bioregistry 0.13.13__tar.gz → 0.13.14__tar.gz

{bioregistry-0.13.13 → bioregistry-0.13.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioregistry
-Version: 0.13.13
+Version: 0.13.14
 Summary: Integrated registry of biological databases and nomenclatures
 Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases,persistent identifiers
 Author: Charles Tapley Hoyt

{bioregistry-0.13.13 → bioregistry-0.13.14}/pyproject.toml

@@ -10,7 +10,7 @@ markers = [
 
 [project]
 name = "bioregistry"
-version = "0.13.13"
+version = "0.13.14"
 description = "Integrated registry of biological databases and nomenclatures"
 readme = "README.md"
 authors = [
@@ -254,7 +254,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.13.13"
+current_version = "0.13.14"
 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-]+)*))?"
 serialize = [
     "{major}.{minor}.{patch}-{release}+{build}",

{bioregistry-0.13.13 → bioregistry-0.13.14}/src/bioregistry/data/bioregistry.json

@@ -1851,8 +1851,8 @@
       "name": "Allotrope Merged Ontology Suite",
       "prefix": "afo",
       "uri_format": "http://purl.allotrope.org/ontologies$1",
-      "version": "2025-06-01",
-      "version.iri": "http://purl.allotrope.org/voc/afo/merged/REC/2025/06/merged-without-qudt-and-inferred"
+      "version": "2025-12-01",
+      "version.iri": "http://purl.allotrope.org/voc/afo/merged/REC/2025/12/merged-without-qudt-and-inferred"
     },
     "ontobee": {
       "library": "Not Specified/No",
@@ -19775,7 +19775,7 @@
       "name": "Cell Ontology",
       "prefix": "CL",
       "repository": "https://github.com/obophenotype/cell-ontology",
-      "version": "2025-11-25"
+      "version": "2025-12-17"
     },
     "biocontext": {
       "prefix": "CL"
@@ -19948,8 +19948,8 @@
       "name": "Cell Ontology",
       "prefix": "cl",
       "tracker": "https://github.com/obophenotype/cell-ontology/issues",
-      "version": "2025-11-25",
-      "version.iri": "http://purl.obolibrary.org/obo/cl/releases/2025-11-25/cl.owl"
+      "version": "2025-12-17",
+      "version.iri": "http://purl.obolibrary.org/obo/cl/releases/2025-12-17/cl.owl"
     },
     "ontobee": {
       "library": "Library",
@@ -21022,7 +21022,7 @@
   "cmo": {
     "aberowl": {
       "description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.",
-      "download_owl": "http://aber-owl.net/media/ontologies/CMO/166/cmo.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/CMO/167/cmo.owl",
       "homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
       "name": "Clinical measurement ontology",
       "prefix": "CMO"
@@ -23572,7 +23572,7 @@
   "cob": {
     "aberowl": {
       "description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.",
-      "download_owl": "http://aber-owl.net/media/ontologies/COB/15/cob.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/COB/16/cob.owl",
       "homepage": "https://obofoundry.org/COB/",
       "name": "Core Ontology for Biology and Biomedicine",
       "prefix": "COB"
@@ -23624,8 +23624,8 @@
       "name": "Core Ontology for Biology and Biomedicine",
       "prefix": "cob",
       "tracker": "https://github.com/OBOFoundry/COB/issues",
-      "version": "2025-06-30",
-      "version.iri": "http://purl.obolibrary.org/obo/cob/releases/2025-06-30/cob.owl"
+      "version": "2025-12-12",
+      "version.iri": "http://purl.obolibrary.org/obo/cob/releases/2025-12-12/cob.owl"
     },
     "ontobee": {
       "library": "Library",
@@ -38505,14 +38505,14 @@
         "email": "efo-users@lists.sourceforge.net",
         "name": "EFO User List"
       },
-      "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. EFO is developed by the EMBL-EBI Samples, Phenotypes and Ontologies Team (SPOT). We also add terms for external users when requested.",
+      "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. EFO is developed by the EMBL-EBI Samples, Phenotypes and Ontologies Team (SPOT). We also add terms for external users when requested., and for projects such as the NHGRI-EBI GWAS catalog. It combines parts of several biological ontologies, Cell Ontology and the Monarch Disease Ontology (MONDO). The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for Open Targets.",
       "example_uri": "http://www.orpha.net/ORDO/Orphanet_1390",
       "homepage": "http://www.ebi.ac.uk/efo/",
       "license": "Apache 2.0 License",
       "name": "Experimental Factor Ontology",
       "prefix": "EFO",
       "repository": "https://github.com/EBISPOT/efo",
-      "version": "3.84.0"
+      "version": "3.85.0"
     },
     "biocontext": {
       "prefix": "EFO"
@@ -38637,14 +38637,14 @@
     },
     "ols": {
       "contact": "efo-users@lists.sourceforge.net",
-      "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for OpenTargets.org",
+      "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the NHGRI-EBI GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, Cell Ontology and the Monarch Disease Ontology (MONDO). The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for Open Targets.",
       "download_owl": "http://www.ebi.ac.uk/efo/efo.owl",
       "homepage": "http://www.ebi.ac.uk/efo",
       "name": "Experimental Factor Ontology",
       "prefix": "efo",
       "uri_format": "http://www.ebi.ac.uk/efo/EFO_$1",
-      "version": "3.84.0",
-      "version.iri": "http://www.ebi.ac.uk/efo/releases/v3.84.0/efo.owl"
+      "version": "3.85.0",
+      "version.iri": "http://www.ebi.ac.uk/efo/releases/v3.85.0/efo.owl"
     },
     "ontobee": {
       "library": "Not Specified/No",
@@ -44562,12 +44562,11 @@
   },
   "exmo": {
     "aberowl": {
-      "description": "A core reference ontology built upon BFO about exercise medicine. This ontology contains the related terms for healthy people, people with chronic conditions and people living with diability to exercise.",
-      "download_owl": "http://aber-owl.net/media/ontologies/EXMO/6/exmo.owl",
+      "description": "A core reference ontology built upon BFO about exercise medicine and it contains the related terms for healthy people, people with chronic conditions and people living with diability to exercise.",
+      "download_owl": "http://aber-owl.net/media/ontologies/EXMO/7/exmo.owl",
       "homepage": "https://github.com/Exercise-Medicine-Ontology/EXMO",
       "name": "Exercise Medicine Ontology",
-      "prefix": "EXMO",
-      "version": "2025-06-05"
+      "prefix": "EXMO"
     },
     "bioportal": {
       "contact": {
@@ -58721,7 +58720,7 @@
   "hgnc": {
     "aberowl": {
       "description": "Human Genome Organisation (HUGO) Gene Nomenclature Committee at the European Bioinformatics Institute approves a gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database.",
-      "download_owl": "http://aber-owl.net/media/ontologies/HGNC/6/hgnc.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/HGNC/7/hgnc.owl",
       "homepage": "http://www.genenames.org/",
       "name": "HUGO Gene Nomenclature",
       "prefix": "HGNC",
@@ -82547,7 +82546,7 @@
   "mmo": {
     "aberowl": {
       "description": "A representation of the variety of methods used to make clinical and phenotype measurements.",
-      "download_owl": "http://aber-owl.net/media/ontologies/MMO/117/mmo.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/MMO/118/mmo.owl",
       "homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000",
       "name": "Measurement method ontology",
       "prefix": "MMO"
@@ -82652,8 +82651,8 @@
       "name": "Measurement method ontology",
       "prefix": "mmo",
       "tracker": "https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues",
-      "version": "2.167",
-      "version.iri": "http://purl.obolibrary.org/obo/mmo/2.167/mmo.owl"
+      "version": "2.168",
+      "version.iri": "http://purl.obolibrary.org/obo/mmo/2.168/mmo.owl"
     },
     "ontobee": {
       "library": "Library",
@@ -85164,7 +85163,7 @@
   "ms": {
     "aberowl": {
       "description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.",
-      "download_owl": "http://aber-owl.net/media/ontologies/MS/227/ms.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/MS/228/ms.owl",
       "homepage": "http://www.psidev.info/groups/controlled-vocabularies",
       "name": "Mass spectrometry ontology",
       "prefix": "MS"
@@ -85257,8 +85256,8 @@
       "name": "Mass spectrometry ontology",
       "prefix": "ms",
       "tracker": "https://github.com/HUPO-PSI/psi-ms-CV/issues",
-      "version": "4.1.221",
-      "version.iri": "http://purl.obolibrary.org/obo/ms/4.1.221/ms.owl"
+      "version": "4.1.223",
+      "version.iri": "http://purl.obolibrary.org/obo/ms/4.1.223/ms.owl"
     },
     "ontobee": {
       "library": "Library",
@@ -88120,8 +88119,8 @@
       "prefix": "ncbitaxon",
       "tracker": "https://github.com/obophenotype/ncbitaxon/issues",
       "uri_format": "http://purl.obolibrary.org/obo/NCBITaxon_$1",
-      "version": "2025-09-11",
-      "version.iri": "http://purl.obolibrary.org/obo/ncbitaxon/2025-09-11/ncbitaxon.owl"
+      "version": "2025-12-03",
+      "version.iri": "http://purl.obolibrary.org/obo/ncbitaxon/2025-12-03/ncbitaxon.owl"
     },
     "ontobee": {
       "library": "Library",
@@ -102316,7 +102315,7 @@
   "peco": {
     "aberowl": {
       "description": "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.",
-      "download_owl": "http://aber-owl.net/media/ontologies/PECO/31/peco.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/PECO/32/peco.owl",
       "homepage": "http://planteome.org/",
       "name": "Plant Experimental Conditions Ontology",
       "prefix": "PECO"
@@ -102337,7 +102336,7 @@
         "https://doi.org/10.3732/ajb.1200222"
       ],
       "repository": "https://github.com/Planteome/plant-experimental-conditions-ontology",
-      "version": "July 2023"
+      "version": "December 2025"
     },
     "biocontext": {
       "prefix": "PECO"
@@ -110092,7 +110091,7 @@
         "email": "cooperl@oregonstate.edu",
         "name": "Laurel Cooper"
       },
-      "description": "The Plant Stress Ontology (PSO) describes biotic and abiotic stresses that a plant may encounter. An ontology containing biotic and abiotic plant stresses. Part of the Planteome suite of reference ontologies.",
+      "description": "The Plant Stress Ontology (PSO) describes biotic and abiotic stresses that a plant may encounter. An ontology containing biotic and abiotic plant stresses. Part of the Planteome suite of reference ontologies., An ontology describing biotic and abiotic plant stresses.",
       "example_uri": "http://purl.obolibrary.org/obo/PSO_0000013",
       "homepage": "https://planteome.org/",
       "license": "CC-BY-4.0",
@@ -110103,7 +110102,7 @@
         "https://planteome.org/references"
       ],
       "repository": "https://github.com/Planteome/plant-stress-ontology",
-      "version": "2023-11-14"
+      "version": "2025-12-16"
     },
     "bioportal": {
       "contact": {
@@ -110176,8 +110175,8 @@
       "name": "Plant Stress Ontology",
       "prefix": "pso",
       "tracker": "https://github.com/Planteome/plant-stress-ontology/issues",
-      "version": "2023-11-14",
-      "version.iri": "http://purl.obolibrary.org/obo/pso/releases/2023-11-14/pso.owl"
+      "version": "2025-12-16",
+      "version.iri": "http://purl.obolibrary.org/obo/pso/releases/2025-12-16/pso.owl"
     },
     "ontobee": {
       "library": "Library",
@@ -111388,8 +111387,8 @@
       "name": "Pathway ontology",
       "prefix": "pw",
       "tracker": "https://github.com/rat-genome-database/PW-Pathway-Ontology/issues",
-      "version": "7.95",
-      "version.iri": "http://purl.obolibrary.org/obo/pw/7.95/pw.owl"
+      "version": "7.96",
+      "version.iri": "http://purl.obolibrary.org/obo/pw/7.96/pw.owl"
     },
     "ontobee": {
       "library": "Library",
@@ -112111,7 +112110,7 @@
   "rbo": {
     "aberowl": {
       "description": "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.",
-      "download_owl": "http://aber-owl.net/media/ontologies/RBO/38/rbo.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/RBO/39/rbo.owl",
       "homepage": "https://github.com/Radiobiology-Informatics-Consortium/RBO",
       "name": "Radiation Biology Ontology",
       "prefix": "RBO"
@@ -112178,8 +112177,8 @@
       "name": "Radiation Biology Ontology",
       "prefix": "rbo",
       "tracker": "https://github.com/Radiobiology-Informatics-Consortium/RBO/issues",
-      "version": "2025-11-26",
-      "version.iri": "http://purl.obolibrary.org/obo/rbo/releases/2025-11-26/rbo.owl"
+      "version": "2025-12-11",
+      "version.iri": "http://purl.obolibrary.org/obo/rbo/releases/2025-12-11/rbo.owl"
     },
     "ontobee": {
       "library": "Library",
@@ -116353,7 +116352,7 @@
   "rs": {
     "aberowl": {
       "description": "Ontology of rat strains",
-      "download_owl": "http://aber-owl.net/media/ontologies/RS/202/rs.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/RS/203/rs.owl",
       "homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html",
       "name": "Rat Strain Ontology",
       "prefix": "RS"
@@ -122701,7 +122700,7 @@
   "slso": {
     "aberowl": {
       "description": "The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data.",
-      "download_owl": "http://aber-owl.net/media/ontologies/SLSO/12/slso.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/SLSO/13/slso.owl",
       "homepage": "https://github.com/nasa/LSDAO",
       "name": "Space Life Sciences Ontology",
       "prefix": "SLSO"
@@ -122753,8 +122752,8 @@
       "name": "Space Life Sciences Ontology",
       "prefix": "slso",
       "tracker": "https://github.com/nasa/LSDAO/issues",
-      "version": "2025-12-09",
-      "version.iri": "http://purl.obolibrary.org/obo/slso/releases/2025-12-09/slso.owl"
+      "version": "2025-12-11",
+      "version.iri": "http://purl.obolibrary.org/obo/slso/releases/2025-12-11/slso.owl"
     },
     "ontobee": {
       "library": "Library",
@@ -135699,7 +135698,8 @@
     "bartoc": {
       "abbreviation": "time",
       "description": "OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing the temporal properties of resources in the world or described in Web pages. The ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. Time positions and durations may be expressed using either the conventional (Gregorian) calendar and clock, or using another temporal reference system such as Unix-time, geologic time, or different calendars.",
-      "homepage": "http://www.w3.org/2006/time",
+      "homepage": "https://www.w3.org/TR/owl-time/",
+      "license": "CC-BY-4.0",
       "name": "Time Ontology",
       "prefix": "18311"
     },

{bioregistry-0.13.13 → bioregistry-0.13.14}/src/bioregistry/data/collections.json

@@ -1483,10 +1483,10 @@
     {
       "authors": [
         {
-          "email": "cthoyt@gmail.com",
-          "github": "cthoyt",
-          "name": "Charles Tapley Hoyt",
-          "orcid": "0000-0003-4423-4370"
+          "email": "damien@gerbi-gmb.de",
+          "github": "gouttegd",
+          "name": "Damien Goutte-Gattat",
+          "orcid": "0000-0002-6095-8718"
         }
       ],
       "description": "A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4BIOIMAGE",
@@ -1505,7 +1505,28 @@
         }
       ],
       "resources": [
-        "bioregistry"
+        "bioregistry",
+        "chebi",
+        "cl",
+        "clo",
+        "cmpo",
+        "dicom",
+        "doid",
+        "edam",
+        "efo",
+        "fbbi",
+        "go",
+        "mesh",
+        "mondo",
+        "mp",
+        "mpath",
+        "ncbitaxon",
+        "obi",
+        "radlex",
+        "snomedct",
+        "swo",
+        "uberon",
+        "uo"
       ]
     },
     {