Merge branch 'main' into import-more-pc

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.64-dev
+current_version = 0.10.9-dev
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P<build>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?

.github/workflows/tests.yml

@@ -60,6 +60,7 @@ jobs:
       matrix:
         os: [ ubuntu-latest, windows-latest ]
         python-version: [ "3.11", "3.8" ]
+        pydantic: [ "pydantic1", "pydantic2" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -72,7 +73,7 @@ jobs:
           pip install tox
       - name: Test with pytest
         run:
-          tox -e py
+          tox -e py-${{ matrix.pydantic }}
       - name: Doctests
         run:
           tox -e doctests

docs/_data/curation.yml

@@ -65,9 +65,6 @@ example:
 - homepage: http://neuinfo.org/
   name: NIF Gross Anatomy
   prefix: nif.grossanatomy
-- homepage: http://www.obofoundry.org/
-  name: Open Biological and Biomedical Ontologies
-  prefix: obo
 - homepage: http://www.plantontology.org
   name: Plant Anatomy Ontology
   prefix: pao
@@ -312,9 +309,6 @@ formatter:
 - homepage: https://taxonomy.nucc.org
   name: National Uniform Claim Committee Taxonomy
   prefix: nucc.taxonomy
-- homepage: http://www.obofoundry.org/
-  name: Open Biological and Biomedical Ontologies
-  prefix: obo
 - homepage: https://pactr.samrc.ac.za/
   name: Pan African Clinical Trials Registry
   prefix: pactr
@@ -836,6 +830,9 @@ pattern:
 - homepage: https://www.hivreagentprogram.org/
   name: NIH HIV Reagent Program
   prefix: hivreagentprogram
+- homepage: https://www.hoelzel-biotech.com
+  name: "H\xF6lzel Diagnostika"
+  prefix: hoelzel
 - homepage: https://horizondiscovery.com/
   name: Horizon Discovery cell line collection
   prefix: horizon_discovery
@@ -999,6 +996,9 @@ pattern:
 - homepage: https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/
   name: NCBI Registry
   prefix: ncbi.resource
+- homepage: https://www.cancer.gov/publications/dictionaries/cancer-drug
+  name: NCI Drug Dictionary ID
+  prefix: nci.drug
 - homepage: https://www.ndexbio.org
   name: Network Data Exchange
   prefix: ndex
@@ -1020,6 +1020,9 @@ pattern:
 - homepage: https://stemcells.nindsgenetics.org
   name: NINDS Human Cell and Data Repository
   prefix: nhcdr
+- homepage: http://chemdb.niaid.nih.gov
+  name: NIAID ChemDB ID
+  prefix: niaid.chemdb
 - homepage: http://neuinfo.org/
   name: NIF Cell
   prefix: nif.cell
@@ -1651,6 +1654,9 @@ wikidata:
 - homepage: http://autism.mindspec.org/autdb/
   name: AutDB
   prefix: autdb
+- homepage: https://monarch-initiative.github.io/babelon/
+  name: Babelon
+  prefix: babelon
 - homepage: http://bacmap.wishartlab.com/
   name: BacMap Biography
   prefix: bacmap.biog
@@ -2724,7 +2730,7 @@ wikidata:
   name: E-cyanobacterium rule
   prefix: ecyano.rule
 - homepage: http://edamontology.org
-  name: Bioinformatics operations, data types, formats, identifiers and topics
+  name: EDAM Ontology
   prefix: edam
 - homepage: http://edamontology.org
   name: EDAM Data
@@ -2741,9 +2747,6 @@ wikidata:
 - homepage: https://bioportal.bioontology.org/ontologies/EDDA
   name: EDDA Study Designs Taxonomy
   prefix: edda
-- homepage: http://www.ebi.ac.uk/efo
-  name: Experimental Factor Ontology
-  prefix: efo
 - homepage: https://ega-archive.org/
   name: European Genome-phenome Archive Dataset
   prefix: ega.dataset
@@ -3441,6 +3444,9 @@ wikidata:
 - homepage: https://lincs.hms.harvard.edu/db/datasets/
   name: HMS Library of Integrated Network-based Cellular Signatures Datasets
   prefix: hms.lincs.dataset
+- homepage: https://www.hoelzel-biotech.com
+  name: "H\xF6lzel Diagnostika"
+  prefix: hoelzel
 - homepage: https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships
   name: Homologous Organ Groups
   prefix: hog
@@ -5821,9 +5827,6 @@ wikidata:
 - homepage: https://github.com/infectious-disease-ontology-extensions/ido-virus
   name: The Virus Infectious Disease Ontology
   prefix: vido
-- homepage: null
-  name: ViolinNet
-  prefix: violinnet
 - homepage: http://viperdb.scripps.edu/
   name: VIPERdb
   prefix: viperdb