bioregistry 0.13.8__py3-none-any.whl → 0.13.10__py3-none-any.whl

bioregistry/data/collections.json

@@ -977,6 +977,7 @@
         "digitalconstruction.energy",
         "dogont",
         "energymarketroles",
+        "meno",
         "oeo",
         "openadr",
         "saref.ener",
@@ -1073,7 +1074,7 @@
         "sosa",
         "ssn",
         "ssn.system",
-        "sweetrealm",
+        "sweet",
         "swo",
         "t4fs",
         "tib.bk",
@@ -1177,6 +1178,11 @@
           "github": "cthoyt",
           "name": "Charles Tapley Hoyt",
           "orcid": "0000-0003-4423-4370"
+        },
+        {
+          "github": "epoz",
+          "name": "Etienne Posthumus",
+          "orcid": "0000-0002-0006-7542"
         }
       ],
       "description": "Prefixes for ontologies relevant for NFDI4Culture.",
@@ -1186,9 +1192,26 @@
         "bot",
         "cidoc.crm",
         "gesah",
+        "iconclass",
         "nfdi4culture.cto",
         "premis"
       ]
+    },
+    {
+      "authors": [
+        {
+          "email": "cthoyt@gmail.com",
+          "github": "cthoyt",
+          "name": "Charles Tapley Hoyt",
+          "orcid": "0000-0003-4423-4370"
+        }
+      ],
+      "description": "Prefixes for ontologies relevant for DAPHNE4NFDI.",
+      "identifier": "0000026",
+      "name": "DAPHNE4NFDI Ontologies",
+      "resources": [
+        "emg"
+      ]
     }
   ]
 }

bioregistry/data/curated_papers.tsv

@@ -1,4 +1,8 @@
 pubmed	relevant	orcid	date_curated	relevancy_type	pr_added	notes
+30380085	1	0009-0009-3402-8013	2025-10-07	new_prefix	1714	Publication for dbamp
+31836719	1	0009-0009-3402-8013	2025-10-09	new_prefix	1724	Publication for nfportal.tool
+34850155	1	0009-0009-3402-8013	2025-10-07	new_publication	1714	Publication for dbamp 2.0
+38530613	1	0009-0009-3402-8013	2025-10-30	new_provider	1730	Publication for dotad
 38991828	0	0009-0009-5240-7463	2024-09-28	irrelevant_other	1193	
 38991851	1	0009-0009-5240-7463	2024-09-28	unclear	1193	identifiers for sharing, retrieving, and validating sample metadata. Unclear if this should be curated as a prefix, provider or a separate registry
 39005357	0	0009-0009-5240-7463	2024-10-05	irrelevant_other	1193	
@@ -94,6 +98,7 @@ pubmed	relevant	orcid	date_curated	relevancy_type	pr_added	notes
 39535044	1	0009-0009-5240-7463	2024-12-16	new_publication	1333	Publication for insdc
 39535054	1	0009-0009-5240-7463	2024-12-14	new_prefix	1330	Identifiers for clinical and pre-clinical biomarkers
 39535874	1	0009-0009-5240-7463	2024-12-05	not_notable	1296	This database website is very low quality and fails to resolve many of its own IDs
+39540425	1	0009-0009-3402-8013	2025-10-07	new_publication	1714	Publication for dbamp 3.0
 39540428	1	0009-0009-5240-7463	2024-12-14	new_publication	1329	Publication for pfam
 39540430	1	0009-0009-5240-7463	2024-12-10	new_prefix	1301	Identifiers for secondary metabolite biosynthetic gene clusters and sources
 39540736	0	0009-0009-5240-7463	2024-12-11	irrelevant_other	1305	
@@ -285,6 +290,7 @@ pubmed	relevant	orcid	date_curated	relevancy_type	pr_added	notes
 40337913	1	0009-0008-8406-631X	2025-06-16	new_provider	1596	
 40343712	1	0009-0008-8406-631X	2025-05-05	new_provider	1585	
 40355757	1	0009-0008-8406-631X	2025-05-05	new_provider	1584	
+40402563	1	0009-0009-3402-8013	2025-10-11	new_prefix	1727	Publication for aacdb
 40450118	0	0009-0000-6974-6386	2025-07-22	not_identifiers_resource	1623	
 40450355	0	0009-0000-6974-6386	2025-07-17	non_resource_paper	1623	
 40455150	0	0009-0000-6974-6386	2025-07-21	not_identifiers_resource	1623	
@@ -350,5 +356,8 @@ pubmed	relevant	orcid	date_curated	relevancy_type	pr_added	notes
 40574262	0	0009-0000-6974-6386	2025-07-16	not_identifiers_resource	1623	
 40575554	0	0009-0000-6974-6386	2025-07-22	not_identifiers_resource	1623	
 40578340	0	0009-0000-6974-6386	2025-07-21	not_identifiers_resource	1623	
+40716733	1	0009-0009-3402-8013	2025-10-07	new_prefix	1717	Publication for kdbirp
+40767478	1	0009-0009-3402-8013	2025-10-11	new_prefix	1720	Publication for funggrowth
 40779104	1	0009-0009-3402-8013	2025-09-24	new_provider	1709	Publication for cedar
+40811252	1	0009-0009-3402-8013	2025-09-30	new_provider	1710	Publication for abpdb
 40812678	1	0009-0009-3402-8013	2025-09-13	new_prefix	1700	Publication for tsrna

bioregistry/data/metaregistry.json

@@ -1448,7 +1448,7 @@
         "status": "active"
       },
       "homepage": "https://terminology.tib.eu",
-      "license": "https://github.com/TIBHannover/TIB-Terminology-Service-Frontend-2.0/issues/3",
+      "license": "CCO",
       "logo_url": "https://terminology.tib.eu/TIB_Logo_W_W.SVG",
       "name": "TIB Terminology Service",
       "prefix": "tib",

bioregistry/export/rdf_export.py

@@ -32,6 +32,7 @@ from ..constants import (
     SCHEMA_TURTLE_PATH,
 )
 from ..resource_manager import Manager, manager
+from ..schema import Collection, Registry, Resource
 from ..schema.constants import (
     ROR,
     WIKIDATA,
@@ -42,7 +43,6 @@ from ..schema.constants import (
     bioregistry_schema,
     get_schema_rdf,
 )
-from ..schema.struct import Collection, Registry, Resource
 
 logger = logging.getLogger(__name__)
 

bioregistry/export/tables_export.py

@@ -14,7 +14,7 @@ from ..constants import (
     TABLES_SUMMARY_LATEX_PATH,
 )
 from ..resolve import count_mappings
-from ..schema.struct import Registry
+from ..schema import Registry
 from ..schema_utils import read_metaregistry
 from ..summary import BioregistrySummary
 

bioregistry/external/aberowl/processed.json

@@ -221,6 +221,10 @@
     "prefix": "AI-RHEUM",
     "version": "2016AB"
   },
+  "AIDENTIFYAGE": {
+    "name": "AIdentifyAGE",
+    "prefix": "AIDENTIFYAGE"
+  },
   "AIDSCLIN": {
     "description": "This new ontology will cover the knowledge on AIDS and the relevant clinic activities, which imports the HIV ontology at the site https://bioportal.bioontology.org/ontologies/HIVO004 as its main or basic concept system. The new ontology is named AIDSClinic001.owl",
     "download_owl": "http://aber-owl.net/media/ontologies/AIDSCLIN/4/aidsclin.owl",
@@ -742,7 +746,7 @@
   },
   "BIOLINK": {
     "description": "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations",
-    "download_owl": "http://aber-owl.net/media/ontologies/BIOLINK/73/biolink.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/BIOLINK/74/biolink.owl",
     "homepage": "https://biolink.github.io/biolink-model/",
     "name": "Biolink Model",
     "prefix": "BIOLINK",
@@ -1372,7 +1376,7 @@
   },
   "CHEBI": {
     "description": "A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds.",
-    "download_owl": "http://aber-owl.net/media/ontologies/CHEBI/207/chebi.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/CHEBI/208/chebi.owl",
     "homepage": "http://www.ebi.ac.uk/chebi",
     "name": "Chemical Entities of Biological Interest",
     "prefix": "CHEBI"
@@ -1565,7 +1569,7 @@
   },
   "CMO": {
     "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/163/cmo.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/CMO/164/cmo.owl",
     "homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
     "name": "Clinical measurement ontology",
     "prefix": "CMO"
@@ -2374,7 +2378,7 @@
   },
   "DRON": {
     "description": "An ontology to support comparative effectiveness researchers studying claims data.",
-    "download_owl": "http://aber-owl.net/media/ontologies/DRON/32/dron.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/DRON/33/dron.owl",
     "homepage": "https://github.com/ufbmi/dron",
     "name": "The Drug Ontology",
     "prefix": "DRON"
@@ -4255,7 +4259,7 @@
     "description": "A collection of curated and standardized values used by the HuBMAP (Human BioMolecular Atlas Program) and SenNet (Cellular Senescence Network) metadata records to ensure uniformity in the description of samples and single-cell data produced by the consortium.",
     "name": "HuBMAP Research Attributes Value Set",
     "prefix": "HRAVS",
-    "version": "2.13.8"
+    "version": "2.13.10"
   },
   "HRDO": {
     "description": "This resource was designed during a PhD in medical informatics (funded by INSERM, 2010-2012). Its components are (i) a core ontology consistent with a metamodel (disorders and groups of disorders, genes, clinical signs and their relations) and (ii) an instantiation of this metamodel with Orphanet Data (available on http://orphadata.org). </ br> Research experiments demonstrated (i) efficient classifications generation based on SPARQL Construct, (ii) perspectives in semantic audit of a knowledge base, (iii) semantic comparison with OMIM (www.omim.org) using proximity measurements and (iv) opened perspectives in knowledge sharing (LORD, http://lord.bndmr.fr).  Current production services of Orphanet developed ORDO, released in 2014, an ontology synchronized with their production database. This ontology is now available on Bioportal.",
@@ -5802,11 +5806,11 @@
   },
   "METPO": {
     "description": "An ontology of ecophysiological traits of microbes, including tolerated and preferred growth conditions, Microbial ecophysiological trait and phenotype ontology",
-    "download_owl": "http://aber-owl.net/media/ontologies/METPO/15/metpo.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/METPO/16/metpo.owl",
     "homepage": "https://github.com/berkeleybop/metpo",
     "name": "METPO",
     "prefix": "METPO",
-    "version": "2025-11-17"
+    "version": "2025-11-21"
   },
   "MF": {
     "description": "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.",
@@ -5876,7 +5880,7 @@
   },
   "MI": {
     "description": "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.",
-    "download_owl": "http://aber-owl.net/media/ontologies/MI/133/mi.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/MI/134/mi.owl",
     "homepage": "https://github.com/HUPO-PSI/psi-mi-CV",
     "name": "Molecular Interactions Controlled Vocabulary",
     "prefix": "MI"
@@ -6062,7 +6066,7 @@
   },
   "MOD": {
     "description": "PSI-MOD is an ontology consisting of terms that describe protein chemical modifications",
-    "download_owl": "http://aber-owl.net/media/ontologies/MOD/122/mod.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/MOD/123/mod.owl",
     "homepage": "http://www.psidev.info/MOD",
     "name": "Protein modification",
     "prefix": "MOD"
@@ -6136,7 +6140,7 @@
   },
   "MP": {
     "description": "Standard terms for annotating mammalian phenotypic data.",
-    "download_owl": "http://aber-owl.net/media/ontologies/MP/133/mp.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/MP/134/mp.owl",
     "homepage": "https://www.informatics.jax.org/vocab/mp_ontology/",
     "name": "Mammalian Phenotype Ontology",
     "prefix": "MP"
@@ -6171,7 +6175,7 @@
   },
   "MS": {
     "description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.",
-    "download_owl": "http://aber-owl.net/media/ontologies/MS/225/ms.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/MS/226/ms.owl",
     "homepage": "http://www.psidev.info/groups/controlled-vocabularies",
     "name": "Mass spectrometry ontology",
     "prefix": "MS"
@@ -8909,7 +8913,7 @@
   },
   "RS": {
     "description": "Ontology of rat strains",
-    "download_owl": "http://aber-owl.net/media/ontologies/RS/201/rs.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/RS/202/rs.owl",
     "homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html",
     "name": "Rat Strain Ontology",
     "prefix": "RS"
@@ -10145,10 +10149,10 @@
   },
   "UCVA": {
     "description": "The Unwarranted Clinical Variation Analysis ontology (UCVA) is an application ontology that standardizes the representation of local context factors of UCV analysis. It includes numerous instances designed to support the extraction of these factors as covariates in UCV analysis, making it practical and easy to use",
-    "download_owl": "http://aber-owl.net/media/ontologies/UCVA/1/ucva.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/UCVA/2/ucva.owl",
     "name": "Unwarranted Clinical Variation Analysis With Contextual Factors",
     "prefix": "UCVA",
-    "version": "1.0"
+    "version": "1.1"
   },
   "UGANDAFACILITIES": {
     "description": "This is the list of health facilities registered under VODANA Project.",
@@ -10274,10 +10278,10 @@
   },
   "VFB_DRIVERS": {
     "description": "An ontology of Drosophila melanogaster drivers and expression patterns., An ontology of Drosophila melanogaster drivers and expression patterns. All genetic objects are created using data taken directly from FlyBase.",
-    "download_owl": "http://aber-owl.net/media/ontologies/VFB_DRIVERS/191/vfb_drivers.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/VFB_DRIVERS/192/vfb_drivers.owl",
     "name": "vfb_drivers",
     "prefix": "VFB_DRIVERS",
-    "version": "2025-11-17"
+    "version": "2025-11-24"
   },
   "VHO": {
     "description": "Ontology of terms used for annotating data in Virtual Fly Brain, including anatomical templates.",
@@ -10487,7 +10491,7 @@
   },
   "VT": {
     "description": "An ontology of traits covering vertebrates",
-    "download_owl": "http://aber-owl.net/media/ontologies/VT/138/vt.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/VT/139/vt.owl",
     "homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
     "name": "Vertebrate trait ontology",
     "prefix": "VT"
@@ -10655,7 +10659,7 @@
   },
   "XCO": {
     "description": "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.",
-    "download_owl": "http://aber-owl.net/media/ontologies/XCO/152/xco.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/XCO/153/xco.owl",
     "homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000",
     "name": "Experimental condition ontology",
     "prefix": "XCO"
@@ -10674,7 +10678,7 @@
   },
   "XLMOD": {
     "description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.",
-    "download_owl": "http://aber-owl.net/media/ontologies/XLMOD/3/xlmod.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/XLMOD/4/xlmod.owl",
     "homepage": "http://www.psidev.info/groups/controlled-vocabularies",
     "name": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary",
     "prefix": "XLMOD"

bioregistry/external/bartoc/processed.json

@@ -14131,7 +14131,7 @@
     "prefix": "2015"
   },
   "20150": {
-    "description": "It is a specialized encyclopedia for collecting Korean folklore, and is currently working on a compilation project by dividing the subject into eight major categories.\n\"The Korean Folklore Dictionary\", \"The Korean Folk Religion Dictionary\", \"The Korean Folk Literature Dictionary\", \"The Korean Folk Art Dictionary\", \"The Korean Living Dictionary\", \"The Korean Biological Dictionary\", and \"The Korean Folklore Social Dictionary\" are collectively called the Korean Dictionary.",
+    "description": "It is a specialized encyclopedia for collecting Korean folklore, and is currently working on a compilation project by dividing the subject into eight major categories.\n\"The Korean Folklore Dictionary\", \"The Korean Folk Religion Dictionary\", \"The Korean Folk Literature Dictionary\", \"The Korean Folk Art Dictionary\", \"The Korean Living Dictionary\", \"The Korean Biological Dictionary\", and \"The Korean Folklore Social Dictionary\" are collectively called the Korean Dictionary.\nIn addition, since 2021 we have been compiling the Encyclopedia of Korean Folk Symbols, a newly initiated project, and in 2024 we published a special edition of the Encyclopedia of Hallyu to commemorate the 20th anniversary of the compilation of the Encyclopedia of Korean Folk Culture.",
     "homepage": "https://folkency.nfm.go.kr/kr/main",
     "license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
     "name": "Encyclopedia of Korean Folk Culture",
@@ -15747,7 +15747,7 @@
   },
   "20375": {
     "description": "A list of genders.",
-    "homepage": "http://uri.gbv.de/terminology/gender/",
+    "homepage": "https://uri.gbv.de/terminology/gender/",
     "license": "CC0-1.0",
     "name": "Gender",
     "prefix": "20375"
@@ -16832,7 +16832,7 @@
   "20526": {
     "description": "The April Revolution Term Dictionary is a term dictionary provided by the April Revolution Web Dictionary, which was piloted by the Democratic Movement Memorial Society, and provides slogans, synonyms, and related words for the April Revolution. In addition, the April Revolution Web Dictionary provides information such as concepts and definitions, backgrounds and causes, the development of events, major events, historical significance, and the status of commemorative succession.",
     "homepage": "https://419.kdemo.or.kr/terms/419/",
-    "name": "April Revolution",
+    "name": "April Revolution Glossary",
     "prefix": "20526"
   },
   "20527": {
@@ -21451,7 +21451,7 @@
     "wikidata_database": "Q28934016"
   },
   "560": {
-    "description": "The eagle-i research resource ontology (ERO) models research resources such as instruments, protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/). Currently, ERO consists of over 2100 classes of which 1200 were created within the ERO namespace, while the rest come from existent ontologies such as the Ontology for Biomedical Investigation (OBI), the uber-anatomy ontology (Uberon), VIVO, the Ontology for Clinical Research (OCRe), the Sequence Ontology (SO), the Software Ontology (SWO) and we include terms from the NCBI Taxonomy as well.",
+    "description": "This ontology is deprecated!\"\n\n\"The eagle-i research resource ontology (ERO) models research resources such as instruments, protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/). Currently, ERO consists of over 2100 classes of which 1200 were created within the ERO namespace, while the rest come from existent ontologies such as the Ontology for Biomedical Investigation (OBI), the uber-anatomy ontology (Uberon), VIVO, the Ontology for Clinical Research (OCRe), the Sequence Ontology (SO), the Software Ontology (SWO) and we include terms from the NCBI Taxonomy as well.",
     "homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology",
     "name": "eagle-i Research Resource Ontology",
     "prefix": "560"
@@ -21565,7 +21565,6 @@
   },
   "580": {
     "description": "XeO has been created to help plant scientists in documenting and sharing metadata describing the abiotic environment.",
-    "homepage": "http://xeo.codeplex.com/",
     "name": "XEML Environment Ontology",
     "prefix": "580"
   },
@@ -21986,6 +21985,7 @@
   },
   "705": {
     "description": "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.",
+    "homepage": "https://code.google.com/p/vital-sign-ontology/",
     "name": "Vital Sign Ontology",
     "prefix": "705"
   },

bioregistry/external/biolink/processed.json

@@ -392,6 +392,9 @@
   "schema": {
     "uri_format": "http://schema.org/$1"
   },
+  "uspto-patent": {
+    "uri_format": "http://www.uspto.gov/patent/grant/v1/$1"
+  },
   "wgs": {
     "uri_format": "http://www.w3.org/2003/01/geo/wgs84_pos$1"
   }

bioregistry/external/bioportal/agroportal.json

@@ -564,7 +564,7 @@
     "name": "Cell Ontology",
     "prefix": "CL",
     "repository": "https://github.com/obophenotype/cell-ontology",
-    "version": "2025-11-03"
+    "version": "2025-11-25"
   },
   "CLC": {
     "contact": {
@@ -2616,13 +2616,13 @@
       "email": "beichen.wang@wur.nl",
       "name": "Beichen Wang"
     },
-    "description": "The soil health knowledge graph (SHKG) is designed to unify fragmented interpretations of soil health—a concept variably defined across research, policymaking, and agricultural practice—by structuring insights mainly from the European Environment Agency's report Soil Monitoring in Europe: Indicators and Thresholds for Soil Health Assessments. The KG leverages SKOS (Simple Knowledge Organization System) as its core framework to model soil health concepts, soil threat indicators and their critical thresholds, while Dublin Core standardizes metadata for references in the report. Relationships between entities are semantically defined using existing ontologies such as Agrontology and OBO Relation Ontology. The KG is linked to external vocabularies including AGROVOC, GloSIS, ISO 11074:2025, GEMET and INRAE Thesaurus. The SHKG comprises a total of 11,715 RDF triples. These triples describe 2,018 distinct entities. The majority of these entities (1,786) represent soil-related concepts extracted from the knowledge sources. The remaining entities include 158 bibliographic references cited in the source text, along with other supportive entities such as relevant policies, standards, regulations, geographical regions (e.g., cities, continents), and mathematical or quantitative entities (including models, equations, and units of measure). Structurally, the KG leverages 19 classes and 205 properties drawn from the selected ontologies to formally define the types of entities and the relationships between them.",
+    "description": "The soil health knowledge graph (SHKG) is designed to unify fragmented interpretations of soil health—a concept variably defined across research, policymaking, and agricultural practice—by structuring insights mainly from the European Environment Agency's report Soil Monitoring in Europe: Indicators and Thresholds for Soil Health Assessments. The KG leverages SKOS (Simple Knowledge Organization System) as its core framework to model soil health concepts, soil threat indicators and their critical thresholds, while Dublin Core standardizes metadata for references in the report. Relationships between entities are semantically defined using existing ontologies such as Agrontology and OBO Relation Ontology. The KG is linked to external vocabularies including AGROVOC, GloSIS, ISO 11074:2025, GEMET and INRAE Thesaurus. The SHKG comprises a total of 11,719 RDF triples. These triples describe 2,017 distinct entities. The majority of these entities (1,785) represent soil-related concepts extracted from the knowledge sources. The remaining entities include 158 bibliographic references cited in the source text, along with other supportive entities such as relevant policies, standards, regulations, geographical regions (e.g., cities, continents), and mathematical or quantitative entities (including models, equations, and units of measure). Structurally, the KG leverages 19 classes and 205 properties drawn from the selected ontologies to formally define the types of entities and the relationships between them.",
     "homepage": "https://soilwise-he.github.io/soil-health/",
     "license": "CC-BY-4.0",
     "name": "Soil Health Knowledge Graph",
     "prefix": "SHKG",
     "repository": "https://github.com/soilwise-he/soil-health-knowledge-graph",
-    "version": "v0.2.5"
+    "version": "v0.2.6"
   },
   "SIO": {
     "contact": {

bioregistry/external/bioportal/bioportal.json

@@ -60,6 +60,15 @@
     "prefix": "ACVD_ONTOLOGY",
     "version": "2.0"
   },
+  "AD-CDO": {
+    "contact": {
+      "email": "zenan.sun@uth.tmc.edu",
+      "name": "Zenan Sun"
+    },
+    "description": "The Alzheimer’s Disease Common Data Element Ontology for Clinical Trials (AD-CDO) is a semantically enriched, lightweight ontology designed to represent and standardize key eligibility criteria concepts in Alzheimer’s disease (AD) clinical trials. It bridges the gap between broad biomedical ontologies and the task-specific needs of trial modeling. AD-CDO was constructed by extracting high-frequency concepts from over 1,500 AD interventional trials registered on ClinicalTrials.gov. To balance coverage with manageability, the ontology utilizes the Jenks Natural Breaks method to identify the most representative concepts. The key feature of AD-CDO is its extensive mapping to standardized biomedical vocabularies to support data integration and phenotyping.",
+    "name": "Alzheimer's Disease Common Data Element Ontology for Clinical Trials",
+    "prefix": "AD-CDO"
+  },
   "AD-DROP": {
     "contact": {
       "email": "vincent643@gmail.com",
@@ -320,6 +329,17 @@
     ],
     "version": "AIR93"
   },
+  "AIDENTIFYAGE": {
+    "contact": {
+      "email": "cpereira@edu.ulisboa.pt",
+      "name": "Cristiana Palmela Pereira"
+    },
+    "description": "The AIdentifyAGE ontology provides a comprehensive vocabulary description for forensic age assessment using dental biological markers, promoting the transparent assessment processes in forensic odontology and age diagnostics. It formalizes expert knowledge according to IOFOS, AGFAD, ABFO, ADA and ISO standards, ensuring semantic interoperability and ethical AI integration. This ontology is a work in progress developed under the AIdentifyAGE project (FCT Grant 2024.07444.IACDC), within the national investment RE-C05-i08 – More Digital Science, measure RE-C05-i08.M04 – Support to R&D projects for advanced cybersecurity, artificial intelligence and data science systems in public administration. This work is being developed in collaboration with researchers from the University of Lisbon (Portugal), the University of Münster (Germany), and the University of Zagreb (Croatia), within the framework of the AIdentifyAGE international consortium., Base Ontology for use in AIdentifyAGE Project",
+    "license": "CC-BY-4.0",
+    "name": "AIdentifyAGE",
+    "prefix": "AIDENTIFYAGE",
+    "version": "v1.0.1-beta"
+  },
   "AIO": {
     "contact": {
       "email": "MJoachimiak@lbl.gov",
@@ -1850,7 +1870,7 @@
     "publications": [
       "https://www.ncbi.nlm.nih.gov/pubmed/27377652"
     ],
-    "version": "2025-11-03"
+    "version": "2025-11-25"
   },
   "CLAO": {
     "contact": {
@@ -2931,7 +2951,7 @@
     "publications": [
       "https://disease-ontology.org/community/publications"
     ],
-    "version": "2025-10-31"
+    "version": "2025-11-25"
   },
   "DOREMUS-KEYS": {
     "contact": {
@@ -3017,7 +3037,7 @@
     "license": "CC-BY-3.0",
     "name": "The Drug Ontology",
     "prefix": "DRON",
-    "version": "2025-07-19"
+    "version": "2025-11-20"
   },
   "DRPSNPTO": {
     "contact": {
@@ -3276,15 +3296,15 @@
       "email": "herve.menager@pasteur.fr",
       "name": "Hervé Ménager"
     },
-    "description": "EDAM is a domain ontology of data analysis and data management in bio- and other sciences, and science-based applications. It comprises concepts related to analysis, modelling, optimisation, and data life cycle. Targetting usability by diverse users, the structure of EDAM is relatively simple, divided into 4 main sections: Topic, Operation, Data (incl. Identifier), and Format. EDAM is particularly suitable for semantic annotations and categorisation of diverse resources related to data analysis and management: e.g. tools, workflows, learning materials, or standards. EDAM is also useful in data management itself, for recording provenance metadata of processed data. As a reference article (citation), please use https://doi.org/10.7490/f1000research.1118900.1, and Format.",
+    "description": "EDAM is a domain ontology of data analysis and data management in bio- and other sciences, and science-based applications. It comprises concepts related to analysis, modelling, optimisation, and data life cycle. Targetting usability by diverse users, the structure of EDAM is relatively simple, divided into 4 main sections: Topic, Operation, Data (incl. Identifier), and Format. EDAM is particularly suitable for semantic annotations and categorisation of diverse resources related to data analysis and management: e.g. tools, workflows, learning materials, or standards. EDAM is also useful in data management itself, for recording provenance metadata of processed data. As a reference citation, please use https://doi.org/10.7490/f1000research.1118900.1",
     "homepage": "http://edamontology.org",
     "license": "CC BY-SA 4.0",
-    "name": "EDAM - The data analysis and management ontology",
+    "name": "EDAM - The ontology of data analysis and management",
     "prefix": "EDAM",
     "publications": [
       "https://doi.org/10.7490/f1000research.1118900.1"
     ],
-    "version": "1.25-20251106T2339Z-unstable(1.26)"
+    "version": "1.25-20251112T1620Z-unstable(1.26)"
   },
   "EDAM-BIOIMAGING": {
     "contact": {
@@ -4504,12 +4524,12 @@
       "email": "mclarkson@uky.edu",
       "name": "Melissa Clarkson"
     },
-    "description": "For the best browsing experience, see our illustrated browser at https://gdo.endlessforms.info that provides visual depictions of many classes and individuals. The GitHub repository is at https://github.com/endlessforms-info/GDO-GDOA. <br><br> The version of the GDO/A here is the GDOA and the GDO merged. The version number applies to the merged variant. For separate GDOA and GDO artifacts, please visit the GitHub repo above. <br /><br /> The Graphic Descriptor Ontology (GDO) is intended for use in describing graphics that represent the form of objects. The Graphic Descriptor Ontology Anatomy extension (GDOA) extends the GDO to the domain of anatomical graphics by providing classes for anatomical views and anatomically-relevant region mark roles, such as representing a type of body tissue or body fluid., The Graphic Descriptor Ontology (GDO) is intended for use in describing graphics that represent the form of objects. It uses the language of visual communication, illustration, and technical drawing. The GDO is rooted in the Basic Formal Ontology (BFO) and uses several classes from the Information Entity Ontology of the Common Core Ontologies as a mid-level ontology.",
+    "description": "For the best browsing experience, see our illustrated browser at https://gdo.endlessforms.info that provides visual depictions of many classes and individuals. The GitHub repository is at https://github.com/endlessforms-info/GDO-GDOA. <br><br> The version of the GDO/A here is the GDOA and the GDO merged. The version number applies to the merged variant. For separate GDOA and GDO artifacts, please visit the GitHub repo above. <br /><br /> The Graphic Descriptor Ontology (GDO) is intended for use in describing graphics that represent the form of objects. The Graphic Descriptor Ontology Anatomy extension (GDOA) extends the GDO to the domain of anatomical graphics by providing classes for anatomical views and anatomically-relevant region mark roles, such as representing a type of body tissue or body fluid., The Graphic Descriptor Ontology (GDO) is intended for use in describing graphics that represent the form of objects. It uses the language of visual communication, illustration, and technical drawing. The GDO is rooted in the Basic Formal Ontology (BFO) and uses several classes from the Information Entity Ontology of the Common Core Ontologies as a mid-level ontology., The Graphic Descriptor Ontology (GDO) is intended for use in describing graphics that represent the form of objects. The Graphic Descriptor Ontology Anatomy extension (GDOA) extends the GDO to the domain of anatomical graphics by providing classes for anatomical views and anatomically-relevant region mark roles",
     "homepage": "https://gdo.endlessforms.info/",
     "license": "CC-BY-4.0",
     "name": "Graphic Descriptor Ontology Anatomy Extension",
     "prefix": "GDOA",
-    "version": "1.1.2"
+    "version": "1.1.3"
   },
   "GECCO": {
     "contact": {
@@ -5407,7 +5427,7 @@
     "publications": [
       "http://human-phenotype-ontology.github.io/license.html"
     ],
-    "version": "2025-10-22"
+    "version": "2025-11-24"
   },
   "HPIO": {
     "contact": {
@@ -5458,7 +5478,7 @@
     "description": "A collection of curated and standardized values used by the HuBMAP (Human BioMolecular Atlas Program) and SenNet (Cellular Senescence Network) metadata records to ensure uniformity in the description of samples and single-cell data produced by the consortium.",
     "name": "HuBMAP Research Attributes Value Set",
     "prefix": "HRAVS",
-    "version": "2.13.8"
+    "version": "2.13.10"
   },
   "HRDO": {
     "contact": {
@@ -7341,7 +7361,7 @@
     "license": "CC-BY-4.0",
     "name": "METPO",
     "prefix": "METPO",
-    "version": "2025-11-17"
+    "version": "2025-11-25"
   },
   "MF": {
     "contact": {
@@ -7791,7 +7811,7 @@
     "homepage": "http://www.informatics.jax.org/searches/MP_form.shtml",
     "name": "Mammalian Phenotype Ontology",
     "prefix": "MP",
-    "version": "2025-10-23"
+    "version": "2025-11-19"
   },
   "MPATH": {
     "contact": {
@@ -8882,7 +8902,7 @@
     "license": "CC-BY-4.0",
     "name": "Ontology of Dental Care-Related Fear and Anxiety",
     "prefix": "ODFA",
-    "version": "2025-08-28"
+    "version": "2025-11-25"
   },
   "ODHT": {
     "contact": {
@@ -8915,6 +8935,14 @@
     "prefix": "OF",
     "version": "1.0"
   },
+  "OFDSIPT": {
+    "contact": {
+      "email": "lina.dadic.ld@gmail.com",
+      "name": "Lina"
+    },
+    "name": "Ontology for Data Science in Practice (trial)",
+    "prefix": "OFDSIPT"
+  },
   "OFL": {
     "contact": {
       "email": "nico.fra97@icloud.com",
@@ -10968,7 +10996,7 @@
     "publications": [
       "https://doi.org/10.1080/09553002.2023.2173823"
     ],
-    "version": "2025-09-17"
+    "version": "2025-11-26"
   },
   "RCD": {
     "contact": {
@@ -12625,7 +12653,7 @@
     "description": "The Unwarranted Clinical Variation Analysis ontology (UCVA) is an application ontology that standardizes the representation of local context factors of UCV analysis. It includes numerous instances designed to support the extraction of these factors as covariates in UCV analysis, making it practical and easy to use",
     "name": "Unwarranted Clinical Variation Analysis With Contextual Factors",
     "prefix": "UCVA",
-    "version": "1.0"
+    "version": "1.1"
   },
   "UGANDA_DISEASES": {
     "contact": {
@@ -12791,7 +12819,7 @@
     "license": "CC-BY-4.0",
     "name": "vfb_drivers",
     "prefix": "VFB_DRIVERS",
-    "version": "2025-11-17"
+    "version": "2025-11-24"
   },
   "VHOG": {
     "contact": {
@@ -13060,7 +13088,7 @@
     "publications": [
       "https://www.animalgenome.org/bioinfo/projects/vt/"
     ],
-    "version": "2025-11-18"
+    "version": "2025-11-25"
   },
   "VTO": {
     "contact": {

bioregistry/external/cellosaurus/processed.json

@@ -182,7 +182,7 @@
     "category": "Chemistry resources",
     "homepage": "https://www.ebi.ac.uk/chebi/",
     "name": "Chemical Entities of Biological Interest",
-    "uri_format": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$1"
+    "uri_format": "https://www.ebi.ac.uk/chebi/search?query=$1"
   },
   "ChEMBL-Cells": {
     "category": "Chemistry resources",
@@ -497,9 +497,9 @@
   },
   "KCLB": {
     "category": "Cell line collections (Providers)",
-    "homepage": "https://cellbank.snu.ac.kr/eng/",
+    "homepage": "https://cellbank.snu.ac.kr/en",
     "name": "Korean Cell Line Bank",
-    "uri_format": "https://cellbank.snu.ac.kr/main/tmpl/sub_main.php?m_cd=6&m_id=0201&strQ=$1"
+    "uri_format": "https://cellbank.snu.ac.kr/cellline/search?sc=y&q=$1"
   },
   "KYinno": {
     "category": "Cell line collections (Providers)",