bioregistry 0.13.11__py3-none-any.whl → 0.13.13__py3-none-any.whl

bioregistry/external/bioportal/agroportal.json

@@ -64,6 +64,17 @@
     "name": "Agriculture and Forestry Ontology",
     "prefix": "AFO"
   },
+  "AFY": {
+    "contact": {
+      "email": "raphael.condesalazar@online.fr",
+      "name": "Raphaël CONDE SALAZAR"
+    },
+    "description": "Agroforestry Ontology is a knowledge model that provides a unifying framework for structuring agroforestry data and knowledge., Ontologie des systèmes agroforestiers, Ontology of agroforestry systems",
+    "license": "CC-BY-4.0",
+    "name": "Agroforestry Ontology",
+    "prefix": "AFY",
+    "version": "1.0.0"
+  },
   "AGFOOD": {
     "contact": {
       "email": "contact-terminologietal@inist.fr",
@@ -1927,7 +1938,7 @@
     "license": "CC-BY-4.0",
     "name": "A lexicon of water related textual and geophysicla data - Un lexique de données textuelles et géophysiques sur l'eau",
     "prefix": "LEXEAU",
-    "version": "2.2"
+    "version": "2.3"
   },
   "LHO": {
     "contact": {
@@ -2199,13 +2210,18 @@
   },
   "ONTOPFAS": {
     "contact": {
-      "email": "abrouk@lirmm.fr",
-      "name": "Lylia ABROUK"
+      "email": "lylia.abrouk@u-bourgogne.fr",
+      "name": "Lylia Abrouk"
     },
     "description": "OntoPFAS is a conceptualization of the PFAS domain, concerning its exposure, measurement, and spread aspects. Combining chemical, geographical, and sensor data, it aims to represent a hub for practitioners of different fields willing to contribute with data, models, or artificial intelligence applications.",
     "license": "CC-BY-4.0",
-    "name": "OntoPFAS",
-    "prefix": "ONTOPFAS"
+    "name": "OntoPFAS: an Ontology for the Forever Chemicals",
+    "prefix": "ONTOPFAS",
+    "publications": [
+      "https://hal.science/hal-05189813"
+    ],
+    "repository": "https://github.com/davide1797/OntoPFAS",
+    "version": "1"
   },
   "OWSD": {
     "contact": {
@@ -2938,7 +2954,7 @@
     "license": "http://publications.europa.eu/resource/authority/access-right/PUBLIC",
     "name": "PO2/TransformON",
     "prefix": "TRANSFORMON",
-    "version": "22.0"
+    "version": "23.0"
   },
   "TRANSMAT": {
     "contact": {

bioregistry/external/bioportal/ecoportal.json

@@ -950,8 +950,7 @@
     "homepage": "https://ecoportal.lifewatch.eu/ontologies/TRAITS_THES",
     "license": "CC-BY-4.0",
     "name": "Traits Thesaurus",
-    "prefix": "TRAITS_THES",
-    "version": "2.0.1"
+    "prefix": "TRAITS_THES"
   },
   "WISE_CLASS": {
     "contact": {

bioregistry/external/fairsharing/processed.json

@@ -1158,7 +1158,7 @@
   },
   "FAIRsharing.2b4316": {
     "abbreviation": "PMCID",
-    "description": "Identifier schema for PubMed Central, a U.S. National Institutes of Health's National Library of Medicine (NIH/NLM) free full-text archive of biomedical and life sciences journal literature.",
+    "description": "Identifier schema for PubMed Central, a U.S. National Institutes of Health's National Library of Medicine (NIH/NLM) free full-text archive of biomedical and life sciences journal literature, which gives the public access to papers at no cost. Papers collected under the NIH or participating funder's public access policy are archived in PMC. Each paper in PMC is assigned a unique identification number. A PMCID may be used by authors and awardees to demonstrate compliance with a funder's public access policy. A PMCID is assigned to an NIHMS submission when the following two criteria are met: the Final Approval step is complete, and the article has been matched to a PubMed record.",
     "domains": [
       "centrally registered identifier"
     ],
@@ -1170,7 +1170,7 @@
   },
   "FAIRsharing.2b9b61": {
     "abbreviation": "PMID",
-    "description": "The PubMed Unique Identifier (PMID) is a 1- to 8-digit accession number with no leading zeros for managing and disseminating records at the PubMed repository. The PMID is a unique reference number for PubMed citations and is a distinctly different number from the PMCID and is used only for PubMed records. PMIDs are not reused after records are deleted. Prior to the 2004 version of PubMed (available December 3, 2003), many records contained a MEDLINE Unique Identifier in addition to the PMID. NLM no longer displays the MEDLINE Unique Identifier. The PMID has become the unique identifier for the MEDLINE record.",
+    "description": "The PubMed Unique Identifier (PMID) is a 1- to 8-digit accession number with no leading zeros for managing and disseminating records at the PubMed repository. PubMed is a citation and abstract database for biomedical literature, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher websites. The PMID is a unique reference number for PubMed citations and is a distinctly different number from the PMCID and is used only for PubMed records. PMIDs are not reused after records are deleted. Prior to the 2004 version of PubMed (available December 3, 2003), many records contained a MEDLINE Unique Identifier in addition to the PMID. NLM no longer displays the MEDLINE Unique Identifier. The PMID has become the unique identifier for the MEDLINE record. Each citation record in PubMed is assigned a unique identification number. A PMID is not the same as a PMCID and cannot be used to demonstrate compliance with the NIH or another participating funder's public access policy. ",
     "homepage": "https://www.nihms.nih.gov/help/glossary/#pmid",
     "name": "PubMed Unique Identifier",
     "subjects": [
@@ -6556,7 +6556,8 @@
       "Resource metadata",
       "Annotation",
       "Data retrieval",
-      "centrally registered identifier"
+      "centrally registered identifier",
+      "FAIR"
     ],
     "homepage": "https://www.rrids.org/",
     "name": "Research Resource Identifier",
@@ -6598,6 +6599,10 @@
       "Omics",
       "Biology",
       "Chemistry"
+    ],
+    "user_defined_tags": [
+      "Resource Discovery",
+      "community resource"
     ]
   },
   "FAIRsharing.DbFnKV": {
@@ -9932,9 +9937,9 @@
     "twitter": "sparontologies"
   },
   "FAIRsharing.d88s6e": {
-    "abbreviation": "SNOMEDCT",
+    "abbreviation": "SNOMED CT",
     "description": "The Systematized Nomenclature of Medicine Clinical Terms is a reference terminology that can be used to cross-map standardized healthcare languages across healthcare disciplines.",
-    "homepage": "http://www.snomed.org/snomed-ct/five-step-briefing",
+    "homepage": "https://www.snomed.org/what-is-snomed-ct",
     "name": "Systematized Nomenclature of Medicine-Clinical Terms",
     "publications": [
       {

bioregistry/external/integbio/processed.json

@@ -460,7 +460,7 @@
   "maintainer": "Tokyo Medical and Dental University Medical Research Institute",
   "name": "CGH Data Base",
   "prefix": "NBDC00026",
-  "status": "Active",
+  "status": "Inactive",
   "target_keywords": [
    "Genetic variation",
    "Health/Disease"
@@ -641,6 +641,7 @@
   "pubmeds": [
    "17211581"
   ],
+  "status": "Closed",
   "target_keywords": [
    "Genome/Gene"
   ]
@@ -718,7 +719,7 @@
    "7971946",
    "2330366"
   ],
-  "status": "Active",
+  "status": "Inactive",
   "target_keywords": [
    "Protein"
   ]
@@ -1021,7 +1022,7 @@
  "nbdc00054": {
   "description": "ENSEMBL is a collection of automatically annotated genome databases for vertebrates and a number of eukaryotes, integrated with all other relevant biological data available.\nThe repository covers data on gene annotation, microarray probeset mapping and comparative genomics among many other topics.\nInformation may be downloaded by a variety of means: \nFor small amounts of data, an export option is suggested.\nFor larger amounts of data, an FTP site is provided from where a complete database may be downloaded in one of various formats, from flat files to MySQL dumps.",
   "fairsharing": "biodbcore-000330",
-  "homepage": "http://uswest.ensembl.org/index.html",
+  "homepage": "https://www.ensembl.org/index.html",
   "information_keywords": [
    "Sequence"
   ],
@@ -1068,7 +1069,7 @@
   "maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
   "name": "ENU Mutants (A large Scale Mutagenesis Project in Riken GSC)",
   "prefix": "NBDC00056",
-  "status": "Active",
+  "status": "Inactive",
   "target_keywords": [
    "Genome/Gene",
    "Organism"
@@ -1670,7 +1671,7 @@
  "nbdc00088": {
   "alt_name": "A Database for Triticeae and Avena",
   "description": "Graingenes provides information on wheat and barley research. Users can browse through class data such as references, authors, genes, polymorphisms, proteins, and sequences. Each record is linked to associated databases and web resources. Users can also use BLAST, CMap, and GenomeBrowser.",
-  "homepage": "https://wheat.pw.usda.gov/GG3/",
+  "homepage": "https://graingenes.org//GG3/",
   "information_keywords": [
    "Sequence",
    "Image/Movie"
@@ -2107,7 +2108,7 @@
  "nbdc00111": {
   "alt_name": "Japan Drosophila Database",
   "description": "JDD is an introductory database on genetics and taxonomy of Drosophila. JDD stores images of wild-types and mutants, cytological maps, information on taxonomy of Drosophilidae and proteome atlas with search function. This database provides search systems of gene symbols, species name and taxonomic references. English page of each content is not constructed, and the home page of JDD provides only links to the Japanese pages.",
-  "homepage": "http://www.dgrc.kit.ac.jp/~jdd/index_en.html",
+  "homepage": "http://www.drosophila.jp/jdd/",
   "information_keywords": [
    "Image/Movie",
    "Bibliography/Documents",
@@ -13543,7 +13544,7 @@
  },
  "nbdc00851": {
   "description": "ELKUType is a database of information on type specimens preserved in the Entomological Laboratory, Kyushu University (ELKU). ELKUType is based on the holotypes, which are used in the original description for establishment of a new taxon. Each record consists of 17 items including a image of the holotype, scientific names (family, genus and species), the Japanese name and distribution data. Users can search records by keywords from these items.",
-  "homepage": "https://insectdb.kyushu-u.ac.jp/elkutype/",
+  "homepage": "http://elkutype.aiic.jp/",
   "information_keywords": [
    "Ontology/Terminology/Nomenclature",
    "Image/Movie"
@@ -20626,7 +20627,7 @@
   "pubmeds": [
    "20194625"
   ],
-  "status": "Active"
+  "status": "Inactive"
  },
  "nbdc01544": {
   "description": "This Plant gene Database contains plant gene information focusing on the secondary metabolism and the transport mechanism of plants. The data was obtained by analyzing EST information from S. flavescensplant and L. erythrorhizon cells which were cultured in the selected cell-suspension culture systems where photosynthetic genes and those for morphogenesis are strongly suppressed. The database provides keyword search and BLAST search services useful for homology-based cloning of genes, identification of conserved amino acid domains and motif and phylogenetic analyses.",
@@ -29114,7 +29115,7 @@
   "pubmeds": [
    "22058129"
   ],
-  "status": "Active",
+  "status": "Closed",
   "target_keywords": [
    "Genome/Gene",
    "Genetic variation",
@@ -31572,7 +31573,7 @@
   "pubmeds": [
    "26772741"
   ],
-  "status": "Inactive",
+  "status": "Closed",
   "target_keywords": [
    "Drug",
    "Genome/Gene",

bioregistry/external/obofoundry/processed.json

@@ -5232,7 +5232,7 @@
     "homepage": "https://github.com/monarch-initiative/vertebrate-breed-ontology",
     "license": "CC BY 4.0",
     "license.url": "https://creativecommons.org/licenses/by/4.0/",
-    "logo": "https://github.com/tis-lab/closed-illustrations/blob/15058315cba1018e09572b28ebeee262a458b1c6/logos/vbo-logo/VBO-black-logo-stackedv2.png",
+    "logo": "https://raw.githubusercontent.com/tis-lab/closed-illustrations/master/logos/vbo-logo/VBO-black-logo-stackedv2.png",
     "name": "Vertebrate Breed Ontology",
     "preferredPrefix": "VBO",
     "publications": [

bioregistry/external/ols/processed.json

@@ -129,8 +129,8 @@
     "name": "The Behaviour Change Intervention Ontology",
     "prefix": "bcio",
     "uri_format": "http://humanbehaviourchange.org/ontology/BCIO_$1",
-    "version": "2025-11-07",
-    "version.iri": "http://humanbehaviourchange.org/ontology/bcio.owl/2025-11-07"
+    "version": "2025-12-05",
+    "version.iri": "http://humanbehaviourchange.org/ontology/bcio.owl/2025-12-05"
   },
   "bco": {
     "description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.",
@@ -366,8 +366,8 @@
     "name": "Clinical measurement ontology",
     "prefix": "cmo",
     "tracker": "https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues",
-    "version": "2.259",
-    "version.iri": "http://purl.obolibrary.org/obo/cmo/2.259/cmo.owl"
+    "version": "2.260",
+    "version.iri": "http://purl.obolibrary.org/obo/cmo/2.260/cmo.owl"
   },
   "cmpo": {
     "contact": "jupp@ebi.ac.uk",
@@ -718,6 +718,15 @@
     "prefix": "evorao",
     "uri_format": "https://w3id.org/evorao/$1"
   },
+  "exmo": {
+    "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://purl.obolibrary.org/obo/exmo.owl",
+    "homepage": "https://github.com/Exercise-Medicine-Ontology/EXMO",
+    "name": "EXMO",
+    "prefix": "exmo",
+    "tracker": "https://github.com/Exercise-Medicine-Ontology/EXMO/issues",
+    "version.iri": "http://purl.obolibrary.org/obo/exmo/2025-06-05/exmo.owl"
+  },
   "exo": {
     "description": "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.",
     "download_owl": "http://purl.obolibrary.org/obo/exo.owl",
@@ -1322,8 +1331,8 @@
     "name": "Measurement method ontology",
     "prefix": "mmo",
     "tracker": "https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues",
-    "version": "2.166",
-    "version.iri": "http://purl.obolibrary.org/obo/mmo/2.166/mmo.owl"
+    "version": "2.167",
+    "version.iri": "http://purl.obolibrary.org/obo/mmo/2.167/mmo.owl"
   },
   "mmusdv": {
     "description": "Life cycle stages for Mus Musculus",
@@ -1414,8 +1423,8 @@
     "name": "Mass spectrometry ontology",
     "prefix": "ms",
     "tracker": "https://github.com/HUPO-PSI/psi-ms-CV/issues",
-    "version": "4.1.216",
-    "version.iri": "http://purl.obolibrary.org/obo/ms/4.1.216/ms.owl"
+    "version": "4.1.221",
+    "version.iri": "http://purl.obolibrary.org/obo/ms/4.1.221/ms.owl"
   },
   "msio": {
     "description": "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.",
@@ -1857,8 +1866,8 @@
     "name": "Plant Experimental Conditions Ontology",
     "prefix": "peco",
     "tracker": "https://github.com/Planteome/plant-experimental-conditions-ontology/issues",
-    "version": "2023-11-10",
-    "version.iri": "http://purl.obolibrary.org/obo/peco/releases/2023-11-10/peco.owl"
+    "version": "2025-12-02",
+    "version.iri": "http://purl.obolibrary.org/obo/peco/releases/2025-12-02/peco.owl"
   },
   "phipo": {
     "description": "Ontology of species-neutral phenotypes observed in pathogen-host interactions.",
@@ -2071,8 +2080,8 @@
     "name": "Rat Strain Ontology",
     "prefix": "rs",
     "tracker": "https://github.com/rat-genome-database/RS-Rat-Strain-Ontology/issues",
-    "version": "6.262",
-    "version.iri": "http://purl.obolibrary.org/obo/rs/6.262/rs.owl"
+    "version": "6.263",
+    "version.iri": "http://purl.obolibrary.org/obo/rs/6.263/rs.owl"
   },
   "rxno": {
     "contact": "chemistry-ontologies@googlegroups.com",
@@ -2172,8 +2181,8 @@
     "name": "Space Life Sciences Ontology",
     "prefix": "slso",
     "tracker": "https://github.com/nasa/LSDAO/issues",
-    "version": "2025-09-16",
-    "version.iri": "http://purl.obolibrary.org/obo/slso/releases/2025-09-16/slso.owl"
+    "version": "2025-12-09",
+    "version.iri": "http://purl.obolibrary.org/obo/slso/releases/2025-12-09/slso.owl"
   },
   "snomed": {
     "description": "SNOMED CT or SNOMED Clinical Terms is a systematically organized computer processable collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting.",
@@ -2341,8 +2350,8 @@
     "name": "Uber-anatomy ontology",
     "prefix": "uberon",
     "tracker": "https://github.com/obophenotype/uberon/issues",
-    "version": "2025-08-15",
-    "version.iri": "http://purl.obolibrary.org/obo/uberon/releases/2025-08-15/uberon.owl"
+    "version": "2025-12-04",
+    "version.iri": "http://purl.obolibrary.org/obo/uberon/releases/2025-12-04/uberon.owl"
   },
   "unimod": {
     "contact": "psidev-ms-vocab@lists.sourceforge.net",

bioregistry/external/re3data/processed.json

@@ -278,7 +278,7 @@
   "r3d100000037": {
     "description": "The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biogeochemical dynamics is one of the National Aeronautics and Space Administration (NASA) Earth Observing System Data and Information System (EOSDIS) data centers managed by the Earth Science Data and Information System (ESDIS) Project. The ORNL DAAC archives data produced by NASA's Terrestrial Ecology Program. The DAAC provides data and information relevant to biogeochemical dynamics, ecological data, and environmental processes, critical for understanding the dynamics relating to the biological, geological, and chemical components of Earth's environment.",
     "doi": "10.17616/R3SG61",
-    "homepage": "https://daac.ornl.gov/",
+    "homepage": "https://www.earthdata.nasa.gov/centers/ornl-daac/data-access-tools",
     "name": "Oak Ridge National Laboratory Distributed Active Archive Center for Biogeochemical Dynamics",
     "prefix": "r3d100000037",
     "synonyms": [
@@ -4728,7 +4728,7 @@
     ]
   },
   "r3d100010492": {
-    "description": "Lithuanian Data Archive for Social Sciences and Humanities (LiDA) is a virtual digital infrastructure for SSH data and research resources acquisition, long-term preservation and dissemination. All the data and research resources are documented in both English and Lithuanian according to international standards. Access to the resources is provided via Dataverse repository. LiDA curates different types of resources and they are published into catalogues according to the type: Survey Data, Aggregated Data (including Historical Statistics), Encoded Data (including News Media Studies), and Textual Data. Also, LiDA holds collections of social sciences and humanities data deposited by Lithuanian science and higher education institutions and Lithuanian state institutions (Data of Other Institutions).\n\nLiDA is hosted by the Centre for Data Analysis and Archiving of Kaunas University of Technology (data.ktu.edu).",
+    "description": "Lithuanian Data Archive for Social Sciences and Humanities (LiDA) is a virtual digital infrastructure for SSH data and research resources acquisition, long-term preservation and dissemination. All the data and research resources are documented in both English and Lithuanian according to international standards. Access to the resources is provided via Dataverse repository. LiDA curates different types of resources and they are published into catalogues according to the type: Survey Data, Aggregated Data (including Historical Statistics), Encoded Data (including News Media Studies), and Textual Data. Also, LiDA holds collections of social sciences and humanities data deposited by Lithuanian science and higher education institutions and Lithuanian state institutions (Data of Other Institutions).\nLiDA is the Lithuanian national service provider for the CESSDA ERIC.",
     "doi": "10.17616/R34S5V",
     "homepage": "https://lida.dataverse.lt",
     "license": "CC",
@@ -24417,9 +24417,9 @@
     ]
   },
   "r3d100012928": {
-    "description": "The MicroScope platform is an informatics infrastructure dedicated to the annotation and comparative analysis of microbial genomes and metagenomes.",
+    "description": "The MicroScope is a web platform for the analysis of prokaryotic genomes and expert functional annotation.",
     "doi": "10.17616/R31NJMGW",
-    "homepage": "https://mage.genoscope.cns.fr/microscope/home/index.php",
+    "homepage": "https://mage.genoscope.cns.fr/microscope/",
     "name": "MicroScope",
     "prefix": "r3d100012928",
     "synonyms": [
@@ -34885,7 +34885,7 @@
     ]
   },
   "r3d100014604": {
-    "description": "Das Repositorium der Herzog August Bibliothek bietet Zugriff auf Publikationen der Bibliothek, auf Forschungsdaten, auf digitale Editionen sowie auf weitere Medien. Die Veröffentlichung im Repositorium der Herzog August Bibliothek folgt den Grundsätzen von Open Access und den FAIR-Data-Prinzipien.",
+    "description": "The repository of the Herzog August Bibliothek provides access to publications of the library, research data, digital editions and other media. Publishing in the repository of the Herzog August Bibliothek follows the principles of Open Access and the FAIR data principles.",
     "doi": "10.17616/R31NJNRG",
     "homepage": "https://repo.hab.de/home",
     "name": "Repositorium der Herzog August Bibliothek",
@@ -35563,6 +35563,7 @@
   },
   "r3d100014736": {
     "description": "Datarepository Unive is the institutional, free, and open repository that collects, stores, and preserves research data produced by Ca' Foscari University researchers according to the highest international standards and best practices. Datasets published in the archive have a set of metadata that ensure proper description and discoverability.",
+    "doi": "10.17616/R31NJNV4",
     "homepage": "https://datarepository.unive.it/",
     "license": "CC",
     "name": "Datarepository Unive",
@@ -35570,8 +35571,56 @@
   },
   "r3d100014737": {
     "description": "A data sharing platform for the MRC CoRE in Restorative Neural Dynamics, and the Brain Network Dynamics Unit. Nuffield Department of Clinical Neurosciences, University of Oxford.",
+    "doi": "10.17616/R31NJNV5",
     "homepage": "https://data.mrc.ox.ac.uk/",
     "name": "Cambium",
     "prefix": "r3d100014737"
+  },
+  "r3d100014738": {
+    "description": "The MNXref namespace (the database for MetaNetX) is a comprehensive resource for the reconciliation and integration of metabolic information across diverse biochemical databases. MNXref integrates biochemical data from a broad range of resources, including ChEBI, KEGG, Rhea, BiGG, The SEED, and the recently added VHM. Each source is parsed, standardized, and mapped to MetaNetX identifiers through a combination of automated pipelines and manual curation.",
+    "doi": "10.17616/R31NJNV6",
+    "homepage": "https://www.metanetx.org",
+    "license": "CC",
+    "name": "MetaNetX",
+    "prefix": "r3d100014738",
+    "synonyms": [
+      "MNXref"
+    ]
+  },
+  "r3d100014739": {
+    "description": "The Croatian Social Science Data Archive (CROSSDA) is a national infrastructure public service whose role is to ensure the long-term preservation and dissemination of social science research data. CROSSDA is committed to providing data management support for researchers during the entire lifecycle of the project, from hypothesis development and grant preparation to data collection and data analysis. The data archive will make sure that the data are preserved and reusable in the long-term. CROSSDA is the national service provider for Croatia in the Consortium of European Social Science Data Archives CESSDA ERIC.",
+    "doi": "10.17616/R31NJNV7",
+    "homepage": "https://data.crossda.hr",
+    "name": "Croatian Social Science Data Archive",
+    "prefix": "r3d100014739",
+    "synonyms": [
+      "CROSSDA",
+      "Hrvatski arhiv podataka za društvene znanosti"
+    ]
+  },
+  "r3d100014740": {
+    "description": "The International Soil Moisture Network (ISMN) provides free access to long-term, harmonised and quality-controlled in situ soil moisture observations, covering the near-surface zone down to the deep-root zone. These observations are collected from around 3.000 sites belonging to various organisations that supply ISMN with data on a voluntary basis. Other relevant hydrometeorological variables such as rainfall and temperature are also stored in the database. Services provided by ISMN have made a major contribution towards calibrating/validating and improving global satellite soil moisture products and land surface models.",
+    "homepage": "https://ismn.earth",
+    "name": "International Soil Moisture Network",
+    "prefix": "r3d100014740",
+    "synonyms": [
+      "ISMN"
+    ]
+  },
+  "r3d100014741": {
+    "description": "GRANTS Data is a data repository operated by the Japan Science and Technology Agency (JST). GRANTS Data is a platform that securely stores and publishes data for researchers who wish to share the findings of their publicly funded research with the public. The purpose of this service is to promote the publication and utilization of research data, and ultimately to contribute to the promotion and advancement of science and technology.\n\nData Published through GRANTS Data will automatically be assigned a DOI and will be distributed worldwide as open access* data, which means that the data can be cited, shared, reused, and otherwise used under the conditions set by the copyright holder.\n\n*Open access: Anyone can access it for free, and the scope of permitted secondary use is clearly stated.\n\nNote: Please be aware that some of the data included in GRANTS Data is not linked to any research paper, meaning that it has not been academically evaluated or verified by researchers.",
+    "homepage": "https://grantsdata.jst.go.jp/",
+    "name": "GRANTS Data",
+    "prefix": "r3d100014741"
+  },
+  "r3d100014742": {
+    "description": "Telkom University Dataverse is the institutional research data repository of Universitas Telkom (Telkom University), Indonesia. It provides Telkom University researchers, lecturers, students, and partners with a trusted platform to deposit, preserve, and share research data, software, and other reproducible research outputs across all disciplines. The repository assigns DataCite DOIs to datasets, supports standard data citation and Make Data Count metrics (views, downloads, citations), and follows FAIR data principles to promote open science, long-term stewardship, and global visibility and re-use of Telkom University research data. The service is operated by the Directorate of Information Technology Center (PuTI) of Telkom University.",
+    "homepage": "https://dataverse.telkomuniversity.ac.id/",
+    "license": "CC",
+    "name": "Dataverse Telkom University",
+    "prefix": "r3d100014742",
+    "synonyms": [
+      "Dataverse Universitas Telkom"
+    ]
   }
 }

bioregistry/resource_manager.py

@@ -222,6 +222,10 @@ class Manager:
             self._converter.add_prefix(resource.prefix, uri_prefix)
             # TODO what about synonyms
 
+    def add_collection(self, collection: Collection) -> None:
+        """Add a collection."""
+        self.collections[collection.identifier] = collection
+
     def add_to_collection(self, collection: str | Collection, resource: str | Resource) -> None:
         """Add a resource to the collection."""
         if isinstance(collection, Collection):

bioregistry/schema/schema.json

@@ -147,6 +147,7 @@
         },
         "description": {
           "description": "A description of the collection",
+          "minLength": 30,
           "title": "Description",
           "type": "string"
         },
@@ -155,6 +156,7 @@
           "items": {
             "type": "string"
           },
+          "minItems": 1,
           "title": "Resources",
           "type": "array"
         },
@@ -163,9 +165,27 @@
           "items": {
             "$ref": "#/$defs/Author"
           },
+          "minItems": 1,
           "title": "Authors",
           "type": "array"
         },
+        "organizations": {
+          "anyOf": [
+            {
+              "items": {
+                "$ref": "#/$defs/Organization"
+              },
+              "minItems": 1,
+              "type": "array"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "description": "A list of organizations that contribute to this collection",
+          "title": "Organizations"
+        },
         "context": {
           "anyOf": [
             {
@@ -329,7 +349,7 @@
       "type": "object"
     },
     "Organization": {
-      "description": "Model for organizataions.",
+      "description": "Model for organizations.",
       "properties": {
         "ror": {
           "anyOf": [

bioregistry/schema/struct.py

@@ -185,7 +185,7 @@ class MetaprefixAnnotatedValue(Generic[X]):
 
 
 class Organization(BaseModel):
-    """Model for organizataions."""
+    """Model for organizations."""
 
     ror: str | None = Field(
         default=None,
@@ -3112,14 +3112,22 @@ class Collection(BaseModel):
     description: str = Field(
         ...,
         description="A description of the collection",
+        min_length=30,
     )
     resources: list[str] = Field(
         ...,
         description="A list of prefixes of resources appearing in the collection",
+        min_length=1,
     )
     authors: list[Author] = Field(
         ...,
         description="A list of authors/contributors to the collection",
+        min_length=1,
+    )
+    organizations: list[Organization] | None = Field(
+        None,
+        description="A list of organizations that contribute to this collection",
+        min_length=1,
     )
     context: str | None = Field(default=None, description="The JSON-LD context's name")
     references: list[str] | None = Field(default=None, description="URL references")

bioregistry/schema_utils.py

@@ -218,7 +218,12 @@ def write_collections(collections: Mapping[str, Collection], *, path: Path | Non
         collection.resources = sorted(set(collection.resources))
     with open(path or COLLECTIONS_PATH, encoding="utf-8", mode="w") as file:
         json.dump(
-            {"collections": [c.model_dump(exclude_none=True) for c in values]},
+            {
+                "collections": [
+                    c.model_dump(exclude_none=True, exclude_defaults=True, exclude_unset=True)
+                    for c in values
+                ]
+            },
             file,
             indent=2,
             sort_keys=True,

bioregistry/validate/cli.py

@@ -102,3 +102,19 @@ def validate_virtuoso(
         url, strict=not relax, use_preferred=use_preferred, context=context
     )
     click_write_messages(messages, tablefmt=tablefmt)
+
+
+@validate.command(name="linkml")
+@click.argument("url")
+@RELAX_OPTION
+@CONTEXT_OPTION
+@PREFERRED_OPTION
+@FORMAT_OPTION
+def validate_linkml(
+    url: str, relax: bool, use_preferred: bool, context: str | None, tablefmt: str | None
+) -> None:
+    """Validate prefixes in a LinkMK YAML configuration."""
+    from .utils import click_write_messages, validate_linkml
+
+    messages = validate_linkml(url, strict=not relax, use_preferred=use_preferred, context=context)
+    click_write_messages(messages, tablefmt=tablefmt)

bioregistry/validate/utils.py

@@ -5,7 +5,7 @@ from __future__ import annotations
 import json
 from collections.abc import Callable, Mapping
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Literal
+from typing import TYPE_CHECKING, Any, Literal, cast
 
 import click
 from pydantic import BaseModel
@@ -18,6 +18,7 @@ __all__ = [
     "Message",
     "click_write_messages",
     "validate_jsonld",
+    "validate_linkml",
     "validate_ttl",
     "validate_virtuoso",
 ]
@@ -150,6 +151,13 @@ def validate_virtuoso(url: str, **kwargs: Any) -> list[Message]:
     return _get_all_messages(inputs, **kwargs)
 
 
+def validate_linkml(url: str, **kwargs: Any) -> list[Message]:
+    """Validate a LinkML YAML configuration's prefix map."""
+    prefix_map = get_linkml_prefix_map(url)
+    inputs: list[tuple[str, str, int | None]] = [(k, v, None) for k, v in prefix_map.items()]
+    return _get_all_messages(inputs, **kwargs)
+
+
 def _get_all_messages(
     inputs: list[tuple[str, str, int | None]],
     *,
@@ -309,3 +317,22 @@ def get_virtuoso_prefix_map(url: str) -> dict[str, str]:
         )
     rv = {left.text: right.text for left, right in table_body_tag.find_all("tr")}
     return rv
+
+
+def get_linkml_prefix_map(url: str) -> dict[str, str]:
+    """Get the prefix map from a LinkML YAML configuration.
+
+    :param url: The URL for the LinkML YAML configuration. Examples:
+
+        - https://github.com/HendrikBorgelt/CatCore/raw/refs/heads/main/src/catcore/schema/catcore.yaml
+        - https://github.com/mapping-commons/sssom/raw/refs/heads/master/src/sssom_schema/schema/sssom_schema.yaml
+
+    :returns: The prefix map defined in the LinkML configuration
+    """
+    import requests
+    import yaml
+
+    res = requests.get(url, timeout=5)
+    res.raise_for_status()
+    data = yaml.safe_load(res.text)
+    return cast(dict[str, str], data["prefixes"])

bioregistry/version.py

@@ -11,7 +11,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.13.11"
+VERSION = "0.13.13"
 
 
 def get_git_hash() -> str | None: