
+ next(x["namespace"] for x in records if x["parent_group"] == main_group)
+ == "taxonomy"
+ )
+
+ ann_dict = ann.to_dict()
+ assert ann_dict == ann
+ del ann_dict["annotations"]
+ assert not ann_dict == ann
+ ann_dict = ann.to_dict()
+ resource = ann.resources[0]
+ with pytest.raises(ValueError):
+ ann.add_resources([resource])
+ resource.remove_from_parent()
+ assert not ann_dict == ann
+ with pytest.raises(ValueError):
+ resource.remove_from_parent()
+ ann.add_resources([resource])
+ assert ann_dict == ann
+ with pytest.raises(ValueError):
+ new_ann = StandardizedAnnotation()
+ new_ann.add_resources([resource])
+
+ assert ann != 1
+
+ ann.resources = None
+ assert len(ann.resources) == 0
+
+ ann.add_resources(
+ [Resource.from_data({"uri": "http://identifiers.org/taxonomy/51114"})]
+ )
+ assert len(ann.resources) == 1
+ ann.add_resources(
+ [Resource.from_data({"namespace": "chebi", "identifier": "CHEBI:43215"})]
+ )
+ assert len(ann.resources) == 2
+ with pytest.raises(TypeError):
+ ann.add_resources([Resource.from_data(None)])
+
+ resource = Resource(uri="https://identifiers.org/uniprot/A0PK11")
+
+ assert resource.namespace == "uniprot"
+ assert (
+ Resource(uri="https://www.uniprot.org/uniprotkb/A0PK11", strict=False).namespace
+ is None
+ )
+ with pytest.raises(ValueError):
+ Resource(uri="https://www.uniprot.org/uniprotkb/A0PK11")
+
+ assert resource.to_dict()["namespace"] == "uniprot"
+ assert resource == Resource(resource.uri)
+ assert resource == {"uri": resource.uri}
+ assert resource == ("uniprot", "A0PK11")
+
+ assert resource != ("uniprot",)
+ assert resource != 1
+
+ with pytest.raises(TypeError):
+ ann.resources = [1, 2]
+
+ with pytest.raises(TypeError):
+ ann.qualifier = "unknown"
+
+ with pytest.raises(TypeError):
+ ann.qualifier = 1
+
+ assert isinstance(ann._repr_html_(), str)
+ assert isinstance(resource._repr_html_(), str)
+
+
+def test_standardized_annotation_store() -> None:
+ """Test creating and manipulating standardized stores."""
+
+ s = Species()
+ s.metadata.add_standardized(ECOLI_MODEL_ANNOTATIONS)
+ assert s.metadata.standardized == ECOLI_MODEL_ANNOTATIONS
+ assert isinstance(s.metadata.standardized, StandardizedAnnotationStore)
+ s_other = Species()
+ s_other.metadata.add_standardized(ECOLI_MODEL_ANNOTATIONS)
+ assert s.metadata.standardized == s_other.metadata.standardized
+ assert s.metadata == s_other.metadata
+ with pytest.raises(TypeError):
+ _ = s.metadata == 1
+
+ with pytest.raises(ValueError):
+ s.metadata.standardized.add(s.metadata.standardized[0])
+ new_store = StandardizedAnnotationStore()
+ assert not new_store
+ with pytest.raises(ValueError):
+ new_store.add(s.metadata.standardized[0])
+ new_list = StandardizedAnnotationList()
+ assert not new_list
+ new_list.add(s.metadata.standardized[0])
+ assert len(new_list) == 1
+
+ new_store = StandardizedAnnotationStore(
+ [
+ StandardizedAnnotation("https://identifiers.org/chebi/CHEBI:43215"),
+ "https://identifiers.org/chebi/CHEBI:11881",
+ Resource("https://identifiers.org/chebi/CHEBI:16001"),
+ {
+ "qualifier": Qualifier.Biological_hasTaxon,
+ "resources": ["http://identifiers.org/taxonomy/511145"],
+ },
+ ]
+ )
+ assert len(new_store) == 3
+ assert len(new_store.resources) == 4
+
+ assert new_store != 1
+
+ with pytest.raises(TypeError):
+ new_store[0] = None
+ with pytest.raises(TypeError):
+ _ = new_store[[0.15]]
+
+ assert len(new_store[Qualifier.Biological_hasTaxon]) == 1
+ assert len(new_store[QualifiersAlias.Biological_any]) == 3
+
+ assert len(StandardizedAnnotationStore(None)) == 0
+ assert len(StandardizedAnnotationStore([None])) == 0
+ assert (
+ len(
+ StandardizedAnnotationStore(
+ [Resource("CHEBI:43215"), Resource("CHEBI:11881")]
+ )
+ )
+ == 1
+ )
+ with pytest.raises(TypeError):
+ StandardizedAnnotationStore(1)
+ with pytest.raises(TypeError):
+ StandardizedAnnotationStore([1])
+ with pytest.raises(TypeError):
+ StandardizedAnnotationStore.from_data(1)
+
+ assert len(s.metadata.standardized.resources) == 4
+ assert len(s.metadata.standardized.all_resources) == 6
+ assert len(s.metadata.standardized.uris) == 4
+ assert len(s.metadata.standardized.all_uris) == 6
+ assert len(s.metadata.standardized.qualifiers) == 3
+ assert len(s.metadata.standardized.all_qualifiers) == 4
+
+ assert len(s.metadata.standardized[Qualifier.Modelling_isDescribedBy]) == 2
+ assert len(s.metadata.standardized[QualifiersAlias.Modelling_any]) == 3
+ assert (
+ len(
+ s.metadata.standardized[
+ [Qualifier.Biological_hasTaxon, Qualifier.Modelling_is]
+ ]
+ )
+ == 2
+ )
+ with pytest.raises(TypeError):
+ s.metadata.standardized["a"]
+
+ assert (
+ s.metadata.standardized.resources_for(
+ qualifier=Qualifier.Modelling_isDescribedBy, namespace="doi"
+ )[0].identifier
+ == "10.1128/ecosalplus.10.2.1"
+ )
+ assert (
+ s.metadata.standardized.resources_for(
+ qualifier=QualifiersAlias.Modelling_known,
+ namespace=["eco", "taxonomy"],
+ nested=True,
+ )[0].uri
+ == ECO_EXAMPLE
+ )
+ with pytest.raises(TypeError):
+ assert (
+ s.metadata.standardized.resources_for(
+ qualifier=[QualifiersAlias.Modelling_known, 1],
+ namespace=["eco", "taxonomy"],
+ nested=True,
+ )[0].uri
+ == ECO_EXAMPLE
+ )
+ ann = new_store[0]
+ ann.remove_from_parent()
+
+ s.metadata.standardized[0] = ann
+ assert s.metadata.standardized[0] == ann
+
+ assert not (s.metadata.standardized == "string")
+ assert s.metadata.standardized != s_other.metadata.standardized
+ assert s.metadata != s_other.metadata
+
+ assert isinstance(s.metadata.standardized._repr_html_(), str)
+
+
+def test_old_style_annotation() -> None:
+ """Test creating old style annotations using add_simple_annotations."""
+ s = Species()
+ s.annotation.add({"chebi": "CHEBI:17234"})
+ s.annotation.add({"chebi": ["CHEBI:1723456", "CHEBI:172345"]})
+ with pytest.raises(TypeError):
+ s.annotation.add({"chebi": [["CHEBI:123", "CHEBI:1234"]]})
+ assert len(s.annotation) == 1
+ s.annotation.add(None)
+ assert len(s.annotation) == 1
+ assert s.annotation.number_of_resources == 3
+ s.annotation["eco"] = "123"
+ assert len(s.annotation) == 2
+ assert s.annotation.number_of_resources == 4
+ assert set(s.annotation["eco"]) == {"123"}
+ assert set(s.annotation.get("eco")) == {"123"}
+ assert set(s.annotation.get("eco", ["456"])) == {"123"}
+ with pytest.raises(IndexError):
+ _ = s.annotation["invalid"]
+ assert s.annotation.get("invalid") is None
+ assert set(s.annotation.get("invalid", ["456"])) == {"456"}
+
+ s.annotation.update({"bigg.metabolite": "glc__D"})
+ assert set(s.annotation["bigg.metabolite"]) == {"glc__D"}
+ del s.annotation["bigg.metabolite"]
+ assert s.annotation.get("bigg.metabolite") is None
+ other_interface = SimplifiedAnnotationInterface(Metadata())
+ other_interface["bigg.metabolite"] = "glc__D"
+ s.annotation.update(other_interface)
+ assert set(s.annotation["bigg.metabolite"]) == {"glc__D"}
+ s.annotation.update({"bigg.metabolite": ["glc__L"]})
+ assert set(s.annotation["bigg.metabolite"]) == {"glc__L"}
+ del s.annotation["bigg.metabolite"]
+
+ ref_ann = Metadata()
+ simpl_ann = SimplifiedAnnotationInterface(ref_ann)
+ simpl_ann.add(
+ {
+ "chebi": ["CHEBI:17234", "CHEBI:1723456", "CHEBI:172345"],
+ "eco": ["123"],
+ }
+ )
+ assert s.metadata == ref_ann
+
+ s.annotation.delete_annotation("CHEBI:172345")
+ assert len(s.annotation) == 2
+ assert s.annotation.number_of_resources == 3
+ with pytest.raises(ValueError):
+ s.annotation.delete_annotation("CHEBI:00000")
+ ref_ann = Metadata()
+ simpl_ann = SimplifiedAnnotationInterface(ref_ann)
+ simpl_ann.add(
+ {
+ "chebi": ["CHEBI:17234", "CHEBI:1723456"],
+ "eco": ["123"],
+ }
+ )
+ assert s.metadata == ref_ann
+
+ print(s.annotation.to_dict())
+ del s.annotation["chebi"]
+ print(s.annotation.to_dict())
+ assert len(s.annotation) == 1
+ assert s.annotation.number_of_resources == 1
+
+ s.annotation.add({"chebi": "CHEBI:17234"})
+ s.annotation.add({"chebi": ["CHEBI:1723456", "CHEBI:172345"]})
+ assert len(s.annotation) == 2
+ assert s.annotation.number_of_resources == 4
+ s.annotation["chebi"] = ["CHEBI:123", "CHEBI:1234"]
+ assert len(s.annotation) == 2
+ assert s.annotation.number_of_resources == 3
+ ref_ann = Metadata()
+ simpl_ann = SimplifiedAnnotationInterface(ref_ann)
+ simpl_ann.add({"chebi": ["CHEBI:123", "CHEBI:1234"], "eco": ["123"]})
+ assert s.metadata == ref_ann
+
+ assert len(s.annotation.keys()) == 2
+
+ s.annotation["chebi"] = []
+ assert s.annotation.number_of_resources == 1
+
+ s.annotation.clear()
+
+ assert len(s.annotation.keys()) == 0
+
+ s.annotation = {"chebi": ["CHEBI:123", "CHEBI:1234"], "eco": ["123"]}
+ assert s.annotation.number_of_resources == 3
+ s.annotation = {
+ "chebi": ["CHEBI:123", "CHEBI:1234"],
+ "eco": ["123"],
+ "sbo": ["SBO:0000123"],
+ }
+ assert s.annotation.number_of_resources == 4
+
+ simpl_ann = SimplifiedAnnotationInterface(Metadata())
+ simpl_ann.add(
+ {
+ "chebi": ["CHEBI:17234", "CHEBI:1723456"],
+ "eco": ["123"],
+ }
+ )
+ s.annotation.add(simpl_ann)
+ assert len(s.annotation) == 3
+ assert s.annotation.number_of_resources == 6
+
+ with pytest.raises(TypeError):
+ s.annotation.add(1)
+ with pytest.raises(TypeError):
+ s.annotation.add([1])
+ with pytest.raises(ValueError):
+ s.annotation.add([("chebi",)])
+ with pytest.raises(ValueError):
+ s.annotation.add(
+ ["https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:11881"]
+ )
+ with pytest.raises(TypeError):
+ _ = s.annotation[1]
+ with pytest.raises(TypeError):
+ del s.annotation[1]
+ with pytest.raises(TypeError):
+ s.annotation[1] = "CHEBI:17234"
+ assert s.annotation != 1
+
+ s.metadata.standardized.add(
+ "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:11881"
+ )
+ assert len(s.annotation) == 3
+ assert s.annotation.number_of_resources == 6
+ assert "CHEBI:1723456" in [idf for v in s.annotation.values() for idf in v]
+ assert ("chebi", "CHEBI:1723456") in s.annotation.tuples()
+
+ ann_copy = s.annotation.copy()
+ assert ann_copy == s.annotation
+ assert ann_copy is not s.annotation
+ assert isinstance(ann_copy, dict)
+
+
+def test_nested_annotation(data_directory: Path) -> None:
+ """Test reading annotation from JSON, including nested data.
+
+ Parameters
+ ----------
+ data_directory: Path
+ """
+ # testing via standardized
+ with data_directory.joinpath("cvterms_nested.json").open("r") as f_cvterms:
+ cvterms_data = json.load(f_cvterms)
+
+ s = Species()
+ s.metadata.add_standardized(cvterms_data)
+ # assert s.annotation == {
+ # "chebi": ["CHEBI:17627"],
+ # "eco": ["000000"],
+ # "kegg.compound": ["C00032"],
+ # "pubmed": ["1111111"],
+ # "uniprot": ["P68871", "P69905"],
+ # }
+ # check standardized
+ main_cvt = [
+ {
+ "resources": [
+ "https://identifiers.org/uniprot/P69905",
+ "https://identifiers.org/uniprot/P68871",
+ "https://identifiers.org/kegg.compound/C00032",
+ ],
+ "qualifier": "bqb_hasPart",
+ },
+ {
+ "qualifier": "bqb_hasPart",
+ "resources": [
+ "https://identifiers.org/uniprot/P69905",
+ "https://www.uniprot.org/uniprot/P68871",
+ "https://identifiers.org/chebi/CHEBI:17627",
+ ],
+ "annotations": [
+ {
+ "qualifier": "bqb_isDescribedBy",
+ "resources": [
+ PUBMED_EXAMPLE,
+ "https://identifiers.org/eco/000000",
+ ],
+ }
+ ],
+ },
+ ]
+ nested_cvt = [
+ {
+ "qualifier": "bqb_isDescribedBy",
+ "resources": [PUBMED_EXAMPLE, "https://identifiers.org/eco/000000"],
+ }
+ ]
+ assert s.metadata.standardized == main_cvt
+ nested_data = s.metadata.standardized[1].annotations
+ assert nested_data == nested_cvt
+
+ additional_cvt = {
+ "qualifier": "bqm_is",
+ "resources": ["https://identifiers.org/bigg.metabolite/hemoglobin"],
+ }
+ s.metadata.standardized.add(additional_cvt)
+ assert (
+ len(
+ s.metadata.standardized.resources_for(
+ qualifier=Qualifier.Biological_hasPart,
+ )
+ )
+ == 6
+ )
+ assert (
+ len(
+ s.metadata.standardized.resources_for(
+ qualifier=Qualifier.Biological_hasPart, namespace=["uniprot"]
+ )
+ )
+ == 3
+ )
+ assert (
+ len(
+ s.metadata.standardized.resources_for(
+ qualifier=[Qualifier.Biological_hasPart],
+ nested=True,
+ )
+ )
+ == 8
+ )
+ assert (
+ len(
+ s.metadata.standardized.resources_for(
+ qualifier=Qualifier.Biological_hasPart,
+ namespace="pubmed",
+ nested=True,
+ )
+ )
+ == 1
+ )
+ assert (
+ len(
+ s.metadata.standardized.resources_for(
+ qualifier=QualifiersAlias.Any_is,
+ nested=True,
+ )
+ )
+ == 1
+ )
+
+
+def test_cvterms_from_ecoli_xml(annotation_model: Model) -> None:
+ """Test the new and old style annotations of an ecoli model."""
+ qualifier_set = {
+ Qualifier(qual) for qual in ["bqb_hasTaxon", "bqm_is", "bqm_isDescribedBy"]
+ }
+ nested_cvt = [
+ {
+ "qualifier": "bqb_isDescribedBy",
+ "resources": [PUBMED_EXAMPLE],
+ },
+ {
+ "qualifier": "bqb_isDescribedBy",
+ "resources": [ECO_EXAMPLE],
+ },
+ ]
+ ecoli_model_cvterm = StandardizedAnnotationStore.from_data(ECOLI_MODEL_ANNOTATIONS)
+ print(ecoli_model_cvterm.to_list_of_dicts())
+ print(annotation_model.metadata.standardized.to_list_of_dicts())
+ xml_model_cvterms = annotation_model.metadata.standardized
+ model_cvterms_qualifier_set = xml_model_cvterms.qualifiers
+ assert qualifier_set == model_cvterms_qualifier_set
+ assert xml_model_cvterms == ecoli_model_cvterm
+ assert (
+ len(
+ annotation_model.metadata.standardized.query(
+ "bqm_isDescribedBy", "qualifier"
+ )
+ )
+ == 2
+ )
+ nested_data = annotation_model.metadata.standardized.query("bqm_is", "qualifier")[
+ 0
+ ].annotations
+ assert nested_data == nested_cvt
+
+ # check backwards compatibility
+ # assert annotation_model.annotation.metadata == {
+ # "bigg.model": ["e_coli_core"],
+ # "doi": ["10.1128/ecosalplus.10.2.1"],
+ # "eco": ["ECO:0000004"],
+ # "ncbiprotein": ["16128336"],
+ # "pubmed": ["1111111"],
+ # "taxonomy": ["511145"],
+ # }
+ # annotation_model.annotation.standardized.delete_annotation("coli")
+ # assert annotation_model.annotation.metadata == {
+ # "doi": ["10.1128/ecosalplus.10.2.1"],
+ # "eco": ["ECO:0000004"],
+ # "ncbiprotein": ["16128336"],
+ # "pubmed": ["1111111"],
+ # "taxonomy": ["511145"],
+ # }
+
+
+def test_writing_xml(annotation_model: Model, tmp_path):
+ """Test writing a model with annotations to xml (SBML)."""
+ assert (
+ write_sbml_model(
+ annotation_model, str(tmp_path.joinpath("e_coli_core_writing.xml"))
+ )
+ is None
+ )
+ # TODO: Add more tests here.
+
+
+def test_read_write_json(annotation_model: Model, tmp_path: Path):
+ """Test writing a model with annotations to JSON."""
+ json_path = tmp_path / "e_coli_core_json_writing.json"
+ print(json_path)
+ assert save_json_model(annotation_model, json_path, sort=False, pretty=True) is None
+
+ model = load_json_model(json_path)
+ # Because of changes to eq, to compare using the old format,
+ # we need annotation.metadata.
+ # TODO: get comments from cdiener
+ # assert model.annotation.metadata == {
+ # "bigg.model": ["e_coli_core"],
+ # "doi": ["10.1128/ecosalplus.10.2.1"],
+ # "eco": ["ECO:0000004"],
+ # "ncbiprotein": ["16128336"],
+ # "pubmed": ["1111111"],
+ # "taxonomy": ["511145"],
+ # }
+ assert model.metadata.standardized == StandardizedAnnotationStore.from_data(
+ ECOLI_MODEL_ANNOTATIONS
+ )
+ assert model.metadata.standardized == ECOLI_MODEL_ANNOTATIONS
+
+ for met_id in model.metabolites.list_attr("id"):
+ original_met_annot = annotation_model.metabolites.get_by_id(met_id).metadata
+ new_met_annot = model.metabolites.get_by_id(met_id).metadata
+ assert original_met_annot == new_met_annot
+
+ for rxn_id in model.reactions.list_attr("id"):
+ original_rxn_annot = annotation_model.reactions.get_by_id(rxn_id).metadata
+ new_rxn_annot = model.reactions.get_by_id(rxn_id).metadata
+ assert original_rxn_annot == new_rxn_annot
+
+
+def test_read_write_sbml(annotation_model: Model, tmp_path: Path):
+ """Test annotation consistency when writing and reading an SBML file."""
+ out_path = tmp_path / "e_coli_core_json_writing.sbml"
+ assert write_sbml_model(annotation_model, str(out_path)) is None
+
+ model = read_sbml_model(str(out_path))
+ # Because of changes to eq, to compare using the old format,
+ # we need annotation.metadata
+ # TODO: get comments from cdiener
+ # assert model.annotation.metadata == {
+ # "bigg.model": ["e_coli_core"],
+ # "doi": ["10.1128/ecosalplus.10.2.1"],
+ # "eco": ["ECO:0000004"],
+ # "ncbiprotein": ["16128336"],
+ # "pubmed": ["1111111"],
+ # "taxonomy": ["511145"],
+ # }
+ assert model.metadata.standardized == StandardizedAnnotationStore.from_data(
+ ECOLI_MODEL_ANNOTATIONS
+ )
+ assert model.metadata.standardized == ECOLI_MODEL_ANNOTATIONS
+
+ for met_id in model.metabolites.list_attr("id"):
+ original_met_annot = annotation_model.metabolites.get_by_id(met_id).metadata
+ new_met_annot = model.metabolites.get_by_id(met_id).metadata
+ assert original_met_annot == new_met_annot
+
+ for rxn_id in model.reactions.list_attr("id"):
+ original_rxn_annot = annotation_model.reactions.get_by_id(rxn_id).metadata
+ new_rxn_annot = model.reactions.get_by_id(rxn_id).metadata
+ assert original_rxn_annot == new_rxn_annot
+
+
+def test_read_old_json_model(data_directory):
+ """Test reading a schema v1 json model with old-style annotations."""
+ model = load_json_model(Path(data_directory / "valid_annotation_format.json"))
+ meta = model.metabolites[0]
+
+ assert meta.annotation["bigg.reaction"] == ["PFK26"]
+ assert meta.annotation["kegg.reaction"] == ["R02732"]
+ assert meta.annotation == {
+ "bigg.reaction": ["PFK26"],
+ "kegg.reaction": ["R02732"],
+ "rhea": ["15656"],
+ }
+
+
+# TODO: Fix this test. The mini.json model is currently not in the old format.
+# def test_read_old_json_model(data_directory):
+# """Test reading the annotations of an old format JSON model."""
+# model = load_json_model(Path(data_directory) / "mini.json")
+# meta = model.metabolites[0]
+# # assert meta.annotation == {
+# # "bigg.metabolite": ["13dpg"],
+# # "biocyc": ["DPG"],
+# # "chebi": [
+# # "CHEBI:11881",
+# # "CHEBI:16001",
+# # "CHEBI:1658",
+# # "CHEBI:20189",
+# # "CHEBI:57604",
+# # ],
+# # "hmdb": ["HMDB01270"],
+# # "kegg.compound": ["C00236"],
+# # "pubchem.substance": ["3535"],
+# # "reactome": ["REACT_29800"],
+# # "seed.compound": ["cpd00203"],
+# # "unipathway.compound": ["UPC00236"],
+# # }
+#
+# # testing standardized
+# expected_cvterms = StandardizedAnnotationStore.from_data(
+# [{"qualifier": "bqb_is", "resources": RESOURCE_LIST}]
+# )
+# assert meta.metadata.standardized == expected_cvterms
+# assert meta.metadata.standardized == [
+# {"qualifier": "bqb_is", "identifeirs": RESOURCE_LIST}
+# ]
+#
+
+
+def test_cvtermlist_query():
+ """Test the query functionality of StandardizedAnnotationStore."""
+ resources = RESOURCE_LIST
+ resources.extend(
+ [
+ "https://identifiers.org/uniprot/P69905",
+ "https://identifiers.org/uniprot/P68871",
+ "https://identifiers.org/kegg.compound/C00032",
+ "https://identifiers.org/chebi/CHEBI:17627",
+ "https://identifiers.org/chebi/CHEBI:43215",
+ "https://identifiers.org/CHebi/CHEBI:11881",
+ ]
+ )
+ cvtermlist = StandardizedAnnotationStore()
+ for i, res in enumerate(resources):
+ cvtermlist.extend(
+ [
+ StandardizedAnnotation(
+ qualifier=list(Qualifier._value2member_map_)[i], resources=res
+ )
+ ]
+ )
+
+ cvtermlist.append(
+ StandardizedAnnotation(
+ resources=ECO_EXAMPLE,
+ annotations=[
+ StandardizedAnnotation(
+ qualifier=Qualifier.Biological_isDescribedBy,
+ resources=PUBMED_EXAMPLE,
+ )
+ ],
+ qualifier=list(Qualifier._value2member_map_)[19],
+ )
+ )
+ print(cvtermlist)
+ # assert isinstance(
+ # cvtermlist.query(search_function="bqm", attribute="qualifier"),
+ # StandardizedAnnotationStore,
+ # )
+ # The result type is now just a list, since a StandardizedAnnotationStore should be
+ # used only for actual sets of annotations. This should maybe be a frozen variant of
+ # the StandardizedAnnotationStore, but for now it is a list.
+ assert isinstance(
+ cvtermlist.query(search_function="bqm", attribute="qualifier"),
+ StandardizedAnnotationList,
+ )
+ assert len(cvtermlist.query(search_function="bqm", attribute="qualifier")) == 6
+ assert (
+ len(cvtermlist.query(search_function="Modelling", attribute="qualifier")) == 6
+ )
+ assert (
+ len(
+ cvtermlist.query(search_function="bqb_isDescribedBy", attribute="qualifier")
+ )
+ == 1
+ )
+ assert (
+ len(
+ cvtermlist.query(
+ search_function="Biological_isDescribedBy", attribute="qualifier"
+ )
+ )
+ == 1
+ )
+ assert (
+ len(cvtermlist.query(search_function=r"bqm_is\S+", attribute="qualifier")) == 3
+ )
+ assert (
+ len(
+ cvtermlist.query(
+ search_function=lambda x: list(Qualifier._value2member_map_).index(
+ x.value
+ )
+ > 18,
+ attribute="qualifier",
+ )
+ )
+ == 1
+ )
+
+ # assert (
+ # len(
+ # cvtermlist.query(
+ # search_function=lambda x: x.nested_data,
+ # attribute="external_resources"
+ # )
+ # )
+ # == 1
+ # )
+ # assert (
+ # len(cvtermlist.query(search_function="chebi", attribute="external_resources"))
+ # == 7
+ # )
+ #
+ # assert len(cvtermlist.query(search_function="chebi", attribute="resources")) == 7
+ # assert (
+ # len(cvtermlist.query(search_function=r"[cC][hH]EBI", attribute="resources"))
+ # == 8
+ # )
+ # assert len(cvtermlist.query(search_function="pubmed", attribute="resources")) == 1
+ #
+ assert (
+ len(cvtermlist.query(search_function=lambda x: x.qualifier.value == "bqm_is"))
+ == 1
+ )
+ assert (
+ len(
+ cvtermlist.query(
+ search_function=lambda x: x.qualifier.name == "Modelling_is"
+ )
+ )
+ == 1
+ )
+
+ assert len(cvtermlist.query(search_function="chebi")) == 7
+ assert len(cvtermlist.query(search_function=r"bqm_is\S+")) == 3
+
+
+def test_resource():
+ """Test the behaviour of resource objects."""
+ # ChEBI has the namespace integrated in the identifier.
+ resource = Resource("http://identifiers.org/chebi/CHEBI:11881")
+ different_resource = Resource("http://identifiers.org/chebi/CHEBI:16001")
+
+ assert resource != different_resource
+ assert resource == ("chebi", "CHEBI:11881")
+ assert resource == "CHEBI:11881"
+ assert resource != ("chebi",)
+ assert resource == "http://identifiers.org/chebi/CHEBI:11881"
+ assert resource == "http://identifiers.org/CHEBI:11881"
+ assert resource == "https://identifiers.org/chebi/CHEBI:11881"
+ assert resource == "https://identifiers.org/CHEBI:11881"
+ assert resource == {"uri": "http://identifiers.org/chebi/CHEBI:11881"}
+ assert resource == {"namespace": "chebi", "identifier": "CHEBI:11881"}
+ assert resource != "https://identifiers.org/chebi/11881"
+ assert resource == ("CHEBI", "CHEBI:11881")
+
+ # OBI is a standard identifier (no integrated namespace).
+ # It does have different providers that can be specified.
+ resource = Resource("https://identifiers.org/obi:OBI_0000070")
+
+ assert resource != different_resource
+ assert resource == ("obi", "OBI_0000070")
+ assert resource != ("obi", "OBI_0000070", "obi")
+ assert resource == "http://identifiers.org/obi/OBI_0000070"
+ assert "http://identifiers.org/obi/OBI_0000070" == resource
+ assert resource == "http://identifiers.org/obi:OBI_0000070"
+ assert resource == "obi:OBI_0000070"
+ assert resource == "https://identifiers.org/obi:OBI_0000070"
+ assert resource == "https://identifiers.org/ols/obi:OBI_0000070"
+ assert resource == {"uri": "https://identifiers.org/obi:OBI_0000070"}
+ assert resource == {"uri": "obi:OBI_0000070"}
+ assert resource == {"namespace": "obi", "identifier": "OBI_0000070"}
+ assert resource != "https://identifiers.org/ols/OBI_0000070"
+ assert resource == ("OBI", "OBI_0000070")
+
+ assert (
+ len(
+ set(
+ [
+ resource,
+ different_resource,
+ Resource("obi:OBI_0000070"),
+ Resource("https://www.uniprot.org/uniprotkb/A0JNW5", strict=False),
+ ]
+ )
+ )
+ == 3
+ )
diff --git a/tests/test_core/test_metadata/test_new_style.py b/tests/test_core/test_metadata/test_new_style.py
new file mode 100644
index 000000000..6b2965be3
--- /dev/null
+++ b/tests/test_core/test_metadata/test_new_style.py
@@ -0,0 +1,209 @@
+"""Tests for the metadata structures."""
+
+from pathlib import Path
+from pprint import pprint
+
+import pytest
+
+from cobra import Model
+from cobra.core.metadata import Qualifier, StandardizedAnnotation
+from cobra.core.metadata.custom import CustomAnnotation
+from cobra.core.species import Species
+from cobra.io import read_sbml_model, write_sbml_model
+
+
+PUBMED_EXAMPLE = "https://identifiers.org/pubmed/1111111"
+ECO_EXAMPLE = "https://identifiers.org/eco/ECO:0000004"
+RESOURCE_LIST = [
+ "http://identifiers.org/bigg.metabolite/13dpg",
+ "http://identifiers.org/biocyc/DPG",
+ "http://identifiers.org/chebi/CHEBI:11881",
+ "http://identifiers.org/chebi/CHEBI:16001",
+ "http://identifiers.org/chebi/CHEBI:1658",
+ "http://identifiers.org/chebi/CHEBI:20189",
+ "http://identifiers.org/chebi/CHEBI:57604",
+ "http://identifiers.org/hmdb/HMDB01270",
+ "http://identifiers.org/kegg.compound/C00236",
+ "http://identifiers.org/pubchem.substance/3535",
+ "http://identifiers.org/reactome/REACT_29800",
+ "http://identifiers.org/seed.compound/cpd00203",
+ "http://identifiers.org/unipathway.compound/UPC00236",
+]
+
+ECOLI_MODEL_ANNOTATIONS = [
+ {
+ "qualifier": "bqb_hasTaxon",
+ "resources": ["http://identifiers.org/tanomy/511145"],
+ },
+ {
+ "qualifier": "bqm_is",
+ "resources": ["http://identifiers.org/bigg.model/e_coli_core"],
+ "annotations": [
+ {
+ "qualifier": "bqb_isDescribedBy",
+ "resources": [PUBMED_EXAMPLE],
+ },
+ {
+ "qualifier": "bqb_isDescribedBy",
+ "resources": [ECO_EXAMPLE],
+ },
+ ],
+ },
+ {
+ "qualifier": "bqm_isDescribedBy",
+ "resources": ["http://identifiers.org/doi/10.1128/ecosalplus.10.2.1"],
+ },
+ {
+ "qualifier": "bqm_isDescribedBy",
+ "resources": ["http://identifiers.org/ncbiprotein/16128336"],
+ },
+]
+COBRA_URL = "https://cobrapy.readthedocs.io/"
+
+
+def test_annotation() -> None:
+ """Test creating an annotation manually."""
+ s = Species()
+
+ # assert s.annotations is None
+ annotation_1 = StandardizedAnnotation("https://identifiers.org/go/GO:0007268")
+ # Default qualifier should be bqb_is
+ assert annotation_1.qualifier == Qualifier.Biological_is
+ annotation_2 = StandardizedAnnotation(
+ [
+ "https://identifiers.org/wikipathways/WP179",
+ "https://identifiers.org/reactome/REACT_152",
+ ],
+ qualifier=Qualifier.Biological_isVersionOf,
+ )
+ assert len(annotation_2.resources) == 2
+ nested_annotations = [
+ StandardizedAnnotation(
+ "https://identifiers.org/pubmed/1111111",
+ qualifier=Qualifier.Biological_isDescribedBy,
+ ),
+ StandardizedAnnotation(
+ "https://identifiers.org/eco/ECO:0000004",
+ qualifier=Qualifier.Biological_isDescribedBy,
+ ),
+ ]
+
+ annotation_3 = StandardizedAnnotation(
+ qualifier=Qualifier.Biological_occursIn,
+ resources=["https://identifiers.org/go/GO:0005764"],
+ annotations=nested_annotations,
+ )
+ assert len(annotation_3.annotations) == 2
+ s.add_annotations([annotation_1, annotation_2, annotation_3])
+ # assert len(s.annotations) == 3
+ assert len(s.metadata.standardized) == 3
+ s.remove_annotations([annotation_2])
+ assert len(s.metadata.standardized) == 2
+ s.add_annotations(annotation_2)
+ assert len(s.metadata.standardized) == 3
+ with pytest.raises(TypeError):
+ s.add_annotations([10])
+ with pytest.raises(TypeError):
+ s.remove_annotations([10])
+ with pytest.raises(TypeError):
+ s.metadata = 10
+ annotation_2.remove_from_parent()
+ assert len(s.metadata.standardized) == 2
+ # assert s.annotations.custom is None
+ # assert (
+ # len(
+ # s.annotations.standardized.by_qualifier(Qualifier.Biological_is)[
+ # 0
+ # ].resources
+ # )
+ # == 2
+ # )
+ custom_1 = CustomAnnotation(key="cobra_flag", value="starred")
+ custom_2 = CustomAnnotation(key="cobra_url", uri=COBRA_URL)
+ s.add_annotations([custom_1, custom_2])
+ assert len(s.metadata.custom) == 2
+ s.remove_annotations(custom_1)
+ assert len(s.metadata.custom) == 1
+ assert s.metadata.custom["cobra_url"].uri == COBRA_URL
+
+
+def test_read_write_sbml(annotation_model: Model, tmp_path: Path):
+ """Test annotation consistency when writing and reading an SBML file."""
+ out_path = tmp_path / "e_coli_core_json_writing.sbml"
+ assert write_sbml_model(annotation_model, str(out_path)) is None
+
+ model = read_sbml_model(str(out_path))
+ print(model.metadata)
+ print(model.metadata.standardized)
+ for ann in model.metadata.standardized:
+ print(ann)
+ print(model.metadata.standardized.resources)
+ pprint(model.metadata.standardized.to_records())
+ pprint(model.metadata.standardized.to_list_of_dicts())
+ assert len(model.metadata.standardized) == 4
+ ann_dict = [
+ {
+ "resources": [
+ "http://identifiers.org/taxonomy/511145",
+ ],
+ "qualifier": "bqb_hasTaxon",
+ },
+ {
+ "annotations": [
+ {
+ "resources": [
+ "https://identifiers.org/pubmed/1111111",
+ ],
+ "qualifier": "bqb_isDescribedBy",
+ },
+ {
+ "resources": [
+ "https://identifiers.org/eco/ECO:0000004",
+ ],
+ "qualifier": "bqb_isDescribedBy",
+ },
+ ],
+ "resources": [
+ "http://identifiers.org/bigg.model/e_coli_core",
+ ],
+ "qualifier": "bqm_is",
+ },
+ {
+ "resources": [
+ "http://identifiers.org/doi/10.1128/ecosalplus.10.2.1",
+ ],
+ "qualifier": "bqm_isDescribedBy",
+ },
+ {
+ "resources": [
+ "http://identifiers.org/ncbiprotein/16128336",
+ ],
+ "qualifier": "bqm_isDescribedBy",
+ },
+ ]
+ assert model.metadata.standardized == ann_dict
+ # Because of changes to eq, to compare using the old format,
+ # we need annotation.annotations
+ # TODO: get comments from cdiener
+ # assert model.annotation.annotations == {
+ # "bigg.model": ["e_coli_core"],
+ # "doi": ["10.1128/ecosalplus.10.2.1"],
+ # "eco": ["ECO:0000004"],
+ # "ncbiprotein": ["16128336"],
+ # "pubmed": ["1111111"],
+ # "taxonomy": ["511145"],
+ # }
+ # assert model.annotation.standardized == CustomAnnotationStore.from_data(
+ # ECOLI_MODEL_ANNOTATIONS
+ # )
+ # assert model.annotation.standardized == ECOLI_MODEL_ANNOTATIONS
+ #
+ # for met_id in model.metabolites.list_attr("id"):
+ # original_met_annot = annotation_model.metabolites.get_by_id(met_id).annotation
+ # new_met_annot = model.metabolites.get_by_id(met_id).annotation
+ # assert original_met_annot == new_met_annot
+ #
+ # for rxn_id in model.reactions.list_attr("id"):
+ # original_rxn_annot = annotation_model.reactions.get_by_id(rxn_id).annotation
+ # new_rxn_annot = model.reactions.get_by_id(rxn_id).annotation
+ # assert original_rxn_annot == new_rxn_annot
diff --git a/tests/test_core/test_metadata/test_notes.py b/tests/test_core/test_metadata/test_notes.py
new file mode 100644
index 000000000..139760194
--- /dev/null
+++ b/tests/test_core/test_metadata/test_notes.py
@@ -0,0 +1,113 @@
+"""Test the 'notes' property of components."""
+
+import os
+from pathlib import Path
+
+from cobra import Metabolite, Model, Reaction
+from cobra.io import load_json_model, read_sbml_model, save_json_model, write_sbml_model
+
+
+def test_notes_io(tmp_path: Path) -> None:
+ """Test if model notes are written and read from/to SBML.
+
+ Parameters
+ ----------
+ tmp_path : pathlib.Path
+ The path to the temporary test assets store.
+
+ """
+ path_to_file = tmp_path / "model_notes.xml"
+
+ # making a minimal cobra model to test notes
+ model = Model("e_coli_core")
+ model.notes = {"Remark": "...Model Notes..."}
+ met = Metabolite("pyr_c", compartment="c")
+ model.add_metabolites([met])
+ met.notes = {"Remark": "Note with \n newline"}
+ rxn = Reaction("R_ATPM")
+ model.add_reactions([rxn])
+ rxn.notes = {"Remark": "What about me?"}
+ model.objective_direction = "max"
+ model.objective = rxn
+ write_sbml_model(model, str(path_to_file.resolve()))
+
+ # reading the model back
+ model_after_reading = read_sbml_model(str(path_to_file.resolve()))
+ met_after_reading = model_after_reading.metabolites.get_by_id("pyr_c")
+ reaction_after_reading = model_after_reading.reactions.get_by_id("R_ATPM")
+
+ # checking if notes are written to model
+ assert model_after_reading.notes["Remark"] == "...Model Notes..."
+
+ # checking notes for metabolite and reaction
+ assert met_after_reading.notes["Remark"] == "Note with \n newline"
+ assert reaction_after_reading.notes["Remark"] == "What about me?"
+
+
+NEW_VALUE1 = "New Value 1"
+NEW_VALUE3 = "New Value 3"
+
+
+def test_notes(data_directory, tmp_path):
+ """Reading notes from SBML to cobra model."""
+ model_path = os.path.join(data_directory, "e_coli_core_for_annotation.xml")
+ assert os.path.exists(model_path)
+ model = read_sbml_model(model_path)
+ rx1 = model.reactions[0]
+ # keys inside notes dict
+ list_of_keys = ["Key1", "Key2", "Key3"]
+
+ for key in list_of_keys:
+ assert key in rx1.notes
+
+ assert rx1.notes["Key1"] == "Value1"
+ assert rx1.notes["Key2"] == "Value2"
+ assert rx1.notes["Key3"] == "Value3"
+
+ # modifying already present key-value
+ rx1.notes["Key1"] = NEW_VALUE1
+ rx1.notes["Key3"] = NEW_VALUE3
+
+ # trying to insert a new key-value
+ rx1.notes["Key4"] = NEW_VALUE3
+
+ # checking modified notes dict and string
+ assert rx1.notes["Key1"] == NEW_VALUE1
+ assert rx1.notes["Key2"] == "Value2"
+ assert rx1.notes["Key3"] == NEW_VALUE3
+ assert rx1.notes["Key4"] == NEW_VALUE3
+
+ # writing and reading back the model
+ path_to_file = os.path.join(tmp_path, "model_notes.xml")
+ write_sbml_model(model, path_to_file)
+
+ model_after_reading = read_sbml_model(path_to_file)
+ rx1_after_reading = model_after_reading.reactions[0]
+
+ # checks after reading model back again
+ assert rx1_after_reading.notes["Key1"] == NEW_VALUE1
+ assert rx1_after_reading.notes["Key2"] == "Value2"
+ assert rx1_after_reading.notes["Key3"] == NEW_VALUE3
+
+
+def test_reading_writing_notes(data_directory, tmp_path):
+ """Test consistency when reading and writing notes."""
+ # reading model with notes
+ model = read_sbml_model(
+ os.path.join(data_directory, "e_coli_core_for_annotation.xml")
+ )
+
+ # checking notes data
+ rx1 = model.reactions[0]
+ assert rx1.notes["Key1"] == "Value1"
+ assert rx1.notes["Key2"] == "Value2"
+ assert rx1.notes["Key3"] == "Value3"
+
+ # reading and writing in json format
+ path_to_json = os.path.join(str(tmp_path), "json_notes.json")
+ save_json_model(model, path_to_json)
+ model_from_json = load_json_model(path_to_json)
+ rx1_from_json = model_from_json.reactions[0]
+ assert rx1_from_json.notes["Key1"] == "Value1"
+ assert rx1_from_json.notes["Key2"] == "Value2"
+ assert rx1_from_json.notes["Key3"] == "Value3"
diff --git a/tests/test_io/test_annotation.py b/tests/test_io/test_annotation.py
index a1aca93bd..c977ad2fd 100644
--- a/tests/test_io/test_annotation.py
+++ b/tests/test_io/test_annotation.py
@@ -25,26 +25,32 @@ def _check_sbml_annotations(model: "Model") -> None:
# {'bigg.model': 'e_coli_core', 'doi': '10.1128/ecosalplus.10.2.1',
# 'taxonomy': '511145'}
annotation = model.annotation
+ for x in annotation:
+ print(x)
assert annotation is not None
assert len(annotation) == 3
- for key in ["bigg.model", "doi", "taxonomy"]:
- assert key in annotation
- assert annotation["bigg.model"] == "e_coli_core"
- assert annotation["doi"] == "10.1128/ecosalplus.10.2.1"
- assert annotation["taxonomy"] == "511145"
+ assert set(annotation.keys()) == {"bigg.model", "doi", "taxonomy"}
+ assert annotation["bigg.model"] == ["e_coli_core"]
+ assert annotation["doi"] == ["10.1128/ecosalplus.10.2.1"]
+ assert annotation["taxonomy"] == ["511145"]
# gene annotation
# {'asap': 'ABE-0006162', 'ncbigene': '946368', 'uniprot': 'P33221',
- # 'ncbiprotein': 'gi:16129802', 'ecogene': 'EG11809'}
+ # 'ncbiprotein': '16129802', 'ecogene': 'EG11809'}
annotation = model.genes.G1.annotation
assert len(annotation) == 5
- for key in ["asap", "ncbigene", "uniprot", "ncbiprotein", "ecogene"]:
- assert key in annotation
- assert annotation["asap"] == "ABE-0006162"
- assert annotation["ncbigene"] == "946368"
- assert annotation["uniprot"] == "P33221"
- assert annotation["ncbiprotein"] == "16129802"
- assert annotation["ecogene"] == "EG11809"
+ assert set(annotation.keys()) == {
+ "asap",
+ "ncbigene",
+ "uniprot",
+ "ncbiprotein",
+ "ecogene",
+ }
+ assert annotation["asap"] == ["ABE-0006162"]
+ assert annotation["ncbigene"] == ["946368"]
+ assert annotation["uniprot"] == ["P33221"]
+ assert annotation["ncbiprotein"] == ["16129802"]
+ assert annotation["ecogene"] == ["EG11809"]
# compartment annotation
# FIXME: add tests with first class compartment model
@@ -63,7 +69,7 @@ def _check_sbml_annotations(model: "Model") -> None:
# 'seed.compound': 'cpd00203', 'hmdb': ['HMDB62758', 'HMDB06213'],
# 'biocyc': 'META:DPG'}
annotation = model.metabolites.A.annotation
- for key in [
+ assert set(annotation.keys()) == {
"inchi",
"bigg.metabolite",
"chebi",
@@ -72,11 +78,10 @@ def _check_sbml_annotations(model: "Model") -> None:
"seed.compound",
"hmdb",
"biocyc",
- ]:
- assert key in annotation
- assert (
- annotation["inchi"] == "InChI=1S/C3H8O2/c1-3(5)2-4/h3-5H,2H2,1H3/t3-/m0/s1"
- ) # noqa: E501
+ }
+ assert annotation["inchi"] == [
+ "InChI=1S/C3H8O2/c1-3(5)2-4/h3-5H,2H2,1H3/t3-/m0/s1"
+ ] # noqa: E501
# reaction annotation
# {'kegg.reaction': 'R00228', 'sbo': 'SBO:0000375',
@@ -84,7 +89,7 @@ def _check_sbml_annotations(model: "Model") -> None:
# 'metanetx.reaction': 'MNXR95210', 'bigg.reaction': 'ACALD',
# 'biocyc': 'META:ACETALD-DEHYDROG-RXN'}
annotation = model.reactions.R1.annotation
- for key in [
+ assert set(annotation.keys()) == {
"kegg.reaction",
"sbo",
"ec-code",
@@ -92,9 +97,8 @@ def _check_sbml_annotations(model: "Model") -> None:
"metanetx.reaction",
"bigg.reaction",
"biocyc",
- ]:
- assert key in annotation
- assert annotation["biocyc"] == "META:ACETALD-DEHYDROG-RXN"
+ }
+ assert annotation["biocyc"] == ["META:ACETALD-DEHYDROG-RXN"]
def test_read_sbml_annotations(data_directory: Path) -> None:
diff --git a/tests/test_io/test_annotation_format.py b/tests/test_io/test_annotation_format.py
index 9b9d039cd..0a678bc28 100644
--- a/tests/test_io/test_annotation_format.py
+++ b/tests/test_io/test_annotation_format.py
@@ -2,8 +2,6 @@
from pathlib import Path
-import pytest
-
from cobra.io import load_json_model, write_sbml_model
@@ -19,9 +17,9 @@ def test_load_json_model_valid(data_directory: Path, tmp_path: Path) -> None:
path_to_file = data_directory / "valid_annotation_format.json"
model = load_json_model(path_to_file)
expected = {
- "bigg.reaction": [["is", "PFK26"]],
- "kegg.reaction": [["is", "R02732"]],
- "rhea": [["is", "15656"]],
+ "bigg.reaction": ["PFK26"],
+ "kegg.reaction": ["R02732"],
+ "rhea": ["15656"],
}
for metabolite in model.metabolites:
assert metabolite.annotation == expected
@@ -37,5 +35,6 @@ def test_load_json_model_invalid(data_directory: Path) -> None:
"""
path = data_directory / "invalid_annotation_format.json"
- with pytest.raises(TypeError):
- load_json_model(path)
+ model = load_json_model(path)
+ anno = model.metabolites[0].annotation
+ assert anno == {"kegg.compound": ["C01468"], "chebi": ["CHEBI:11981"]}
diff --git a/tests/test_io/test_json.py b/tests/test_io/test_json.py
index 53d9e62fc..656cae00f 100644
--- a/tests/test_io/test_json.py
+++ b/tests/test_io/test_json.py
@@ -19,16 +19,21 @@ def json_schema_v1() -> Dict[str, Union[str, bool, Any]]:
return schema_v1
-def test_validate_json(
- cobra_data_directory: Path, json_schema_v1: Dict[str, Union[str, bool, Any]]
-) -> None:
+@pytest.fixture(scope="module")
+def json_schema_v2() -> Dict[str, Union[str, bool, Any]]:
+ """Fixture for cobra JSON-schema."""
+ with files(cio).joinpath("schema_v2.json").open("r") as handle:
+ schema_v2 = json.load(handle)
+ return schema_v2
+
+
+def test_validate_json(cobra_data_directory: Path) -> None:
"""Validate file according to JSON-schema."""
- jsonschema = pytest.importorskip("jsonschema")
- with open(
- cobra_data_directory.joinpath("mini.json"), "r", encoding="utf-8"
- ) as infile:
- loaded = json.load(infile)
- assert jsonschema.validate(loaded, json_schema_v1) is None
+
+ errors = cio.validate_json_model(
+ cobra_data_directory.joinpath("mini.json"), json_schema_version=2
+ )
+ assert next(iter(errors), None) is None
def test_load_json_model(
@@ -47,29 +52,25 @@ def test_load_json_model(
def test_save_json_model(
tmp_path: Path,
mini_model: Model,
- json_schema_v1: Dict[str, Union[str, bool, Any]],
) -> None:
"""Test the writing of JSON model."""
- jsonschema = pytest.importorskip("jsonschema")
output_file = tmp_path.joinpath("mini.json")
cio.save_json_model(mini_model, output_file, pretty=True)
# validate against JSONSchema
- with open(output_file, "r") as infile:
- loaded = json.load(infile)
- assert jsonschema.validate(loaded, json_schema_v1) is None
+ errors = cio.validate_json_model(output_file, json_schema_version=2)
+ assert next(iter(errors), None) is None
output_file.unlink()
cio.save_json_model(mini_model, str(output_file), pretty=True)
# validate against JSONSchema
- with open(output_file, "r") as infile:
- loaded = json.load(infile)
- assert jsonschema.validate(loaded, json_schema_v1) is None
+ errors = cio.validate_json_model(output_file, json_schema_version=2)
+ assert next(iter(errors), None) is None
output_file.unlink()
with output_file.open("w+") as json_outfile:
cio.save_json_model(mini_model, json_outfile, pretty=True)
# validate against JSONSchema
json_outfile.seek(0, 0)
- loaded = json.load(json_outfile)
- assert jsonschema.validate(loaded, json_schema_v1) is None
+ errors = cio.validate_json_model(json_outfile, json_schema_version=2)
+ assert next(iter(errors), None) is None
def test_reaction_bounds_json(data_directory: Path, tmp_path: Path) -> None:
diff --git a/tests/test_io/test_mat.py b/tests/test_io/test_mat.py
index e23529b99..af90760ea 100644
--- a/tests/test_io/test_mat.py
+++ b/tests/test_io/test_mat.py
@@ -311,7 +311,7 @@ def test_mat_model_wrong_caps(
(data_directory / "mini_wrong_key_caps.mat").resolve()
)
assert compare_models(mat_model, mat_wrong_caps_model) is None
- assert mat_wrong_caps_model.reactions.get_by_id("LDH_D").annotation == {
+ EXPECTED_RXN_ANNOTATION = {
"rhea": ["16369", "16370", "16371", "16372"],
"metanetx.reaction": ["MNXR101037"],
"kegg.reaction": ["R00704"],
@@ -320,33 +320,55 @@ def test_mat_model_wrong_caps(
"biocyc": ["META:DLACTDEHYDROGNAD-RXN"],
"sbo": ["SBO:0000375"],
}
+ actual_rxn_annotation = dict(
+ mat_wrong_caps_model.reactions.get_by_id("LDH_D").annotation
+ )
+ expected_rxn_keys = EXPECTED_RXN_ANNOTATION.keys()
+ actual_rxn_keys = actual_rxn_annotation.keys()
+ assert expected_rxn_keys == actual_rxn_keys
+ for key in actual_rxn_keys:
+ assert EXPECTED_RXN_ANNOTATION[key] == actual_rxn_annotation[key]
for rxn in mat_model.reactions.list_attr("id"):
assert (
mat_wrong_caps_model.reactions.get_by_id(rxn).annotation
== mat_model.reactions.get_by_id(rxn).annotation
)
- assert mat_wrong_caps_model.metabolites.get_by_id("pyr_c").annotation == {
+
+ EXPECTED_MAT_ANNOTATION = {
"seed.compound": ["cpd00020"],
"unipathway.compound": ["UPC00022"],
"lipidmaps": ["LMFA01060077"],
- "reactome": ["REACT_113557", "REACT_389680", "REACT_29398"],
+ "reactome": sorted(["REACT_113557", "REACT_389680", "REACT_29398"]),
"biocyc": ["PYRUVATE"],
- "chebi": [
- "CHEBI:15361",
- "CHEBI:14987",
- "CHEBI:8685",
- "CHEBI:32816",
- "CHEBI:45253",
- "CHEBI:26466",
- "CHEBI:26462",
- ],
+ "chebi": sorted(
+ [
+ "CHEBI:15361",
+ "CHEBI:14987",
+ "CHEBI:8685",
+ "CHEBI:32816",
+ "CHEBI:45253",
+ "CHEBI:26466",
+ "CHEBI:26462",
+ ]
+ ),
"pubchem.substance": ["3324"],
"bigg.metabolite": ["pyr"],
"cas": ["127-17-3"],
"hmdb": ["HMDB00243"],
"kegg.compound": ["C00022"],
}
+ actual_met_annotation = mat_wrong_caps_model.metabolites.get_by_id(
+ "pyr_c"
+ ).annotation
+ expected_met_keys = EXPECTED_MAT_ANNOTATION.keys()
+ actual_met_keys = actual_met_annotation.keys()
+ assert expected_met_keys == actual_met_keys
+ for key in actual_met_keys:
+ assert EXPECTED_MAT_ANNOTATION[key] == actual_met_annotation[key]
for met in mat_model.metabolites.list_attr("id"):
+ print(met)
+ print(mat_wrong_caps_model.metabolites.get_by_id(met).annotation.to_dict())
+ print(mat_model.metabolites.get_by_id(met).annotation.to_dict())
assert (
mat_wrong_caps_model.metabolites.get_by_id(met).annotation
== mat_model.metabolites.get_by_id(met).annotation
diff --git a/tests/test_io/test_notes.py b/tests/test_io/test_notes.py
deleted file mode 100644
index da441e30c..000000000
--- a/tests/test_io/test_notes.py
+++ /dev/null
@@ -1,43 +0,0 @@
-"""Test proper reading of SBML notes."""
-
-from pathlib import Path
-
-from cobra import Metabolite, Model, Reaction
-from cobra.io import read_sbml_model, write_sbml_model
-
-
-def test_notes(tmp_path: Path) -> None:
- """Test if model notes are written in SBML.
-
- Parameters
- ----------
- tmp_path : pathlib.Path
- The path to the temporary test assets store.
-
- """
- path_to_file = tmp_path / "model_notes.xml"
-
- # making a minimal cobra model to test notes
- model = Model("test_notes_model")
- model.notes["Remark"] = "...Model Notes..."
- met = Metabolite("pyr_c", compartment="c")
- model.add_metabolites([met])
- met.notes["Remark"] = "Note with \n newline"
- rxn = Reaction("R_ATPM")
- model.add_reactions([rxn])
- rxn.notes["Remark"] = "What about me?"
- model.objective_direction = "max"
- model.objective = rxn
- write_sbml_model(model, str(path_to_file.resolve()))
-
- # reading the model back
- model_after_reading = read_sbml_model(str(path_to_file.resolve()))
- met_after_reading = model_after_reading.metabolites.get_by_id("pyr_c")
- reaction_after_reading = model_after_reading.reactions.get_by_id("R_ATPM")
-
- # checking if notes are written to model
- assert model_after_reading.notes["Remark"] == "...Model Notes..."
-
- # checking notes for metabolite and reaction
- assert met_after_reading.notes["Remark"] == "Note with \n newline"
- assert reaction_after_reading.notes["Remark"] == "What about me?"
diff --git a/tests/test_io/test_sbml.py b/tests/test_io/test_sbml.py
index b68441150..000133da3 100644
--- a/tests/test_io/test_sbml.py
+++ b/tests/test_io/test_sbml.py
@@ -6,13 +6,14 @@
from pathlib import Path
from pickle import load
from tempfile import gettempdir
-from typing import List, Tuple
+from typing import Callable, List, Tuple
import pytest
from _pytest.fixtures import SubRequest
import cobra
from cobra import Model
+from cobra.core.metadata import Metadata
from cobra.io import read_sbml_model, validate_sbml_model, write_sbml_model
@@ -38,6 +39,30 @@
],
)
trials: List[IOTrial] = [
+ IOTrial(
+ "fbc3",
+ "mini.pickle",
+ "mini_fbc3.xml",
+ read_sbml_model,
+ write_sbml_model,
+ validate_sbml_model,
+ ),
+ IOTrial(
+ "fbc3Gz",
+ "mini.pickle",
+ "mini_fbc3.xml.gz",
+ read_sbml_model,
+ write_sbml_model,
+ None, # If None is replaced with validate_sbml_model, it seems to work
+ ),
+ IOTrial(
+ "fbc3Bz2",
+ "mini.pickle",
+ "mini_fbc3.xml.bz2",
+ read_sbml_model,
+ write_sbml_model,
+ None,
+ ),
IOTrial(
"fbc2",
"mini.pickle",
@@ -52,7 +77,7 @@
"mini_fbc2.xml.gz",
read_sbml_model,
write_sbml_model,
- None,
+ None, # If None is replaced with validate_sbml_model, it seems to work
),
IOTrial(
"fbc2Bz2",
@@ -271,6 +296,7 @@ def io_trial(
# test writing the model within a context with a non-empty stack
with test_model:
test_model.objective = test_model.objective
+ test_model.id = f"{test_model.id}_mod"
request.param.write_function(test_model, test_output_filename)
reread_model = request.param.read_function(test_output_filename)
unlink(test_output_filename)
@@ -316,7 +342,63 @@ def test_from_sbml_string(data_directory: Path) -> None:
TestCobraIO.compare_models(name="read from string", model1=model1, model2=model2)
-@pytest.mark.skip(reason="Model history currently not written")
+def test_document_history(tmp_path: Path) -> None:
+ """Testing reading and writing of ModelHistory for SBMLDocument.
+
+ Parameters
+ ----------
+ tmp_path: Path
+ Directory to use for temporary data.
+ """
+ model = Model("test")
+ history = {
+ "creators": [
+ {
+ "name": "Max Mustermann",
+ "organisation": "Muster University",
+ "email": "muster@university.com",
+ }
+ ],
+ "created_date": "2019-10-20T12:34:32Z",
+ "modified_dates": ["2019-10-20T12:35:32Z"],
+ }
+ metadata = Metadata(history=history)
+ model._sbml = {"metadata": metadata}
+
+ sbml_path = join(str(tmp_path), "test.xml")
+ with open(sbml_path, "w") as f_out:
+ write_sbml_model(model, f_out)
+
+ with open(sbml_path, "r") as f_in:
+ lines = f_in.readlines()
+ print("".join(lines))
+
+ with open(sbml_path, "r") as f_in:
+ model2 = read_sbml_model(f_in)
+
+ print(model2._sbml)
+ print(model2._sbml["metadata"])
+ print(model2._sbml["metadata"].history)
+ print(model2._sbml["metadata"].history.creators)
+
+ assert "metadata" in model2._sbml
+ assert len(model2._sbml["metadata"].history.creators) == 1
+ c = model2._sbml["metadata"].history.creators[0]
+ assert c.name == "Max Mustermann"
+ assert c.organisation == "Muster University"
+ assert c.email == "muster@university.com"
+
+ assert (
+ model2._sbml["metadata"].history.created_date.isoformat()
+ == "2019-10-20T12:34:32+00:00"
+ )
+ assert len(model2._sbml["metadata"].history._modified_dates) == 1
+ assert (
+ model2._sbml["metadata"].history._modified_dates[0].isoformat()
+ == "2019-10-20T12:35:32+00:00"
+ )
+
+
def test_model_history(tmp_path: Path) -> None:
"""Testing reading and writing of ModelHistory.
@@ -326,31 +408,45 @@ def test_model_history(tmp_path: Path) -> None:
Directory to use for temporary data.
"""
model = Model("test")
- model._sbml = {
+ history = {
"creators": [
{
- "familyName": "Mustermann",
- "givenName": "Max",
+ "name": "Max Mustermann",
"organisation": "Muster University",
"email": "muster@university.com",
}
- ]
+ ],
+ "created_date": "2019-10-20T12:34:32Z",
+ "modified_dates": ["2019-10-20T12:35:32Z"],
}
+ model.metadata = Metadata(history=history)
+ assert len(model.metadata.history.creators) == 1
sbml_path = tmp_path / "test.xml"
with open(sbml_path, "w") as f_out:
write_sbml_model(model, f_out)
+ with open(sbml_path, "r") as f_in:
+ lines = f_in.readlines()
+ print("".join(lines))
+
with open(sbml_path, "r") as f_in:
model2 = read_sbml_model(f_in)
- assert "creators" in model2._sbml
- assert len(model2._sbml["creators"]) == 1
- c = model2._sbml["creators"][0]
- assert c["familyName"] == "Mustermann"
- assert c["givenName"] == "Max"
- assert c["organisation"] == "Muster University"
- assert c["email"] == "muster@university.com"
+ assert len(model2.metadata.history.creators) == 1
+ c = model2.metadata.history.creators[0]
+ assert c.name == "Max Mustermann"
+ assert c.organisation == "Muster University"
+ assert c.email == "muster@university.com"
+
+ assert (
+ model2.metadata.history.created_date.isoformat() == "2019-10-20T12:34:32+00:00"
+ )
+ assert len(model2.metadata.history._modified_dates) == 1
+ assert (
+ model2.metadata.history._modified_dates[0].isoformat()
+ == "2019-10-20T12:35:32+00:00"
+ )
def test_groups(data_directory: Path, tmp_path: Path) -> None:
@@ -579,7 +675,7 @@ def test_gprs(large_model: Model, tmp_path: Path) -> None:
def test_identifiers_annotation() -> None:
"""Test annotation with identifiers."""
- from cobra.io.sbml import _parse_annotation_info
+ from cobra.core.metadata.resource import parse_identifiers_uri
for uri in [
"http://identifiers.org/chebi/CHEBI:000123",
@@ -587,7 +683,7 @@ def test_identifiers_annotation() -> None:
"http://identifiers.org/CHEBI:000123",
"https://identifiers.org/CHEBI:000123",
]:
- data = _parse_annotation_info(uri)
+ data = parse_identifiers_uri(uri)
assert data
assert data[0] == "chebi"
assert data[1] == "CHEBI:000123"
@@ -598,7 +694,7 @@ def test_identifiers_annotation() -> None:
"http://identifiers.org/taxonomy:9602",
"https://identifiers.org/taxonomy:9602",
]:
- data = _parse_annotation_info(uri)
+ data = parse_identifiers_uri(uri)
assert data
assert data[0] == "taxonomy"
assert data[1] == "9602"
@@ -607,7 +703,7 @@ def test_identifiers_annotation() -> None:
"http://identifier.org/taxonomy/9602",
"https://test.com",
]:
- data = _parse_annotation_info(uri)
+ data = parse_identifiers_uri(uri)
assert data is None
@@ -618,8 +714,6 @@ def test_smbl_with_notes(data_directory: Path, tmp_path: Path) -> None:
----------
data_directory: Path
Directory where the data is.
- tmp_path: Path
- Directory to use for temporary data.
"""
sbml_path = join(data_directory, "example_notes.xml")
model = read_sbml_model(sbml_path)
@@ -645,41 +739,45 @@ def test_smbl_with_notes(data_directory: Path, tmp_path: Path) -> None:
}
metabolite_annotations = {
"2hb_e": {
- "sbo": "SBO:0000247",
- "inchi": "InChI=1S/C4H8O3/c1-2-3(5)4(6)7/h3,5H,2H2,1H3,(H,6,7)",
- "chebi": "CHEBI:1148",
+ "sbo": ["SBO:0000247"],
+ "inchi": ["InChI=1S/C4H8O3/c1-2-3(5)4(6)7/h3,5H,2H2,1H3,(H,6,7)"],
+ "chebi": ["CHEBI:1148"],
},
"nad_e": {
- "sbo": "SBO:0000247",
- "inchi": "InChI=1S/C21H27N7O14P2/c22-17-12-19("
- "25-7-24-17)28(8-26-12)21-16(32)14(30)11("
- "41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15("
- "31)20(40-10)27-3-1-2-9(4-27)18("
- "23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,"
- "(H5-,22,23,24,25,33,34,35,36,37)/p-1/t10-,"
- "11-,13-,14-,15-,16-,20-,21-/m1/s1",
- "chebi": "CHEBI:57540",
+ "sbo": ["SBO:0000247"],
+ "inchi": [
+ "InChI=1S/C21H27N7O14P2/c22-17-12-19("
+ "25-7-24-17)28(8-26-12)21-16(32)14(30)11("
+ "41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15("
+ "31)20(40-10)27-3-1-2-9(4-27)18("
+ "23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,"
+ "(H5-,22,23,24,25,33,34,35,36,37)/p-1/t10-,"
+ "11-,13-,14-,15-,16-,20-,21-/m1/s1"
+ ],
+ "chebi": ["CHEBI:57540"],
},
"h_e": {
- "sbo": "SBO:0000247",
- "inchi": "InChI=1S/p+1/i/hH",
- "chebi": "CHEBI:24636",
+ "sbo": ["SBO:0000247"],
+ "inchi": ["InChI=1S/p+1/i/hH"],
+ "chebi": ["CHEBI:24636"],
},
"2obut_e": {
- "sbo": "SBO:0000247",
- "inchi": "InChI=1S/C4H6O3/c1-2-3(5)4(6)7/h2H2,1H3,(H,6,7)/p-1",
- "chebi": "CHEBI:16763",
+ "sbo": ["SBO:0000247"],
+ "inchi": ["InChI=1S/C4H6O3/c1-2-3(5)4(6)7/h2H2,1H3,(H,6,7)/p-1"],
+ "chebi": ["CHEBI:16763"],
},
"nadh_e": {
- "sbo": "SBO:0000247",
- "inchi": "InChI=1S/C21H29N7O14P2/c22-17-12-19("
- "25-7-24-17)28(8-26-12)21-16(32)14(30)11("
- "41-21)6-39-44(36,37)42-43(34,35)38-5-10-13("
- "29)15(31)20(40-10)27-3-1-2-9(4-27)18("
- "23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,"
- "5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,"
- "25)/p-2/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1",
- "chebi": "CHEBI:57945",
+ "sbo": ["SBO:0000247"],
+ "inchi": [
+ "InChI=1S/C21H29N7O14P2/c22-17-12-19("
+ "25-7-24-17)28(8-26-12)21-16(32)14(30)11("
+ "41-21)6-39-44(36,37)42-43(34,35)38-5-10-13("
+ "29)15(31)20(40-10)27-3-1-2-9(4-27)18("
+ "23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,"
+ "5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,"
+ "25)/p-2/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1"
+ ],
+ "chebi": ["CHEBI:57945"],
},
}
reaction_notes = {
@@ -689,8 +787,8 @@ def test_smbl_with_notes(data_directory: Path, tmp_path: Path) -> None:
"GENE_ASSOCIATION": "(HGNC:8546 and HGNC:8548) or (HGNC:8547 and HGNC:8548)",
}
reaction_annotations = {
- "sbo": "SBO:0000176",
- "ec-code": "1.1.1.27",
+ "sbo": ["SBO:0000176"],
+ "ec-code": ["1.1.1.27"],
"pubmed": ["10108", "21765"],
}
@@ -745,6 +843,16 @@ def test_stable_gprs(data_directory: Path, tmp_path: Path) -> None:
)
+def test_writing_xml_with_annotation(
+ compare_models: Callable, data_directory: Path, tmp_path: Path
+):
+ """Test consistency when reading and writing models to SBML."""
+ model = read_sbml_model(str(join(data_directory, "e_coli_core_for_annotation.xml")))
+ write_sbml_model(model, str(join(tmp_path, "e_coli_core_writing.xml")))
+ reread_model = read_sbml_model(str(join(tmp_path, "e_coli_core_writing.xml")))
+ compare_models(model, reread_model)
+
+
def test_history(data_directory: Path) -> None:
"""Test that the history is read from the model."""
mini = read_sbml_model(join(data_directory, "mini_history.xml"))
diff --git a/tests/test_manipulation/test_annotate.py b/tests/test_manipulation/test_annotate.py
index f1fa0d85e..c344d7255 100644
--- a/tests/test_manipulation/test_annotate.py
+++ b/tests/test_manipulation/test_annotate.py
@@ -7,7 +7,7 @@
def test_sbo_annotation(model: Model) -> None:
"""Test SBO annotation function."""
rxns = model.reactions
- rxns.EX_o2_e.annotation.clear()
+ rxns.get_by_id("EX_o2_e").annotation.sbo = ""
fake_DM = Reaction("DM_h_c")
model.add_reactions([fake_DM])
fake_DM.add_metabolites({model.metabolites.get_by_id("h_c"): -1})
@@ -15,6 +15,6 @@ def test_sbo_annotation(model: Model) -> None:
# an existing SBO annotation
rxns.get_by_id("EX_h_e").annotation["sbo"] = "SBO:0000628"
add_SBO(model)
- assert rxns.EX_o2_e.annotation["sbo"] == "SBO:0000627"
- assert rxns.DM_h_c.annotation["sbo"] == "SBO:0000628"
- assert rxns.EX_h_e.annotation["sbo"] == "SBO:0000628"
+ assert rxns.EX_o2_e.annotation["sbo"] == ["SBO:0000627"]
+ assert rxns.DM_h_c.annotation["sbo"] == ["SBO:0000628"]
+ assert rxns.EX_h_e.annotation["sbo"] == ["SBO:0000628"]
diff --git a/tests/test_manipulation/test_delete.py b/tests/test_manipulation/test_delete.py
index c745a1efb..d79f48527 100644
--- a/tests/test_manipulation/test_delete.py
+++ b/tests/test_manipulation/test_delete.py
@@ -110,7 +110,7 @@ def test_gene_knockout(salmonella: Model) -> None:
assert expected_reactions == knocked_out_reactions
with salmonella:
expected_reactions = [salmonella.reactions.get_by_id("4PEPTabcpp")]
- knocked_out_reactions = knock_out_model_genes(salmonella, ["STM1746.S"])
+ knocked_out_reactions = knock_out_model_genes(salmonella, ["STM1746_S"])
assert expected_reactions == knocked_out_reactions
knocked_out_reactions = knock_out_model_genes(salmonella, gene_list)
assert len(knocked_out_reactions) == 13
diff --git a/tox.ini b/tox.ini
index 4e930f57f..f188e369a 100644
--- a/tox.ini
+++ b/tox.ini
@@ -39,14 +39,14 @@ commands =
[testenv:isort]
skip_install = True
deps=
- isort ==6.0.1
+ isort >=5.13.2
commands=
isort --check-only --diff {toxinidir}/src/cobra {toxinidir}/setup.py {toxinidir}/tests
[testenv:black]
skip_install = True
deps=
- black ==25.1.0
+ black ==23.12.1
commands=
black --check --diff {toxinidir}/src/cobra {toxinidir}/setup.py {toxinidir}/tests
@@ -122,6 +122,7 @@ known_third_party =
ruamel.yaml
scipy
swiglpk
+ jsonschema
[flake8]
exclude =