bioregistry 0.13.9__py3-none-any.whl → 0.13.11__py3-none-any.whl

bioregistry/external/fairsharing/processed.json

@@ -832,6 +832,33 @@
       "Anatomy"
     ]
   },
+  "FAIRsharing.23b8a3": {
+    "abbreviation": "GAIDeT",
+    "contact": {
+      "email": "serhii.nazarovets@gmail.com",
+      "name": "Serhii Nazarovets ",
+      "orcid": "0000-0002-5067-4498"
+    },
+    "description": "GAIDeT (Generative AI Delegation Taxonomy) is a taxonomy and ontology for transparently disclosing which research and writing tasks were delegated to generative AI tools. GAIDeT provides a structured framework for documenting GAI’s role in scholarly research. It classifies research activities into key domains – conceptualization, literature review, methodology, data analysis, writing, supervision, and ethical review – ensuring transparency and human accountability.\n",
+    "homepage": "https://doi.org/10.1080/08989621.2025.2544331",
+    "name": "Generative AI Delegation Taxonomy",
+    "publications": [
+      {
+        "doi": "10.1080/08989621.2025.2544331",
+        "title": "GAIDeT (Generative AI Delegation Taxonomy): A taxonomy for humans to delegate tasks to generative artificial intelligence in scientific research and publishing",
+        "year": 2025
+      },
+      {
+        "doi": "10.59350/psjb9-z1x39",
+        "title": "GAIDeT: a practical taxonomy for declaring AI use in research and publishing",
+        "year": 2025
+      }
+    ],
+    "repository": "https://github.com/panbibliotekar/gaidet-declaration",
+    "subjects": [
+      "Artificial Intelligence"
+    ]
+  },
   "FAIRsharing.23th83": {
     "abbreviation": "GeoSpecies",
     "contact": {
@@ -1678,13 +1705,13 @@
     ]
   },
   "FAIRsharing.322dc0": {
-    "description": "Identifier schema for BioSamples. The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.",
+    "description": "Identifier schema for BioSamples. Submissions to BioSamples result in accession numbers. These are a unique set of characters that identify each sample. e.g. SAMEA116043744. The unique identifier can be used to cross-reference BioSamples with other archives, such as ENA or EGA, and also serves as a permanent identifier for the sample.",
     "domains": [
       "Sample annotation",
       "centrally registered identifier",
       "sequencing assay"
     ],
-    "homepage": "https://registry.identifiers.org/registry/biosample",
+    "homepage": "https://read-docs-biosamples.readthedocs.io/en/latest/submit/general-guide/accession-numbers.html",
     "name": "BioSamples identifier",
     "publications": [
       {
@@ -3711,6 +3738,37 @@
       "Life Science"
     ]
   },
+  "FAIRsharing.654931": {
+    "abbreviation": "OSO",
+    "contact": {
+      "email": "steven.piel@ifremer.fr",
+      "name": "Steven PIEL",
+      "orcid": "0009-0008-1759-5254"
+    },
+    "description": "OSO (Observatories of Seas Ontology) is a lightweight and multilingual ontology developed to describe and interlink marine observing systems, including their infrastructures, platforms, sites, equipment, and responsible organisations.\nIt is maintained by Ifremer and designed to support metadata harmonisation across European marine research infrastructures such as EMSO ERIC. The ontology uses standard vocabularies (OWL, DCAT, Dublin Core, FOAF, SKOS, etc.) and aligns with external identifiers (ROR, EDMO, DOI). OSO aims to improve semantic interoperability, enable FAIR metadata publication, and support long-term data stewardship in the marine domain.",
+    "domains": [
+      "marine coral reef biome",
+      "marine environment",
+      "marine metagenome"
+    ],
+    "homepage": "https://w3id.org/earthsemantics/OSO",
+    "license": "CC-BY-4.0",
+    "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdGdHIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--44d6c2d157aad1fd2aea08ddc6bee8effe6ba67d/oso.png?disposition=inline",
+    "name": "Observatories of Seas Ontology ",
+    "repository": "https://github.com/emso-eric/oso-ontology",
+    "subjects": [
+      "Marine Biology",
+      "Earth Science"
+    ],
+    "user_defined_tags": [
+      "earth observation",
+      "Marine Chemistry",
+      "Marine Litter",
+      "marine energy",
+      "semantic web",
+      "marine observatories"
+    ]
+  },
   "FAIRsharing.658tcg": {
     "abbreviation": "OMOP Standardized Vocabularies",
     "description": "The Standardized Vocabularies contain all of the code sets, terminologies, vocabularies, nomenclatures, lexicons, thesauri, ontologies, taxonomies, classifications, abstractions, and other such data that are needed for: Generation of the transformed (i.e., standardized) data from the raw source dataset into the OMOP CDM, Searching, querying, and extraction of the transformed data, browsing and navigating the hierarchies of classes and abstractions inherent in the transformed data, and Interpreting the meanings of the data. These Standardized Vocabularies are an integral part of the OMOP CDM.",
@@ -6998,7 +7056,7 @@
       "Transcription Factor",
       "binding site"
     ],
-    "homepage": "http://tfclass.bioinf.med.uni-goettingen.de/index.jsf",
+    "homepage": "http://tfclass.bioinf.med.uni-goettingen.de/",
     "name": "Transcription Factor Class",
     "publications": [
       {
@@ -11300,7 +11358,7 @@
     "domains": [
       "centrally registered identifier"
     ],
-    "homepage": "https://www.cstr.cn/doc/specification/",
+    "homepage": "https://www.cstr.cn/doc/specification",
     "name": "Common Science and Technology Resource Identifier",
     "subjects": [
       "Subject Agnostic"
@@ -11345,6 +11403,34 @@
       "Political Science"
     ]
   },
+  "FAIRsharing.f31b8f": {
+    "abbreviation": "SPLASH",
+    "contact": {
+      "email": "ofiehn@ucdavis.edu",
+      "name": "Oliver Fiehn",
+      "orcid": "0000-0002-6261-8928"
+    },
+    "description": "The SPLASH (SPectraL hASH) identifier is a unique and unambiguous database-independent spectral identifier for chemical structures. It contains four separate blocks that define different layers of information, separated by dashes. The first block is the SPLASH identifier, the second and third are spectral summary blocks, and the fourth is the full spectrum hash block. The first block (splash10) encodes the SPLASH identifier, starting with letters for semantic web compatibility, followed by a number representing the measurement type (1 for MS, 2 and above for other data types to be included in the future) and the SPLASH version number, starting at 0, to allow future specification updates. The the second and third blocks are , intensities are summed over fixed (but different) bin sizes and wrapped over ten bins. The second block (0002) is formed using a reduced spectrum (the top ten or fewer ions greater than 10% of the base peak). This reduced spectrum is summed over bins of 5 Da. Each bin is then scaled to a single-digit integral value in base 3 (0–2), and the resulting 10 digit histogram is converted to a base 36 number, resulting in a 4-digit block. In the third block (0900000000) the intensities are summed over 100-Da bin sizes, each bin is then scaled to a single-digit, integral base-10 digit (0–9). The fourth block (full spectrum hash) is represented by a Secure Hash Algorithm SHA256 (numbers and lowercase letters only), calculated in hexadecimal notation and truncated to 20 characters. The full spectrum string of m/z and relative intensity pairs are sorted by ascending m/z and then by descending intensity. The m/z value is multiplied by 10^6, cast to a long (64-bit) integer and joined with the normalized intensity as strings separated by a colon. The resulting ion pairs are then joined, delimited by a single space.",
+    "domains": [
+      "Mass spectrum"
+    ],
+    "homepage": "https://splash.fiehnlab.ucdavis.edu/",
+    "name": "The Spectral Hash Identifier",
+    "publications": [
+      {
+        "doi": "10.1038/nbt.3689",
+        "pubmed": "27824832",
+        "title": "SPLASH, a hashed identifier for mass spectra",
+        "year": 2016
+      }
+    ],
+    "repository": "https://github.com/berlinguyinca/spectra-hash",
+    "subjects": [
+      "Lipidomics",
+      "Metabolomics",
+      "Proteomics"
+    ]
+  },
   "FAIRsharing.f50cc0": {
     "abbreviation": "IVOA-UAT",
     "contact": {
@@ -18663,6 +18749,12 @@
         "pubmed": "23180794",
         "title": "TFClass: an expandable hierarchical classification of human transcription factors",
         "year": 2012
+      },
+      {
+        "doi": "10.1093/nar/gkx987",
+        "pubmed": "29087517",
+        "title": "TFClass: expanding the classification of human transcription factors to their mammalian orthologs",
+        "year": 2017
       }
     ],
     "subjects": [

bioregistry/external/integbio/processed.json

@@ -940,6 +940,7 @@
   "maintainer": "NITE (National Institute of Technology and Evaluation)",
   "name": "DOGAN",
   "prefix": "NBDC00050",
+  "status": "Closed",
   "target_keywords": [
    "Genome/Gene",
    "Protein",
@@ -1644,7 +1645,7 @@
   "maintainer": "Pennsylvania State University",
   "name": "Globin Gene Server",
   "prefix": "NBDC00086",
-  "status": "Inactive",
+  "status": "Active",
   "target_keywords": [
    "Genome/Gene",
    "Health/Disease"
@@ -1843,7 +1844,7 @@
  "nbdc00097": {
   "alt_name": "The Human Gene Mutation Database",
   "description": "HGMD is a integrated database of germ-line mutations which are underlying or associated with human inherited disease in nuclear genes. This database contains all germ-line disease-causing mutations and disease-associated/functional polymorphisms reported in the literature. Furthermore, it includes the data about single base-pair substitutions in coding (e.g. missense and nonsense), regulatory and splicing-relevant regions of human nuclear genes, micro-deletions and micro-insertions, indels, repeat expansions, as well as gross gene lesions (deletions, insertions and duplications) and complex gene rearrangements. These data are provided in a readily accessible format to all interested parties, whether they are from an academic, clinical or commercial background.",
-  "homepage": "http://www.hgmd.org/",
+  "homepage": "https://www.hgmd.cf.ac.uk",
   "information_keywords": [
    "Sequence"
   ],
@@ -2288,7 +2289,7 @@
   "maintainer": "Kyushu University Faculty of Agriculture",
   "name": "KONCHU",
   "prefix": "NBDC00121",
-  "status": "Inactive",
+  "status": "Active",
   "target_keywords": [
    "Organism"
   ]
@@ -2511,6 +2512,7 @@
    "15088387",
    "12477932"
   ],
+  "status": "Closed",
   "target_keywords": [
    "cDNA/EST"
   ]
@@ -4856,7 +4858,7 @@
   ]
  },
  "nbdc00271": {
-  "description": "Flytrap is an HTML-based repository on gene expression.\nThis database provides information on gene expression patterns in the brain of the fruit fly Drosophila.\nThe P-element transposon of Drosophila makes it possible to develop enhancer-trap elements containing minimal promoter regions, which induce transcription.\nThe data is displayed as a list of all the lines studied. This list still needs to be completed and many images have not been annotated or mapped yet.\nThe final list will, after completion, contain 300 lines.\nA basic keyword search option is available.",
+  "description": "Flytrap is an HTML-based repository on gene expression. This database provides information on gene expression patterns in the brain of the fruit fly Drosophila.\nThe P-element transposon of Drosophila makes it possible to develop enhancer-trap elements containing minimal promoter regions, which induce transcription. The data is displayed as a list of all the lines studied. This list still needs to be completed and many images have not been annotated or mapped yet. The final list will, after completion, contain 300 lines. A basic keyword search option is available.",
   "homepage": "http://www.fly-trap.org/",
   "information_keywords": [
    "Expression",

bioregistry/external/lov/processed.json

@@ -8036,6 +8036,16 @@
       "Services"
     ]
   },
+  "vas": {
+    "name": "VAS. A Semantic Model for Earth Observation Remote Sensing",
+    "prefix": "vas",
+    "uri_prefix": "https://robotica.uv.es/proyectos/ASOTVAS/def/ciencia-tecnologia/vas#$1",
+    "description": "The VAS ontological model enables the semantic integration of the heterogeneous observations used in ASOTVAS project ( https://robotica.uv.es/proyectos/ASOTVAS/ ), including ground measurements, UAV acquisitions and satellite products. Built as an extension of the W3C SOSA ontology (Janowicz et al., 2018), it incorporates a domain-specific vocabulary tailored to the needs of the Valencia Anchor Station as a CEOS LPV supersite.\nThe model provides additional classes and properties to represent, in a homogeneous way, the different observational platforms: field sensors installed at VAS stations, UAVs equipped with multispectral cameras, and satellite missions such as Sentinel-2 and Sentinel-3. All observations follow a common SOSA pattern and share the same structure for results, units and timestamps.\nBy aligning field, UAV and satellite observations under a unified semantic framework, the VAS ontology supports interoperable data access, consistent representation across scales, and integrated analysis of the multi-source measurements collected in ASOTVAS.",
+    "keywords": [
+      "IoT"
+    ],
+    "homepage": "https://robotica.uv.es/proyectos/ASOTVAS/def/ciencia-tecnologia/vas"
+  },
   "saref": {
     "name": "SAREF: the Smart Appliances REFerence ontology",
     "prefix": "saref",

bioregistry/external/obofoundry/processed.json

@@ -550,6 +550,10 @@
     "name": "Chemical Entities of Biological Interest",
     "preferredPrefix": "CHEBI",
     "publications": [
+      {
+        "id": "https://doi.org/10.1093/nar/gkaf1271",
+        "title": "ChEBI: re-engineered for a sustainable future"
+      },
       {
         "id": "https://www.ncbi.nlm.nih.gov/pubmed/26467479",
         "title": "ChEBI in 2016: Improved services and an expanding collection of metabolites."

bioregistry/external/ols/processed.json

@@ -266,7 +266,7 @@
     "name": "Chemical Entities of Biological Interest",
     "prefix": "chebi",
     "tracker": "https://github.com/ebi-chebi/ChEBI/issues",
-    "version": "246"
+    "version": "247"
   },
   "cheminf": {
     "description": "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.",
@@ -326,8 +326,8 @@
     "name": "Cell Ontology",
     "prefix": "cl",
     "tracker": "https://github.com/obophenotype/cell-ontology/issues",
-    "version": "2025-11-03",
-    "version.iri": "http://purl.obolibrary.org/obo/cl/releases/2025-11-03/cl.owl"
+    "version": "2025-11-25",
+    "version.iri": "http://purl.obolibrary.org/obo/cl/releases/2025-11-25/cl.owl"
   },
   "clao": {
     "description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).",
@@ -366,8 +366,8 @@
     "name": "Clinical measurement ontology",
     "prefix": "cmo",
     "tracker": "https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues",
-    "version": "2.257",
-    "version.iri": "http://purl.obolibrary.org/obo/cmo/2.257/cmo.owl"
+    "version": "2.259",
+    "version.iri": "http://purl.obolibrary.org/obo/cmo/2.259/cmo.owl"
   },
   "cmpo": {
     "contact": "jupp@ebi.ac.uk",
@@ -531,8 +531,8 @@
     "name": "Human Disease Ontology",
     "prefix": "doid",
     "tracker": "https://github.com/DiseaseOntology/HumanDiseaseOntology/issues",
-    "version": "2025-10-31",
-    "version.iri": "http://purl.obolibrary.org/obo/doid/releases/2025-10-31/translations/doid-international.owl"
+    "version": "2025-11-25",
+    "version.iri": "http://purl.obolibrary.org/obo/doid/releases/2025-11-25/translations/doid-international.owl"
   },
   "dpo": {
     "description": "An ontology of commonly encountered and/or high level Drosophila phenotypes.",
@@ -564,6 +564,16 @@
     "version": "2021-02-23",
     "version.iri": "http://purl.obolibrary.org/obo/duo/releases/2021-02-23/duo.owl"
   },
+  "ec": {
+    "contact": "kristian.axelsen@sib.swiss",
+    "description": "The Enzyme Nomenclature (also known as the Enzyme Commission Code) is a species-agnostic controlled vocabulary for specific enzymes and an associated hierarchical classification into 7 main categories.\n\nThe Enzyme Nomenclature is maintained by the [Nomenclature Committee](https://iubmb.org/about/committees/nomenclature-committee/) of the International Union of Biochemistry and Molecular Biology (IUBMB). A detailed history of the nomenclature since the 1950s can be found [here](https://iubmb.qmul.ac.uk/enzyme/history.html).\n\nThere are few notable resources providing access to the Enzyme Nomenclature:\n\n<table class=\"table table-striped\"><thead><tr><th>Website</th><th>Homepage</td><th>Notes</td></tr></thead><tbody><tr><td>ExplorEnz</td><td><a href=\"https://www.enzyme-database.org\">https://www.enzyme-database.org</a></td><td>This is the resource officially recommended by IUBMB</td></tr><tr><td>IUBMB (via by Queen Mary)</td><td><a href=\"https://iubmb.qmul.ac.uk/enzyme\">https://iubmb.qmul.ac.uk/enzyme</a></td><td>This is a web-based version of the <a href=\"https://archive.org/details/enzymenomenclatu0000inte_d6c2\">1992 publication</a>.</td></tr><tr><td>IntEnz</td><td><a href=\"https://www.ebi.ac.uk/intenz\">https://www.ebi.ac.uk/intenz</a></td><td>Shutdown in 2024</td></tr><tr><td>ExPaSy</td><td><a href=\"https://enzyme.expasy.org\">https://enzyme.expasy.org</a></td></tr><tr><td>EnzymePortal</td><td><a href=\"https://www.ebi.ac.uk/enzymeportal\">https://www.ebi.ac.uk/enzymeportal</a></td><td></td></tr></tbody></table> Licensed under CC-BY-4.0.",
+    "download_owl": "https://w3id.org/biopragmatics/resources/ec/ec.owl",
+    "homepage": "https://www.enzyme-database.org/",
+    "name": "Enzyme Nomenclature",
+    "prefix": "ec",
+    "uri_format": "https://www.enzyme-database.org/query.php?ec=$1",
+    "version.iri": "https://w3id.org/biopragmatics/resources/ec/2025-04-09/ec.ofn"
+  },
   "ecao": {
     "description": "None",
     "download_owl": "http://purl.obolibrary.org/obo/ecao.owl",
@@ -793,11 +803,13 @@
   },
   "fma": {
     "description": "This is currently a slimmed down version of FMA",
-    "download_owl": "http://purl.obolibrary.org/obo/fma.owl",
+    "download_owl": "http://purl.org/sig/ont/fma.owl",
     "homepage": "http://si.washington.edu/projects/fma",
     "name": "Foundational Model of Anatomy Ontology (subset)",
     "prefix": "fma",
-    "tracker": "https://bitbucket.org/uwsig/fma/issues"
+    "tracker": "https://bitbucket.org/uwsig/fma/issues",
+    "version": "5.0.0",
+    "version.iri": "http://purl.org/sig/ont/fma_5.0.0.owl"
   },
   "fobi": {
     "description": "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data",
@@ -1019,8 +1031,8 @@
     "name": "Human Phenotype Ontology",
     "prefix": "hp",
     "tracker": "https://github.com/obophenotype/human-phenotype-ontology/issues/",
-    "version": "2025-10-22",
-    "version.iri": "http://purl.obolibrary.org/obo/hp/releases/2025-10-22/hp-international.owl"
+    "version": "2025-11-24",
+    "version.iri": "http://purl.obolibrary.org/obo/hp/releases/2025-11-24/hp-international.owl"
   },
   "hsapdv": {
     "description": "Life cycle stages for Human",
@@ -1310,8 +1322,8 @@
     "name": "Measurement method ontology",
     "prefix": "mmo",
     "tracker": "https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues",
-    "version": "2.164",
-    "version.iri": "http://purl.obolibrary.org/obo/mmo/2.164/mmo.owl"
+    "version": "2.166",
+    "version.iri": "http://purl.obolibrary.org/obo/mmo/2.166/mmo.owl"
   },
   "mmusdv": {
     "description": "Life cycle stages for Mus Musculus",
@@ -1330,8 +1342,8 @@
     "name": "Protein modification",
     "prefix": "mod",
     "tracker": "https://github.com/HUPO-PSI/psi-mod-CV/issues",
-    "version": "1.031.6",
-    "version.iri": "http://purl.obolibrary.org/obo/mod/1.031.6/mod.owl"
+    "version": "1.032.4",
+    "version.iri": "http://purl.obolibrary.org/obo/mod/1.032.4/mod.owl"
   },
   "mondo": {
     "description": "A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.",
@@ -1340,8 +1352,8 @@
     "name": "Mondo Disease Ontology",
     "prefix": "mondo",
     "tracker": "https://github.com/monarch-initiative/mondo/issues",
-    "version": "2025-11-04",
-    "version.iri": "http://purl.obolibrary.org/obo/mondo/releases/2025-11-04/mondo-international.owl"
+    "version": "2025-12-02",
+    "version.iri": "http://purl.obolibrary.org/obo/mondo/releases/2025-12-02/mondo-international.owl"
   },
   "mop": {
     "contact": "chemistry-ontologies@googlegroups.com",
@@ -1361,8 +1373,8 @@
     "name": "The Mammalian Phenotype Ontology",
     "prefix": "mp",
     "tracker": "https://github.com/mgijax/mammalian-phenotype-ontology/issues",
-    "version": "2025-10-23",
-    "version.iri": "http://purl.obolibrary.org/obo/mp/releases/2025-10-23/mp-international.owl"
+    "version": "2025-11-19",
+    "version.iri": "http://purl.obolibrary.org/obo/mp/releases/2025-11-19/mp-international.owl"
   },
   "mpath": {
     "description": "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes",
@@ -1991,8 +2003,8 @@
     "name": "Radiation Biology Ontology",
     "prefix": "rbo",
     "tracker": "https://github.com/Radiobiology-Informatics-Consortium/RBO/issues",
-    "version": "2025-09-17",
-    "version.iri": "http://purl.obolibrary.org/obo/rbo/releases/2025-09-17/rbo.owl"
+    "version": "2025-11-26",
+    "version.iri": "http://purl.obolibrary.org/obo/rbo/releases/2025-11-26/rbo.owl"
   },
   "rdfs": {
     "name": "The RDF Schema vocabulary (RDFS)",
@@ -2393,8 +2405,8 @@
     "name": "Vaccine Ontology",
     "prefix": "vo",
     "tracker": "https://github.com/vaccineontology/VO/issues",
-    "version": "2025-11-01",
-    "version.iri": "http://purl.obolibrary.org/obo/vo/releases/2025-11-01/vo.owl"
+    "version": "2025-12-03",
+    "version.iri": "http://purl.obolibrary.org/obo/vo/releases/2025-12-03/vo.owl"
   },
   "vsao": {
     "description": "Vertebrate skeletal anatomy ontology.",
@@ -2411,8 +2423,8 @@
     "name": "The Vertebrate Trait Ontology",
     "prefix": "vt",
     "tracker": "https://github.com/AnimalGenome/vertebrate-trait-ontology/issues",
-    "version": "2025-11-18",
-    "version.iri": "http://purl.obolibrary.org/obo/vt/releases/2025-11-18/vt.owl"
+    "version": "2025-12-02",
+    "version.iri": "http://purl.obolibrary.org/obo/vt/releases/2025-12-02/vt.owl"
   },
   "vto": {
     "description": "Comprehensive hierarchy of extinct and extant vertebrate taxa.",
@@ -2481,8 +2493,8 @@
     "name": "Experimental condition ontology",
     "prefix": "xco",
     "tracker": "https://github.com/rat-genome-database/XCO-experimental-condition-ontology/issues",
-    "version": "4.220",
-    "version.iri": "http://purl.obolibrary.org/obo/xco/4.220/xco.owl"
+    "version": "4.221",
+    "version.iri": "http://purl.obolibrary.org/obo/xco/4.221/xco.owl"
   },
   "xlmod": {
     "contact": "psidev-ms-vocab@lists.sourceforge.net",

bioregistry/external/re3data/processed.json

@@ -14876,7 +14876,7 @@
   "r3d100011691": {
     "description": "The ACTRIS DC is designed to assist scientists with discovering and accessing atmospheric data and contains an up-to-date catalogue of available datasets in a number of databases distributed throughout the world. A site like this can never be complete, but we have aimed at including datasets from the most relevant databases to the ACTRIS project, also building on the work and experiences achieved in the EU FP6 research project Global Earth Observation and Monitoring. The focus of the web portal is validated data, but it is also possible to browse the ACTRIS data server for preliminary data (rapid delivery data) through this site.\nThe web site allows you to search in a local metadata catalogue that contains information on actual datasets that are archived in external archives. It is set up so that you can search for data by selecting the chemical/physical variable, the data location, the database that holds the data, the type of data, the data acquisition platform, and the data matrix",
     "doi": "10.17616/R3QD26",
-    "homepage": "https://actris.nilu.no/",
+    "homepage": "https://dc.actris.nilu.no/",
     "name": "ACTRIS Data Centre",
     "prefix": "r3d100011691",
     "synonyms": [
@@ -15467,7 +15467,7 @@
   "r3d100011765": {
     "description": "Web Soil Survey (WSS) provides soil data and information produced by the National Cooperative Soil Survey. It is operated by the USDA Natural Resources Conservation Service (NRCS) and provides access to the largest natural resource information system in the world. NRCS has soil maps and data available online for more than 95 percent of the nation’s counties and anticipates having 100 percent in the near future. The site is updated and maintained online as the single authoritative source of soil survey information.",
     "doi": "10.17616/R3963S",
-    "homepage": "https://www.nrcs.usda.gov/wps/portal/nrcs/main/soils/survey/",
+    "homepage": "https://www.nrcs.usda.gov/resources/data-and-reports/web-soil-survey",
     "name": "Web Soil Survey",
     "prefix": "r3d100011765",
     "synonyms": [
@@ -15482,7 +15482,7 @@
   "r3d100011767": {
     "description": "The tree of life links all biodiversity through a shared evolutionary history. This project will produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientific communities. Assembly of the tree will incorporate previously-published results, with strong collaborations between computational and empirical biologists to develop, test and improve methods of data synthesis. This initial tree of life will not be static; instead, we will develop tools for scientists to update and revise the tree as new data come in. Early release of the tree and tools will motivate data sharing and facilitate ongoing synthesis of knowledge.",
     "doi": "10.17616/R35D27",
-    "homepage": "https://tree.opentreeoflife.org/opentree/argus/opentree13.4@ott93302",
+    "homepage": "https://tree.opentreeoflife.org/opentree/argus/opentree15.1@ott93302",
     "license": "BSD",
     "name": "Open Tree of Life",
     "prefix": "r3d100011767",
@@ -15493,7 +15493,7 @@
   "r3d100011768": {
     "description": "OpenWorm aims to build the first comprehensive computational model of the Caenorhabditis elegans (C. elegans), a microscopic roundworm. With only a thousand cells, it solves basic problems such as feeding, mate-finding and predator avoidance. Despite being extremely well studied in biology, this organism still eludes a deep, principled understanding of its biology. \n\nWe are using a bottom-up approach, aimed at observing the worm behaviour emerge from a simulation of data derived from scientific experiments carried out over the past decade. To do so we are incorporating the data available in the scientific community into software models. We are engineering Geppetto and Sibernetic, open-source simulation platforms, to be able to run these different models in concert. We are also forging new collaborations with universities and research institutes to collect data that fill in the gaps\n\nAll the code we produce in the OpenWorm project is Open Source and available on GitHub.",
     "doi": "10.17616/R31P81",
-    "homepage": "http://www.openworm.org/",
+    "homepage": "https://www.openworm.org/",
     "license": "other",
     "name": "OpenWorm",
     "prefix": "r3d100011768"
@@ -20037,7 +20037,7 @@
   "r3d100012335": {
     "description": "GFZ Data Services is a repository for research data and scientific software across the Earth System Sciences, hosted at GFZ. The curated data are archived, persistently accessible and published with digital object identifier (DOI). They range from large dynamic datasets from global monitoring networks with real-time aquisition, to international services in geodesy and geophysics, to the full suite of small and highly heterogeneous datasets collected by individual researchers or small teams (\"long-tail data\"). In addition to the DOI registration and data archiving itself, GFZ Data Services team offers comprehensive consultation by domain scientists and IT specialists. Among others, GFZ Data Services is data publisher for the IAG Services ICGEM, IGETS and ISG (IAG = Int. Association for Geodesy; ICGEM = Int. Center for Global Earth Models; IGETS = Int. Geodynamics and Earth Tide Service; ISG = Int. Service for the Geoid), the World Stress Map, INTERMAGNET, GEOFON, the Geophysical Instrument Pool Potsdam GIPP, TERENO, EnMAP Flight Campaigns, the Potsdam Institute for Climate Impact Research PIK, the Specialised Information Service for Solid Earth Geosciences (FID GEO) and hosts the GFZ Catalogue for the International Generic Sample Number IGSN.",
     "doi": "10.17616/R3VQ0S",
-    "homepage": "https://dataservices-cms.gfz.de/",
+    "homepage": "https://dataservices.gfz.de/",
     "name": "GFZ Data Services",
     "prefix": "r3d100012335"
   },
@@ -34397,12 +34397,11 @@
   "r3d100014525": {
     "description": "Digitum is the Institutional Repository of the University of Murcia.\nIts objective is to allow free access to the scientific and academic production of the University of Murcia in order to increase the visibility of its contents and guarantee the preservation of these digital archives.",
     "doi": "10.17616/R31NJNP9",
-    "homepage": "https://digitum.um.es/digitum/",
+    "homepage": "https://digitum.um.es",
     "name": "DIGITUM",
     "prefix": "r3d100014525",
     "synonyms": [
-      "Depósito de la Universidad de Murcia",
-      "DigitUM",
+      "Depósito Digital Institucional de la Universidad de Murcia",
       "Institutional Repository of the University of Murcia"
     ]
   },
@@ -34530,6 +34529,7 @@
   },
   "r3d100014542": {
     "description": "NewPsy4u is a secure data archiving and HPC processing system. The NewPsy4u platform uses a robust infrastructure to provide researchers with a simple interface for analysing, searching, retrieving and disseminating their biomedical data. With hundreds of investigators across the globe and more than few thousand of downloadable attributes, NewPsy4u aims to become a widespread resource for brain analyses. NewPsy4u platform guarantees reliability with a fault-tolerant network to prevent system failure.",
+    "doi": "10.17616/R31NJNPQ",
     "homepage": "https://newpsy4u.eu",
     "name": "NewPsy4U",
     "prefix": "r3d100014542"
@@ -35555,9 +35555,23 @@
   },
   "r3d100014734": {
     "description": "Edaphobase is a non-commercial data infrastructure developed and hosted by the Senckenberg Museum of Natural History Görlitz in Germany, combining data from heterogeneous sources on soil animals, their distribution and habitat parameters of their sites of occurrence and making this data available to the public in open access.\n\nEdaphobase currently includes data on Nematoda, Collembola, Oribatida, Gamasina, Chilopoda, Diplopoda, Isopoda, Enchytraeidae, and Lumbricidae. Edaphobase lives from the cooperation with numerous soil zoologists who upload their data to the database and thus make them available for overarching analyses and insight. The database currently focusses on Europe-wide soil-biodiversity data, but includes data from around the globe.\n\nEdaphobase is strongly geared towards common data re-use and provision of data and online analysis tools. It follows the FAIR principles and can offer DOIs for submitted data sets. The data warehouse is publically available (open access) via a web-based browser portal, the Edaphobase data-query portal.\n\nAll data (provided it is not anonymized or in an embargo period) can be queried and collated via multiple filters and be downloaded by registered users. Simple queries are possible as well as more sophisticated analyses of different data groups. Specific applications include, e.g., mapping taxa’s distributions, the elucidation of species-specific habitat preferences (niche space), or environmental correlations with population densities.\n\nEdaphobase is a data provider to the Global Biodiversity Information Facility (GBIF).",
+    "doi": "10.17616/R31NJNV2",
     "homepage": "https://portal.edaphobase.org",
     "license": "CC",
     "name": "Edaphobase",
     "prefix": "r3d100014734"
+  },
+  "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.",
+    "homepage": "https://datarepository.unive.it/",
+    "license": "CC",
+    "name": "Datarepository Unive",
+    "prefix": "r3d100014736"
+  },
+  "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.",
+    "homepage": "https://data.mrc.ox.ac.uk/",
+    "name": "Cambium",
+    "prefix": "r3d100014737"
   }
 }

bioregistry/record_accumulator.py

@@ -12,7 +12,7 @@ import curies
 from curies import Converter, Record
 from curies.w3c import NCNAME_RE
 
-from .schema.struct import Resource
+from .schema import Resource
 
 __all__ = [
     "get_converter",

bioregistry/resolve.py

@@ -11,8 +11,7 @@ from typing import Any, Literal, overload
 import curies
 
 from .resource_manager import MetaresourceAnnotatedValue, manager
-from .schema import Attributable, Resource
-from .schema.struct import AnnotatedURL, Collection
+from .schema import AnnotatedURL, Attributable, Collection, Resource
 
 __all__ = [
     "add_resource",

bioregistry/resource_manager.py

@@ -44,11 +44,11 @@ from .schema import (
     Attributable,
     Collection,
     Context,
+    MetaprefixAnnotatedValue,
     Registry,
     Resource,
     sanitize_model,
 )
-from .schema.struct import MetaprefixAnnotatedValue
 from .schema_utils import (
     _collections_from_path,
     _contexts_from_path,

bioregistry/schema/__init__.py

@@ -1,26 +1,50 @@
 """Data structures."""
 
 from .struct import (
+    AnnotatedURL,
     Attributable,
     Author,
     Collection,
     Context,
+    MetaprefixAnnotatedValue,
+    Organization,
+    Provider,
     Publication,
+    RDFFormat,
     Registry,
+    RegistryGovernance,
+    RegistryQualities,
+    RegistrySchema,
     Resource,
+    StatusCheck,
+    deduplicate_publications,
+    generate_schema,
     get_json_schema,
+    schema_status_map,
 )
 from .utils import sanitize_mapping, sanitize_model
 
 __all__ = [
+    "AnnotatedURL",
     "Attributable",
     "Author",
     "Collection",
     "Context",
+    "MetaprefixAnnotatedValue",
+    "Organization",
+    "Provider",
     "Publication",
+    "RDFFormat",
     "Registry",
+    "RegistryGovernance",
+    "RegistryQualities",
+    "RegistrySchema",
     "Resource",
+    "StatusCheck",
+    "deduplicate_publications",
+    "generate_schema",
     "get_json_schema",
     "sanitize_mapping",
     "sanitize_model",
+    "schema_status_map",
 ]

bioregistry/schema/struct.py

@@ -56,9 +56,12 @@ __all__ = [
     "Organization",
     "Provider",
     "Publication",
+    "RDFFormat",
     "Registry",
     "Resource",
     "ResourceStatus",
+    "StatusCheck",
+    "deduplicate_publications",
     "get_json_schema",
 ]
 

bioregistry/version.py

@@ -11,7 +11,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.13.9"
+VERSION = "0.13.11"
 
 
 def get_git_hash() -> str | None:

{bioregistry-0.13.9.dist-info → bioregistry-0.13.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioregistry
-Version: 0.13.9
+Version: 0.13.11
 Summary: Integrated registry of biological databases and nomenclatures
 Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases,persistent identifiers
 Author: Charles Tapley Hoyt