Merge branch 'main' into ingest-bioportal-purls

.github/workflows/update.yml

@@ -2,7 +2,7 @@ name: Update Data
 on:
   workflow_dispatch:
   schedule:
-    - cron: "0 0 * * *"
+    - cron: "0 0 * * SAT"
 jobs:
   build:
     runs-on: ubuntu-latest

README.md

@@ -46,7 +46,7 @@ https://bioregistry.io.
 The underlying data of the Bioregistry can be downloaded (or edited) directly
 from [here](https://github.com/biopragmatics/bioregistry/blob/main/src/bioregistry/data/).
 Several exports to YAML, TSV, and RDF, including consensus views over the
-registry, are built on a nightly basis and can be downloaded via the
+registry, are built on a weekly basis and can be downloaded via the
 [`exports/`](https://github.com/biopragmatics/bioregistry/tree/main/exports) directory.
 
 The manually curated portions of these data are available under the
@@ -71,7 +71,7 @@ file either through the GitHub interface or locally by [forking the repository](
 
 If you want to make a contribution but don't know where to start, you can check
 [this list](https://biopragmatics.github.io/bioregistry/curation/) of curation
-To-Do's that's automatically generated daily, including more detailed
+To-Do's that's automatically generated weekly, including more detailed
 information on how to contribute.
 
 ## ⚖️ Governance

docs/GOVERNANCE.md

@@ -18,7 +18,7 @@ on https://github.com/biopragmatics/bioregistry/issues/156.
   merging prefixes, splitting prefixes, or updating a prefix's associated
   metadata) must be done either in the form of an issue or a pull request.
 - The only updates that aren't considered manual are the ones done by the CI
-  system on a nightly basis.
+  system on a chronological basis.
 - Manual updates can be accepted if all continuous integration tests pass and a
   member of the Bioregistry Review Team approves. It's best practice that a
   member of the Review Team does not approve their own updates.

docs/source/deployment.rst

@@ -1,7 +1,9 @@
 Deploying the Bioregistry
 =========================
 The Bioregistry web application is a part of the ``bioregistry`` Python package which is updated,
-packaged, and pushed nightly to the `Python Package Index (PyPI) <https://pypi.org/project/bioregistry/>`_.
+packaged, and pushed weekly to the `Python Package Index (PyPI) <https://pypi.org/project/bioregistry/>`_.
+A new deploy can also be triggered by admins using the
+`update workflow <https://github.com/biopragmatics/bioregistry/actions/workflows/update.yml>`_ on GitHub.
 It can be installed and run interactively in the command line with the following commands:
 
 .. code-block:: shell
@@ -20,7 +22,7 @@ It can be installed and run interactively in the command line with the following
     should correspond to the location through which the service is accessed. In this
     example, https://example.com is used as the base.
 
-The Bioregistry is also containerized and pushed nightly to
+The Bioregistry is also containerized and pushed during the weekly build to
 `Docker Hub <https://hub.docker.com/r/biopragmatics/bioregistry>`_.
 You can pull then run the latest in the command line with the following commands:
 

exports/README.md

@@ -9,7 +9,7 @@ the Bioregistry's registry through the derived files below.
 ## Derived
 
 This folder contains the exports derived from the Bioregistry source files for
-the registry, metaregistry, and collections. They are re-generated on a nightly
+the registry, metaregistry, and collections. They are re-generated on a weekly
 basis using GitHub Actions as a continuous integration server.
 
 | Directory                      | Format                                                                                           |

src/bioregistry/app/templates/meta/summary.html

@@ -42,7 +42,7 @@ <h2>What is the Bioregistry?</h2>
         </dd>
         <dt class="col-lg-2 text-right text-nowrap">Automated</dt>
         <dd class="col-lg-10">
-            Continuous integration is used to automatically update the database nightly and align with other
+            Continuous integration is used to automatically update the database weekly and align with other
             registries. It suggests new curations to help maintain the community's semantic health.
         </dd>
         <dt class="col-lg-2 text-right text-nowrap">Extensible</dt>

src/bioregistry/app/templates/meta/sustainability.html

@@ -68,7 +68,7 @@ <h3>Hardware</h3>
     </dl>
     <h3>Containerization</h3>
     <p>
-        A Docker image is automatically built nightly following the
+        A Docker image is automatically built weekly following the
         <a href="https://github.com/biopragmatics/bioregistry/actions/workflows/update.yml">update workflow</a>
         on GitHub Actions and pushed to the <a href="https://hub.docker.com/r/biopragmatics/bioregistry"><i class="fab fa-docker"></i>
         biopragmatics/bioregistry</a> DockerHub repository. This image is built with the Python 3.9 alpine base image,

src/bioregistry/data/README.md

@@ -24,7 +24,7 @@ burden and enables the Bioregistry to benefit from upstream changes in external
 registries.
 
 Several exports to YAML, TSV, and RDF, including consensus views over the
-registry, are built on a nightly basis and can be downloaded via the
+registry, are built on a weekly basis and can be downloaded via the
 [`exports/`](https://github.com/biopragmatics/bioregistry/tree/main/exports)
 directory.
 

src/bioregistry/data/bioregistry.json

@@ -2910,6 +2910,11 @@
     "biocontext": {
       "prefix": "APD"
     },
+    "contact": {
+      "email": "[email protected]",
+      "name": "Guangshun Wang",
+      "orcid": "0000-0002-4841-7927"
+    },
     "fairsharing": {
       "abbreviation": "APD",
       "description": "The Antimicrobial Peptide Database (APD) contains information on antimicrobial peptides from across a wide taxonomic range. It includes a glossary, nomenclature, classification, information search, prediction, design, and statistics of AMPs. The antimicrobial peptides in this database contain less than 100 amino acid residues, are in the mature and active form, and primarily from natural sources, ranging from bacteria, fungi, plants, to animals.",
@@ -10003,6 +10008,11 @@
     "biocontext": {
       "prefix": "BRENDA"
     },
+    "contact": {
+      "email": "[email protected]",
+      "name": "Dietmar Schomburg",
+      "orcid": "0000-0002-3354-822X"
+    },
     "fairsharing": {
       "abbreviation": "BRENDA",
       "description": "BRENDA is the main collection of enzyme functional data available to the scientific community.",