[FIX] Update links that threw warning in CI (#1620)

* fix some links * fix more links * fix moe links * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add line break * format * Apply suggestions from code review Co-authored-by: Chris Markiewicz <[email protected]> * fix a few more 'bare' links --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Chris Markiewicz <[email protected]>
bids-standard · Sep 29, 2023 · f9cfafa · f9cfafa
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diff --git a/mkdocs.yml b/mkdocs.yml
@@ -42,7 +42,7 @@ nav:
         - Cross modality correspondence: appendices/cross-modality-correspondence.md
       - Changelog: CHANGES.md
     - The BIDS Starter Kit:
-      - Website: https://bids-standard.github.io/bids-starter-kit
+      - Website: https://bids-standard.github.io/bids-starter-kit/
       - Tutorials: https://bids-standard.github.io/bids-starter-kit/tutorials/tutorials.html
       - GitHub repository: https://github.com/bids-standard/bids-starter-kit
 theme:

diff --git a/src/appendices/coordinate-systems.md b/src/appendices/coordinate-systems.md
diff --git a/src/appendices/hed.md b/src/appendices/hed.md
@@ -14,7 +14,7 @@ Individual terms are comma-separated and may be grouped using parentheses to ind
 association.
 See [https://www.hedtags.org/display_hed.html](https://www.hedtags.org/display_hed.html)
 to view the HED schema and the
-[HED resources](https://www.hed-resources.org) site for additional information.
+[HED resources](https://www.hed-resources.org/en/latest/) site for additional information.
 
 Starting with HED version 8.0.0, HED allows users to annotate using individual
 terms or partial paths in the HED vocabulary (for example `Red` or `Visual-presentation`)

diff --git a/src/appendices/meg-file-formats.md b/src/appendices/meg-file-formats.md
@@ -57,8 +57,8 @@ A guide for using macros can be found at
    }
 ) }}
 
-To learn more about CTF’s data organization:
-[https://www.fieldtriptoolbox.org/getting_started/ctf](https://www.fieldtriptoolbox.org/getting_started/ctf)
+To learn more about CTF’s data organization
+on the relevant [FieldTrip webpage](https://www.fieldtriptoolbox.org/getting_started/ctf/)
 
 ## Neuromag/Elekta/MEGIN
 
@@ -235,8 +235,8 @@ A guide for using macros can be found at
 
 More information can be found under the following links:
 
--   [Neuromag/Elekta/MEGIN data organization](https://www.fieldtriptoolbox.org/getting_started/neuromag)
--   [BabyMEG](https://www.fieldtriptoolbox.org/getting_started/babysquid)
+-   [Neuromag/Elekta/MEGIN data organization](https://www.fieldtriptoolbox.org/getting_started/neuromag/)
+-   [BabyMEG](https://www.fieldtriptoolbox.org/getting_started/babysquid/)
 
 ### Recording dates in `.fif` files
 
@@ -301,8 +301,8 @@ A guide for using macros can be found at
    }
 ) }}
 
-More about the 4D neuroimaging/BTi data organization at:
-[https://www.fieldtriptoolbox.org/getting_started/bti](https://www.fieldtriptoolbox.org/getting_started/bti)
+More about the 4D neuroimaging/BTi data organization
+on the relevant [FieldTrip webpage](https://www.fieldtriptoolbox.org/getting_started/bti/)
 
 ## KIT/Yokogawa/Ricoh
 
@@ -355,8 +355,8 @@ While the acquisition entity can take any value, it is RECOMMENDED that if
 the two marker measurements occur before and after the raw data acquisition,
 `pre` and `post` are used to differentiate the two situations.
 
-More about the KIT/Yokogawa/Ricoh data organization at:
-[https://www.fieldtriptoolbox.org/getting_started/yokogawa](https://www.fieldtriptoolbox.org/getting_started/yokogawa/)
+More about the KIT/Yokogawa/Ricoh data organization
+on the relevant [FieldTrip webpage](https://www.fieldtriptoolbox.org/getting_started/yokogawa/)
 
 ## KRISS
 

diff --git a/src/introduction.md b/src/introduction.md
@@ -175,7 +175,7 @@ For example:
 ### Research Resource Identifier (RRID)
 
 BIDS has also a
-[Research Resource Identifier (RRID)](https://www.force11.org/group/resource-identification-initiative),
+[Research Resource Identifier (RRID)](https://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)
+-   [`RRID:SCR_016124`](https://scicrunch.org/resources/data/record/nlx_144509-1/SCR_016124/resolver?q=SCR_016124)
diff --git a/src/modality-specific-files/electroencephalography.md b/src/modality-specific-files/electroencephalography.md
@@ -33,7 +33,7 @@ stored in one of the following formats:
 | ------------------------------------------------- | ------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | [European data format](https://www.edfplus.info/) | `.edf`                   | Each recording consists of a single `.edf` file. [`edf+`](https://www.edfplus.info/specs/edfplus.html) files are permitted. The capital `.EDF` extension MUST NOT be used.                           |
 | [BrainVision Core Data Format][bvformat]          | `.vhdr`, `.vmrk`, `.eeg` | Each recording consists of a  `.vhdr`, `.vmrk`, `.eeg` file triplet.                                                                                                                                 |
-| [EEGLAB](https://sccn.ucsd.edu/eeglab)            | `.set`, `.fdt`           | The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab). Each recording consists of a `.set` file with an OPTIONAL `.fdt` file.                                                 |
+| [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php)  | `.set`, `.fdt`           | The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php). Each recording consists of a `.set` file with an OPTIONAL `.fdt` file.                                       |
 | [Biosemi](https://www.biosemi.com/)               | `.bdf`                   | Each recording consists of a single `.bdf` file. [`bdf+`](https://www.teuniz.net/edfbrowser/bdfplus%20format%20description.html) files are permitted. The capital `.BDF` extension MUST NOT be used. |
 
 It is RECOMMENDED to use the European data format, or the BrainVision data
@@ -359,10 +359,10 @@ triangulate the position of other LED-lit electrodes on a research subject's
 head.
 
 -   For more information on the definition of anatomical landmarks, please visit:
-    [https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined)
+    [How are the Left and Right Pre-Auricular (LPA and RPA) points defined? - FieldTrip Toolbox](https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined/)
 
 -   For more information on coordinate systems for coregistration, please visit:
-    [https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined)
+    [How are the different head and MRI coordinate systems defined? - FieldTrip Toolbox](https://www.fieldtriptoolbox.org/faq/coordsys/)
 
 General fields:
 

diff --git a/src/modality-specific-files/intracranial-electroencephalography.md b/src/modality-specific-files/intracranial-electroencephalography.md
@@ -29,13 +29,13 @@ The iEEG community uses a variety of formats for storing raw data, and there is
 no single standard that all researchers agree on. For BIDS, iEEG data MUST be
 stored in one of the following formats:
 
-| **Format**                                                     | **Extension(s)**         | **Description**                                                                                                                                                            |
-| -------------------------------------------------------------- | ------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| [European data format](https://www.edfplus.info/)              | `.edf`                   | Each recording consists of a `.edf` single file. [`edf+`](https://www.edfplus.info/specs/edfplus.html) files are permitted. The capital `.EDF` extension MUST NOT be used. |
-| [BrainVision Core Data Format][bvformat]                       | `.vhdr`, `.vmrk`, `.eeg` | Each recording consists of a  `.vhdr`, `.vmrk`, `.eeg` file triplet.                                                                                                       |
-| [EEGLAB](https://sccn.ucsd.edu/eeglab)                         | `.set`, `.fdt`           | The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab). Each recording consists of a `.set` file with an OPTIONAL `.fdt` file.                       |
-| [Neurodata Without Borders](https://nwb-schema.readthedocs.io) | `.nwb`                   | Each recording consists of a single `.nwb` file.                                                                                                                           |
-| [MEF3](https://osf.io/e3sf9/)                                  | `.mefd`                  | Each recording consists of a `.mefd` directory.                                                                                                                            |
+| **Format**                                                                | **Extension(s)**         | **Description**                                                                                                                                                            |
+| ------------------------------------------------------------------------- | ------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| [European data format](https://www.edfplus.info/)                         | `.edf`                   | Each recording consists of a `.edf` single file. [`edf+`](https://www.edfplus.info/specs/edfplus.html) files are permitted. The capital `.EDF` extension MUST NOT be used. |
+| [BrainVision Core Data Format][bvformat]                                  | `.vhdr`, `.vmrk`, `.eeg` | Each recording consists of a  `.vhdr`, `.vmrk`, `.eeg` file triplet.                                                                                                       |
+| [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php)                          | `.set`, `.fdt`           | The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php). Each recording consists of a `.set` file with an OPTIONAL `.fdt` file.             |
+| [Neurodata Without Borders](https://nwb-schema.readthedocs.io/en/latest/) | `.nwb`                   | Each recording consists of a single `.nwb` file.                                                                                                                           |
+| [MEF3](https://osf.io/e3sf9/)                                             | `.mefd`                  | Each recording consists of a `.mefd` directory.                                                                                                                            |
 
 It is RECOMMENDED to use the European data format, or the BrainVision data
 format. It is furthermore discouraged to use the other accepted formats over

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -9,7 +9,7 @@ MRI acquisition parameters are divided into several categories based on
 ([article](https://doi.org/10.15200/winn.143191.17127)) by Ben Inglis.
 
 When adding additional metadata please use the CamelCase version of
-[DICOM ontology terms](https://scicrunch.org/scicrunch/interlex/dashboard)
+[DICOM ontology terms](https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_d.html)
 whenever possible. See also
 [recommendations on JSON files](../common-principles.md#keyvalue-files-dictionaries).
 

diff --git a/src/modality-specific-files/magnetoencephalography.md b/src/modality-specific-files/magnetoencephalography.md
@@ -408,12 +408,12 @@ A guide for using macros can be found at
 {{ MACROS___make_sidecar_table("meg.MEGCoordsystemFiducialsInformation") }}
 
 For more information on the definition of anatomical landmarks, please visit:
-[https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined)
+    [How are the Left and Right Pre-Auricular (LPA and RPA) points defined? - FieldTrip Toolbox](https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined/)
 
 For more information on typical coordinate systems for MEG-MRI coregistration:
-[https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined),
+    [How are the different head and MRI coordinate systems defined? - FieldTrip Toolbox](https://www.fieldtriptoolbox.org/faq/coordsys/)
 or:
-[https://neuroimage.usc.edu/brainstorm/CoordinateSystems](https://neuroimage.usc.edu/brainstorm/CoordinateSystems)
+[Coordinate Systems - Brainstorm toolbox](https://neuroimage.usc.edu/brainstorm/CoordinateSystems)
 
 ## Landmark photos (`*_photo.<extension>`)
 

diff --git a/src/modality-specific-files/microscopy.md b/src/modality-specific-files/microscopy.md
@@ -434,7 +434,7 @@ sub-02 mus musculus C57BL/6J RRID:IMSR_JAX:000664
         "Description": "name of the strain of the species"
     },
     "strain_rrid": {
-        "Description": "research resource identifier (RRID) of the strain (https://scicrunch.org/resources/Organisms/search)"
+        "Description": "research resource identifier (RRID) of the strain (https://scicrunch.org/resources/data/source/nlx_154697-1/search)"
     }
 }
 ```

diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
@@ -568,7 +568,7 @@ strain_rrid:
   display_name: Strain RRID
   description: |
     For species different from `homo sapiens`, research resource identifier
-    ([RRID](https://scicrunch.org/resources/Organisms/search))
+    ([RRID](https://scicrunch.org/resources/data/source/nlx_154697-1/search))
     of the strain of the species, for example: `RRID:IMSR_JAX:000664`.
   type: string
   format: rrid

diff --git a/src/schema/objects/extensions.yaml b/src/schema/objects/extensions.yaml
@@ -100,9 +100,9 @@ fdt:
   value: .fdt
   display_name: EEGLAB FDT
   description: |
-    An [EEGLAB](https://sccn.ucsd.edu/eeglab) file.
+    An [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php) file.
 
-    The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab).
+    The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php).
     Each recording consists of a `.set` file with an optional `.fdt` file.
 fif:
   value: .fif
@@ -175,8 +175,10 @@ OMEZARR:
   description: |
     An OME-NGFF file.
 
-    OME-NGFF is a [Zarr](https://zarr.readthedocs.io)-based format, organizing data arrays in nested directories.
-    This format was developed by the Open Microscopy Environment to provide data stream access to very large data.
+    OME-NGFF is a [Zarr](https://zarr.readthedocs.io/en/stable/)-based format,
+    organizing data arrays in nested directories.
+    This format was developed by the Open Microscopy Environment
+    to provide data stream access to very large data.
 nii:
   value: .nii
   display_name: NIfTI
@@ -191,7 +193,7 @@ nwb:
   value: .nwb
   display_name: Neurodata Without Borders Format
   description: |
-    A [Neurodata Without Borders](https://nwb-schema.readthedocs.io) file.
+    A [Neurodata Without Borders](https://nwb-schema.readthedocs.io/en/latest/) file.
 
     Each recording consists of a single `.nwb` file.
 OMEBigTiff:
@@ -233,9 +235,9 @@ set:
   value: .set
   display_name: EEGLAB SET
   description: |
-    An [EEGLAB](https://sccn.ucsd.edu/eeglab) file.
+    An [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php) file.
 
-    The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab).
+    The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php).
     Each recording consists of a `.set` file with an optional `.fdt` file.
 snirf:
   value: .snirf

diff --git a/src/schema/objects/files.yaml b/src/schema/objects/files.yaml
@@ -9,8 +9,8 @@ CHANGES:
     Version history of the dataset (describing changes, updates and corrections) MAY be provided in
     the form of a `CHANGES` text file.
     This file MUST follow the
-    [CPAN Changelog convention](https://metacpan.org/pod/release/HAARG/CPAN-Changes-0.400002/lib/\
-    CPAN/Changes/Spec.pod).
+    [CPAN Changelog convention](https://metacpan.org/release/HAARG/CPAN-Changes-0.400002/view\
+    /lib/CPAN/Changes/Spec.pod).
     The `CHANGES` file MUST be either in ASCII or UTF-8 encoding.
 CITATION:
   display_name: CITATION.cff