Skip to content

Commit c87379a

Browse files
anitacarongithub-actions[bot]
anitacaron
authored and
github-actions[bot]
committed
Update dashboard run
1 parent 3c3b1ca commit c87379a

16 files changed

+693
-0
lines changed

‎dashboard/about.html‎

Lines changed: 72 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,72 @@
1+
<!DOCTYPE html>
2+
<html>
3+
<head>
4+
<title>About the </title>
5+
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
6+
<style>
7+
body {
8+
margin: 2em;
9+
}
10+
11+
.tooltip-inner {
12+
max-width: 280px;
13+
}
14+
15+
.check {
16+
text-align: center;
17+
}
18+
19+
.fixedHeader {
20+
position: sticky;
21+
top: 0;
22+
background-color: white;
23+
}
24+
25+
th {
26+
max-width: 4em;
27+
height: 5em;
28+
}
29+
30+
th a {
31+
display: block;
32+
transform: rotate(-45deg);
33+
margin: 0.2em;
34+
}
35+
</style>
36+
</head>
37+
<body>
38+
<h1>OBO Dashboard</h1>
39+
<p><strong>The OBO Dashboard is a new feature under active development.</strong></p>
40+
<p>The OBO Dashboard is being developed by the OBO Operations Committee and members of the Technical Working Group. Our goal is to provide a set of automated tests that establish a minimum level of compliance with OBO Principles and best practises. Keep in mind that automated checks often cannot capture the full intent of a given principle &ndash; we do our best while keeping the automated checks as fast and cheap as possible.</p>
41+
<p>For each ontology, two aspects are checked: the OBO Registry entry, and the latest release of the project&rsquo;s main OWL file. For each check we provide links to the rule text and implementation.</p>
42+
<p><strong>Please give us your feedback!</strong></p>
43+
<p><a href="https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1076">This issue</a> is for general comments, with links to the specific issue for each check.</p>
44+
<hr>
45+
<h2>Limitations</h2>
46+
<p>This is an alpha version of an automated representation of the OBO Foundry principles. Many of the principles contain a subjective aspect, making the checks difficult to implement. These checks are still in review and subject to change.</p>
47+
<p><strong>The result of the OBO Foundry Dashboard is not a reflection of the quality of content of an ontology.</strong> </p>
48+
<p>It is simply a means to alert ontology developers to areas that may need review.</p>
49+
<hr>
50+
<h2>Reading the Dashboard</h2>
51+
<p>The dashboard page contains a table with all results from all OBO Foundry ontologies. These results are sorted in the same order that the ontologies appear on the OBO Foundry homepage: foundry ontologies, active ontologies, orphaned, and finally obsolete ontologies.</p>
52+
<p>Each column after the ontology ID represents one dashboard check. There are four levels of results for each column:</p>
53+
<ol>
54+
<li>Pass - green check</li>
55+
<li>Info - blue <em>i</em></li>
56+
<li>Warning - yellow exclamation point</li>
57+
<li>Error - red <strong>x</strong></li>
58+
</ol>
59+
<p>For details on what constitutes a pass versus an error for each check, click on the column header.</p>
60+
<p>The last column contains a summary of the dashboard check. This column corresponds to the lowest result of all checks. For example, if there are any errors, this column will contain a red <strong>x</strong>. Likewise, if there are any infos, but no errors or warnings, this column will contain a blue <em>i</em>.</p>
61+
<p>Finally, you can download the report summary as a YAML file from the link near the top of the page.</p>
62+
<hr>
63+
<h2>Reading Individual Results</h2>
64+
<p>To view more details on an ontology&rsquo;s results, click on the ontology ID in the first column.</p>
65+
<p>From the dashboard report page, you can see the version IRI that the dashboard was run on (for all OWL file checks) and the date it was run. Some checks include reports, which you can view under the <strong>Resources</strong> column. Each individual report page includes a link to download those reports as TSV files.</p>
66+
<h4>Reading ROBOT Reports</h4>
67+
<p><a href="http://robot.obolibrary.org/report">ROBOT report</a> runs a series of standard queries over the OWL file. More details on these queries can be <a href="http://robot.obolibrary.org/report_queries/">found here</a>. Like the dashboard checks, report has three levels of violations (passing results are not shown in the table): info, warning, and error.</p>
68+
<p>Each row contains the violation level, the rule name (corresponding to a query), the subject of the violation, the property of the violation, and the value of the violation. For specific details on what the rule checks and how to fix it, click on the rule name.</p>
69+
<hr>
70+
<hr/>
71+
</body>
72+
</html>

‎dashboard/analysis.html‎

Lines changed: 270 additions & 0 deletions
Large diffs are not rendered by default.

‎dashboard/assets/check.svg‎

Lines changed: 3 additions & 0 deletions
Loading

‎dashboard/assets/info.svg‎

Lines changed: 4 additions & 0 deletions
Loading

‎dashboard/assets/warning.svg‎

Lines changed: 3 additions & 0 deletions
Loading

‎dashboard/assets/x.svg‎

Lines changed: 3 additions & 0 deletions
Loading

‎dashboard/dashboard-results.json‎

Lines changed: 92 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,92 @@
1+
{
2+
"ontologies": [
3+
{
4+
"base_generated": true,
5+
"base_prefixes": [
6+
"OMO",
7+
"OMOALT",
8+
"OMO"
9+
],
10+
"changed": true,
11+
"failure": "failed_ontology_dashboard",
12+
"last_ontology_dashboard_run_failed": true,
13+
"metrics": {
14+
"Axioms: Breakdown of axiom types": {
15+
"AnnotationAssertion": 523,
16+
"AnnotationPropertyRangeOf": 1,
17+
"ClassAssertion": 19,
18+
"Declaration": 125,
19+
"DifferentIndividuals": 2,
20+
"EquivalentClasses": 3,
21+
"SubAnnotationPropertyOf": 18,
22+
"SubClassOf": 26
23+
},
24+
"Axioms: Number of axioms": 717,
25+
"Entities: % of entities reused": 85.61,
26+
"Entities: Number of annotation properties": 82,
27+
"Entities: Number of classes": 27,
28+
"Entities: Number of data properties": 0,
29+
"Entities: Number of individuals": 20,
30+
"Entities: Number of object properties": 0,
31+
"Entities: Number of unsatisfiable classes": 0,
32+
"Info: Breakdown of OWL class expressions used": {
33+
"Class": 101,
34+
"ObjectOneOf": 3
35+
},
36+
"Info: Does the ontology fall under OWL 2 DL?": true,
37+
"Info: Experimental OBO score": {
38+
"_impact": 0.0,
39+
"_impact_external": 0.25,
40+
"_reuse": 0.856
41+
},
42+
"Info: How many externally documented uses?": 1,
43+
"Info: How many ontologies use it?": 0,
44+
"Info: Logical consistency": true,
45+
"Info: Syntax": "RDF/XML Syntax",
46+
"Info: Usage of namespaces in axioms": {
47+
"IAO": 555,
48+
"OMO": 36,
49+
"dc": 35,
50+
"dc11": 29,
51+
"oboInOwl": 27,
52+
"owl": 1,
53+
"prefix_unknown": 1,
54+
"rdfs": 123,
55+
"xsd": 1
56+
},
57+
"Info: Which ontologies use it?": []
58+
},
59+
"mirror_from": "http://purl.obolibrary.org/obo/omo.owl",
60+
"namespace": "omo",
61+
"sha256_hash": "779c51183f570ef260bf8c2048d567be95bfa605f0427c5d06451f6abef06071"
62+
}
63+
],
64+
"oboscore": {
65+
"dashboard_score_weights": {
66+
"no_base": 5,
67+
"overall_error": 5,
68+
"overall_warning": 0.5,
69+
"overall_info": 0.1,
70+
"report_errors": 0.05,
71+
"report_warning": 0.01,
72+
"report_info": 0.005,
73+
"dashboard": 1,
74+
"impact": 1,
75+
"reuse": 1,
76+
"impact_external": 3
77+
},
78+
"dashboard_score_max_impact": {
79+
"no_base": 5,
80+
"overall_error": 20,
81+
"overall_warning": 10,
82+
"overall_info": 5,
83+
"report_errors": 10,
84+
"report_warning": 5,
85+
"report_info": 3,
86+
"dashboard": 1,
87+
"impact": 1,
88+
"reuse": 1,
89+
"impact_external": 3
90+
}
91+
}
92+
}

‎dashboard/dashboard-results.yml‎

Lines changed: 78 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,78 @@
1+
oboscore:
2+
dashboard_score_max_impact:
3+
dashboard: 1
4+
impact: 1
5+
impact_external: 3
6+
no_base: 5
7+
overall_error: 20
8+
overall_info: 5
9+
overall_warning: 10
10+
report_errors: 10
11+
report_info: 3
12+
report_warning: 5
13+
reuse: 1
14+
dashboard_score_weights:
15+
dashboard: 1
16+
impact: 1
17+
impact_external: 3
18+
no_base: 5
19+
overall_error: 5
20+
overall_info: 0.1
21+
overall_warning: 0.5
22+
report_errors: 0.05
23+
report_info: 0.005
24+
report_warning: 0.01
25+
reuse: 1
26+
ontologies:
27+
- base_generated: true
28+
base_prefixes:
29+
- OMO
30+
- OMOALT
31+
- OMO
32+
changed: true
33+
failure: failed_ontology_dashboard
34+
last_ontology_dashboard_run_failed: true
35+
metrics:
36+
'Axioms: Breakdown of axiom types':
37+
AnnotationAssertion: 523
38+
AnnotationPropertyRangeOf: 1
39+
ClassAssertion: 19
40+
Declaration: 125
41+
DifferentIndividuals: 2
42+
EquivalentClasses: 3
43+
SubAnnotationPropertyOf: 18
44+
SubClassOf: 26
45+
'Axioms: Number of axioms': 717
46+
'Entities: % of entities reused': 85.61
47+
'Entities: Number of annotation properties': 82
48+
'Entities: Number of classes': 27
49+
'Entities: Number of data properties': 0
50+
'Entities: Number of individuals': 20
51+
'Entities: Number of object properties': 0
52+
'Entities: Number of unsatisfiable classes': 0
53+
'Info: Breakdown of OWL class expressions used':
54+
Class: 101
55+
ObjectOneOf: 3
56+
'Info: Does the ontology fall under OWL 2 DL?': true
57+
'Info: Experimental OBO score':
58+
_impact: 0.0
59+
_impact_external: 0.25
60+
_reuse: 0.856
61+
'Info: How many externally documented uses?': 1
62+
'Info: How many ontologies use it?': 0
63+
'Info: Logical consistency': true
64+
'Info: Syntax': RDF/XML Syntax
65+
'Info: Usage of namespaces in axioms':
66+
IAO: 555
67+
OMO: 36
68+
dc: 35
69+
dc11: 29
70+
oboInOwl: 27
71+
owl: 1
72+
prefix_unknown: 1
73+
rdfs: 123
74+
xsd: 1
75+
'Info: Which ontologies use it?': []
76+
mirror_from: http://purl.obolibrary.org/obo/omo.owl
77+
namespace: omo
78+
sha256_hash: 779c51183f570ef260bf8c2048d567be95bfa605f0427c5d06451f6abef06071

‎dashboard/index.html‎

Lines changed: 112 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,112 @@
1+
<head>
2+
<title>OBO Dashboard (2025-08-01)</title>
3+
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/css/bootstrap.min.css" integrity="sha384-Vkoo8x4CGsO3+Hhxv8T/Q5PaXtkKtu6ug5TOeNV6gBiFeWPGFN9MuhOf23Q9Ifjh" crossorigin="anonymous">
4+
<style>
5+
body {
6+
margin: 2em;
7+
}
8+
9+
.tooltip-inner {
10+
max-width: 280px;
11+
}
12+
13+
.check {
14+
text-align: center;
15+
}
16+
17+
th {
18+
max-width: 4em;
19+
height: 5em;
20+
position: sticky;
21+
top: 0;
22+
background-color: white;
23+
}
24+
25+
th a {
26+
display: block;
27+
transform: rotate(-66deg);
28+
margin: 0.2em;
29+
}
30+
</style>
31+
<script src="https://code.jquery.com/jquery-3.4.1.slim.min.js" integrity="sha384-J6qa4849blE2+poT4WnyKhv5vZF5SrPo0iEjwBvKU7imGFAV0wwj1yYfoRSJoZ+n" crossorigin="anonymous"></script>
32+
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/umd/popper.min.js" integrity="sha384-Q6E9RHvbIyZFJoft+2mJbHaEWldlvI9IOYy5n3zV9zzTtmI3UksdQRVvoxMfooAo" crossorigin="anonymous"></script>
33+
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/js/bootstrap.min.js" integrity="sha384-wfSDF2E50Y2D1uUdj0O3uMBJnjuUD4Ih7YwaYd1iqfktj0Uod8GCExl3Og8ifwB6" crossorigin="anonymous"></script>
34+
<script>
35+
$(function () {
36+
$('[data-toggle="tooltip"]').tooltip()
37+
})
38+
</script>
39+
</head>
40+
<body>
41+
<h1>OBO Dashboard (2025-08-01)</h1>
42+
<h4>Dashboard for checking ontology quality. Under construction. <a href="about.html">Learn More!</a></h4>
43+
<p>Created with <a href="http://robot.obolibrary.org/">ROBOT version 1.9.8</a> and <a href="https://github.com/OBOFoundry/OBO-Dashboard/commit/d58e5376ebec3cc910c2986296d4283b3b6ba911">OBO Metadata Schema</a>.</p>
44+
<p>A very basic analysis of the results can be found <a href="analysis.html">here</a>.</p>
45+
<table class="table table-borderless">
46+
<thead>
47+
<tr>
48+
<th>Ontology<br/>(click for details)</th>
49+
<th>
50+
<a href="http://obofoundry.org/principles/fp-001-open.html">Open</a>
51+
</th>
52+
<th>
53+
<a href="http://obofoundry.org/principles/fp-002-format.html">Format</a>
54+
</th>
55+
<th>
56+
<a href="http://obofoundry.org/principles/fp-003-uris.html">URIs</a>
57+
</th>
58+
<th>
59+
<a href="http://obofoundry.org/principles/fp-004-versioning.html">Versioning</a>
60+
</th>
61+
<th>
62+
<a href="http://obofoundry.org/principles/fp-005-delineated-content.html">Scope</a>
63+
</th>
64+
<th>
65+
<a href="http://obofoundry.org/principles/fp-006-textual-definitions.html">Definitions</a>
66+
</th>
67+
<th>
68+
<a href="http://obofoundry.org/principles/fp-007-relations.html">Relations</a>
69+
</th>
70+
<th>
71+
<a href="http://obofoundry.org/principles/fp-008-documented.html">Documented</a>
72+
</th>
73+
<th>
74+
<a href="http://obofoundry.org/principles/fp-009-users.html">Users</a>
75+
</th>
76+
<th>
77+
<a href="http://obofoundry.org/principles/fp-011-locus-of-authority.html">Authority</a>
78+
</th>
79+
<th>
80+
<a href="http://obofoundry.org/principles/fp-012-naming-conventions.html">Naming</a>
81+
</th>
82+
<th>
83+
<a href="http://obofoundry.org/principles/fp-016-maintenance.html">Maintained</a>
84+
</th>
85+
<th>
86+
<a href="http://obofoundry.org/principles/fp-020-responsiveness.html">Responsiveness</a>
87+
</th>
88+
<th>
89+
<a href="http://robot.obolibrary.org/report">ROBOT Report</a>
90+
</th>
91+
<th>
92+
Summary
93+
</th>
94+
</tr>
95+
</thead>
96+
<tbody class="scrollContent">
97+
98+
<tr>
99+
<td><b><a href="omo/dashboard.html">omo</a></b></td>
100+
101+
<td class="table-notchecked" colspan="13">Failed to process ontology: failed_ontology_dashboard</td>
102+
103+
104+
105+
106+
<td class="check table-danger"><img src="assets/x.svg" height="15px"></td>
107+
108+
</tr>
109+
110+
</tbody>
111+
</table>
112+
</body>

‎dashboard/omo/dashboard-qc-badge.json‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
{"schemaVersion": 1, "label": "QC", "message": "Processing error: build dashboard", "color": "red", "logoSvg": "<svg id=\"Layer_1\" data-name=\"Layer 1\" xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"0 0 135.54 133.3\"><defs><style>.cls-1{fill:#fff;}.cls-2{fill:#231f20;}</style></defs><path class=\"cls-1\" d=\"M85.31,20.58l-4-16.64s0,0,0,0c-1.11-.14-2.21-.26-3.33-.35s-2.24-.15-3.36-.18-2.26,0-3.4,0c-.82,0-1.66.06-2.49.11L63.21,19.66c-.22,0-.43.11-.65.15l0,.11c-1.58.3-3.13.68-4.65,1.12s-3,1-4.45,1.53L40.52,11.64c-.58.32-1.17.63-1.74,1-1,.56-1.91,1.14-2.83,1.74s-1.84,1.23-2.73,1.88-1.77,1.31-2.63,2l-.73.6L34.72,35c-.15.16-.28.33-.42.48v0c-1.12,1.18-2.17,2.42-3.17,3.7s-1.95,2.59-2.84,4h-.06v0l-16.83-1c-.31.62-.62,1.23-.91,1.85-.46,1-.88,2-1.29,3.07-.28.69-.53,1.39-.79,2.09-.12.35-.26.7-.38,1.05-.36,1-.69,2.1-1,3.17-.1.33-.17.68-.26,1l13.4,10.13a54.29,54.29,0,0,0-.56,10.73L5.25,84.54c.09.52.16,1,.26,1.55.21,1.08.44,2.16.7,3.23s.54,2.14.85,3.2.65,2.12,1,3.16c.14.42.31.82.46,1.24h0L25.22,97l0,0h.13a51.6,51.6,0,0,0,5.88,9L24.87,122c.61.59,1.21,1.18,1.83,1.74.85.76,1.71,1.49,2.59,2.2S31.06,127.35,32,128s1.62,1.14,2.45,1.69l13.68-9.92c.14.07.3.12.43.19l.1-.07c1.22.59,2.47,1.11,3.73,1.59a19.94,19.94,0,0,1,9.28-28.87A22.89,22.89,0,0,1,72.29,49.46a23.11,23.11,0,0,1,6,.82,19.92,19.92,0,0,1,11.53-27.8l.16-.42A47.65,47.65,0,0,0,85.31,20.58Z\"/><path class=\"cls-2\" d=\"M43.71,37.89V34.77c0-2.89,1.57-4,4.09-4s4.09,1.07,4.09,4v3.12c0,3-1.2,4.17-4.09,4.17S43.71,40.86,43.71,37.89Zm6.4,0V34.77c0-2-.84-2.37-2.31-2.37s-2.32.39-2.32,2.37v3.12c0,2,.73,2.62,2.32,2.62S50.11,39.87,50.11,37.89Z\"/><path class=\"cls-2\" d=\"M60.46,41.87l-.22-1.44a2.71,2.71,0,0,1-2.71,1.5c-2.19,0-3.7-1-3.7-3.94V35.11c0-3,1.4-4.24,3.7-4.24a3,3,0,0,1,2.63.95V27.27H62v14.6Zm-2.54-9.28c-1.59,0-2.31.63-2.31,2.56V38c0,1.79.72,2.26,2.18,2.26s2.37-.71,2.37-2.86V35.05C60.16,33.19,59.51,32.59,57.92,32.59Z\"/><path class=\"cls-2\" d=\"M67,37h-.8v4.85H64.42V27.45H66.2v7.88h.71L70.29,31h2.17l-4,5.13,4.37,5.79H70.7Z\"/><path class=\"cls-1\" d=\"M126.8,64.76a4.35,4.35,0,0,0-3.28,1.52l-6.24-3A8.16,8.16,0,0,0,115.15,55l3.73-5.15a2.7,2.7,0,0,0,.63.07A2.93,2.93,0,1,0,116.58,47a2.87,2.87,0,0,0,.42,1.48l-3.74,5.15a8.21,8.21,0,0,0-12,7.27,7.59,7.59,0,0,0,.11,1.27L84.84,67.27a13.6,13.6,0,0,0-3.38-4.87l10.7-13.85a8.12,8.12,0,0,0,4,1.07,8.24,8.24,0,1,0-5.89-2.5L79.61,61a13.54,13.54,0,1,0-9.5,24.75l-1.3,17.14a8.21,8.21,0,0,0,.55,16.4l.49,0,1.38,6.7a2.3,2.3,0,1,0,2.29-.46l-1.38-6.7a8.21,8.21,0,0,0-1-15.74l1.3-17.13a13.5,13.5,0,0,0,6.26-1.6l8.18,12.51A8.2,8.2,0,0,0,90.48,111L90,116.62a4.39,4.39,0,1,0,2.33.2l.47-5.66A8.21,8.21,0,0,0,99.49,107l7.1,2.71a2.32,2.32,0,1,0,.84-2.18l-7.11-2.71a8.2,8.2,0,0,0-11.48-9.24L80.65,83a13.74,13.74,0,0,0,3.81-4.71L99.14,84a8,8,0,0,0-.22,1.84,8.22,8.22,0,1,0,1-4L85.3,76.12a13.36,13.36,0,0,0,.23-6.62L102,64.42a8.21,8.21,0,0,0,14.27,1l6.24,3a4.41,4.41,0,0,0-.08.73,4.36,4.36,0,1,0,4.36-4.36Z\"/></svg>"}

0 commit comments

Comments
 (0)