[MISC] consolidate BIDS citations in introduction. fixes #525

Author: sappelhoff

src/01-introduction.md

@@ -19,11 +19,11 @@ standard you will benefit in the following ways:
     acquired by a graduate student or postdoc that has already left the lab.
 
 -   There are a growing number of data analysis software packages that can
-    understand data organised according to BIDS (see
-    [http://bids.neuroimaging.io](http://bids.neuroimaging.io) for the most up
-    to date list).
+    understand data organised according to BIDS (see the
+    [up to date list](https://bids.neuroimaging.io/benefits.html)).
 
--   Databases such as OpenNeuro.org accept datasets organised according to BIDS.
+-   Databases such as [OpenNeuro.org](https://openneuro.org/) accept datasets
+    organised according to BIDS.
     If you ever plan to share your data publicly (nowadays some journals require
     this) you can minimize the additional time and energy spent on publication,
     and speed up the curation process by using BIDS to structure and describe
@@ -32,9 +32,12 @@ standard you will benefit in the following ways:
 -   Validation tools such as the [BIDS Validator](https://github.com/bids-standard/bids-validator)
     can check your dataset integrity and help you easily spot missing values.
 
-BIDS is heavily inspired by the format used internally by OpenfMRI.org and has
-been supported by the International Neuroinformatics Coordinating Facility and
-the Neuroimaging Data Sharing Task Force. While working on BIDS we consulted
+BIDS was heavily inspired by the format used internally by the OpenfMRI repository
+that is now known as [OpenNeuro.org](https://openneuro.org/),
+and has been supported by the International Neuroinformatics Coordinating Facility
+([INCF](https://www.incf.org/))
+and the INCF Neuroimaging Data Sharing (NIDASH) Task Force.
+While working on BIDS we consulted
 many neuroscientists to make sure it covers most common experiments, but at the
 same time is intuitive and easy to adopt. The specification is intentionally
 based on simple file formats and folder structures to reflect current lab
@@ -50,19 +53,67 @@ Proposals (BEPs). For more information about the BEP process, see
 
 ## Citing BIDS
 
-When referring to BIDS in context of academic literature please cite:
+When referring to BIDS in context of academic literature, please cite one or
+more of the publications listed below.
+We RECOMMEND that you cite the original publication on BIDS and *additionally*
+the publication regarding the datatype you were using
+(e.g., EEG, MEG, iEEG, if available).
 
-> Gorgolewski, K.J., Auer, T., Calhoun, V.D., Craddock, R.C., Das, S., Duff,
-> E.P., Flandin, G., Ghosh, S.S., Glatard, T., Halchenko, Y.O., Handwerker,
-> D.A., Hanke, M., Keator, D., Li, X., Michael, Z., Maumet, C., Nichols, B.N.,
-> Nichols, T.E., Pellman, J., Poline, J.-B., Rokem, A., Schaefer, G., Sochat,
-> V., Triplett, W., Turner, J.A., Varoquaux, G., Poldrack, R.A., 2016.
-> [The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments](https://www.nature.com/articles/sdata201644).
-> Sci Data 3, 160044.
+For example:
 
-as well as other papers describing specific BIDS extensions (see below).
+> The data used in the study were organized using the
+> Brain Imaging Data Structure (Gorgolewski, K., Auer, T., Calhoun, V. et al., 2016)
+> with the extension for EEG data (Pernet, C.R., Appelhoff, S., Gorgolewski, K.J. et al., 2019).
+
+### original publication
+
+-   Gorgolewski, K.J., Auer, T., Calhoun, V.D., Craddock, R.C., Das, S., Duff,
+    E.P., Flandin, G., Ghosh, S.S., Glatard, T., Halchenko, Y.O., Handwerker,
+    D.A., Hanke, M., Keator, D., Li, X., Michael, Z., Maumet, C., Nichols, B.N.,
+    Nichols, T.E., Pellman, J., Poline, J.-B., Rokem, A., Schaefer, G., Sochat,
+    V., Triplett, W., Turner, J.A., Varoquaux, G., Poldrack, R.A. (2016).
+    **The brain imaging data structure,**
+    **a format for organizing and describing outputs of neuroimaging experiments**.
+    Scientific Data, 3 (160044).
+    [doi:10.1038/sdata.2016.44](https://doi.org/10.1038/sdata.2016.44)
+
+### datatype specific publications
+
+#### EEG
+
+-   Pernet, C. R., Appelhoff, S., Gorgolewski, K.J., Flandin, G., Phillips, C.,
+    Delorme, A., Oostenveld, R. (2019).
+    **EEG-BIDS, an extension to the brain imaging data structure for electroencephalography**. Scientific data, 6 (103).
+    [doi:10.1038/s41597-019-0104-8](https://doi.org/10.1038/s41597-019-0104-8)
+
+#### iEEG
+
+-   Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D'Ambrosio, S.,
+    David, O., Devinsky, O., Dichter, B., Flinker, A., Foster, B. L.,
+    Gorgolewski, K. J., Groen, I., Groppe, D., Gunduz, A., Hamilton, L.,
+    Honey, C. J., Jas, M., Knight, R., Lauchaux, J.-P., Lau, J. C.,
+    Lee-Messer, C., Lundstrom, B. N., Miller, K. J., Ojemann, J. G.,
+    Oostenveld, R., Petridou, N., Piantoni, G., Pigorini, A., Pouratian, N.,
+    Ramsey, N. F., Stolk, A., Swann, N. C., Tadel, F., Voytek, B., Wandell, B. A.,
+    Winawer, J., Whitaker, K., Zehl, L., Hermes, D. (2019).
+    **iEEG-BIDS, extending the Brain Imaging Data Structure specification to**
+    **human intracranial electrophysiology**.
+    Scientific data, 6 (102).
+    [doi:10.1038/s41597-019-0105-7](https://doi.org/10.1038/s41597-019-0105-7)
+
+#### MEG
+
+-   Niso Galan, J.G., Gorgolewski, K.J., Bock, E., Brooks, T.L., Flandin, G.,
+    Gramfort, A., Henson, R.N., Jas, M., Litvak, V., Moreau, J., Oostenveld, R.,
+    Schoffelen, J.-M., Tadel, F., Wexler, J., Baillet, S. (2018).
+    **MEG-BIDS, the brain imaging data structure extended to magnetoencephalography**.
+    Scientific Data, 5 (180110).
+    [doi:10.1038/sdata.2018.110](https://doi.org/10.1038/sdata.2018.110)
+
+### Research Resource Identifier (RRID)
 
 BIDS has also a
-[Research Resource Identifier (RRID)](https://www.force11.org/group/resource-identification-initiative)
--   `RRID:SCR_016124` - which you can also include in your manuscript in addition
-to citing the paper.
+[Research Resource Identifier (RRID)](https://www.force11.org/group/resource-identification-initiative),
+which you can also include in your citations in addition to relevant publications (see above):
+
+-   [`RRID:SCR_016124`](https://scicrunch.org/resources/Any/search?q=SCR_016124&l=SCR_016124)

src/04-modality-specific-files/02-magnetoencephalography.md

@@ -1,14 +1,10 @@
 # Magnetoencephalography
 
-Support for Magnetoencephalography (MEG) was developed as a [BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
-Please cite the following paper when referring to this part of the standard in
-context of the academic literature:
-
-> Niso Galan, J.G., Gorgolewski, K.J., Bock, E., Brooks, T.L., Flandin, G.,
-> Gramfort, A., Henson, R.N., Jas, M., Litvak, V., Moreau, J., Oostenveld, R.,
-> Schoffelen, J.-M., Tadel, F., Wexler, J., Baillet, S. (2018). **MEG-BIDS, the
-> brain imaging data structure extended to magnetoencephalography**. Scientific
-> data, 5. doi: [10.1038/sdata.2018.110](https://doi.org/10.1038/sdata.2018.110)
+Support for Magnetoencephalography (MEG) was developed as a
+[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
+Please see [Citing BIDS](../01-introduction.md#citing-bids)
+on how to appropriately credit this extension when referring to it in the
+context of the academic literature.
 
 ## MEG recording data
 

src/04-modality-specific-files/03-electroencephalography.md

@@ -1,13 +1,10 @@
 # Electroencephalography
 
-Support for Electroencephalography (EEG) was developed as a [BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
-Please cite the following paper when referring to this part of the standard in
-context of the academic literature:
-
-> Pernet, C. R., Appelhoff, S., Gorgolewski, K.J., Flandin, G., Phillips, C.,
-> Delorme, A., Oostenveld, R. (2019). **EEG-BIDS, an extension to the brain
-> imaging data structure for electroencephalography**. Scientific data, 6.
-> doi: [10.1038/s41597-019-0104-8](https://doi.org/10.1038/s41597-019-0104-8)
+Support for Electroencephalography (EEG) was developed as a
+[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
+Please see [Citing BIDS](../01-introduction.md#citing-bids)
+on how to appropriately credit this extension when referring to it in the
+context of the academic literature.
 
 The following example EEG datasets have been formatted using this specification
 and can be used for practical guidance when curating a new dataset.

src/04-modality-specific-files/04-intracranial-electroencephalography.md

@@ -1,19 +1,10 @@
 # Intracranial Electroencephalography
 
-Support for Intracranial Electroencephalography (iEEG) was developed as a [BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
-Please cite the following paper when referring to this part of the standard in
-context of the academic literature:
-
-> Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D'Ambrosio, S.,
-> David, O., Devinsky, O., Dichter, B., Flinker, A., Foster, B. L.,
-> Gorgolewski, K. J., Groen, I., Groppe, D., Gunduz, A., Hamilton, L.,
-> Honey, C. J., Jas, M., Knight, R., Lauchaux, J.-P., Lau, J. C.,
-> Lee-Messer, C., Lundstrom, B. N., Miller, K. J., Ojemann, J. G.,
-> Oostenveld, R., Petridou, N., Piantoni, G., Pigorini, A., Pouratian, N.,
-> Ramsey, N. F., Stolk, A., Swann, N. C., Tadel, F., Voytek, B., Wandell, B. A.,
-> Winawer, J., Whitaker, K., Zehl, L., Hermes, D. (2019). **iEEG-BIDS,
-> extending the Brain Imaging Data Structure specification to human intracranial
-> electrophysiology**. Scientific data, 6. doi: [10.1038/s41597-019-0105-7](https://doi.org/10.1038/s41597-019-0105-7)
+Support Intracranial Electroencephalography (iEEG) was developed as a
+[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
+Please see [Citing BIDS](../01-introduction.md#citing-bids)
+on how to appropriately credit this extension when referring to it in the
+context of the academic literature.
 
 ## iEEG recording data
 

src/04-modality-specific-files/08-genetic-descriptor.md

@@ -1,9 +1,10 @@
 # Genetic Descriptor
 
-Support for genetic descriptors was developed as a [BIDS Extension
-Proposal](../07-extensions.md#bids-extension-proposals).
-The extension was primarily developed by Cyril Pernet and Clara Moreau with
-contributions from Tom Nichols and Jessica Turner.
+Support genetic descriptors was developed as a
+[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
+Please see [Citing BIDS](../01-introduction.md#citing-bids)
+on how to appropriately credit this extension when referring to it in the
+context of the academic literature.
 
 Genetic data are typically stored in dedicated repositories,
 separate from imaging data.