bioregistry 0.13.17__py3-none-any.whl → 0.13.19__py3-none-any.whl

bioregistry/external/bioportal/ecoportal.json

@@ -145,6 +145,19 @@
     ],
     "version": "2.1"
   },
+  "BIOMASSVRE": {
+    "contact": {
+      "email": "jessica.titocci@cnr.it",
+      "name": "Jessica Titocci"
+    },
+    "description": "The Biomass VRE Thesaurus provides a comprehensive set of concepts designed to enhance the interoperability of data related to both aquatic and terrestrial biomass. Its main goal is to facilitate the harmonisation and integration of heterogeneous datasets that include abiotic and biotic variables, measured in situ or derived from remote sensing observations. The thesaurus includes well-defined terms with corresponding labels, definitions, and semantic relationships covering key concepts associated with aquatic and terrestrial biomass. The Biomass VRE Thesaurus ensures compatibility with other data infrastructures and supports the sharing, comparison, and reuse of biomass-related information across different scientific domains and research communities.",
+    "example_uri": "https://kos.lifewatch.eu/thesauri/vrebiomass/c_12bf14d7",
+    "homepage": "https://ecoportal.lifewatch.eu/ontologies/BIOMASSVRE",
+    "license": "CC-BY-4.0",
+    "name": "Biomass VRE Thesaurus",
+    "prefix": "BIOMASSVRE",
+    "version": "1.0.0"
+  },
   "BIOREGIONS": {
     "contact": {
       "email": "cr@eionet.europa.eu",
@@ -550,6 +563,16 @@
       "https://thesaurus.geolba.ac.at/bibl_res.html?proj=GeologicUnit"
     ]
   },
+  "GEOSP": {
+    "contact": {
+      "email": "mohamed-el-amine.boukerfa@inrae.fr",
+      "name": "LOV Migration"
+    },
+    "description": "The GeoSpecies Ontology is used to describe geographical distribution of living species.",
+    "name": "GeoSpecies Ontology",
+    "prefix": "GEOSP",
+    "version": "v2012-10-02"
+  },
   "GEO_STRUCTURES": {
     "contact": {
       "email": "thesaurus@geologie.ac.at",
@@ -820,6 +843,17 @@
     "repository": "https://github.com/PopulationAndCommunityOntology/pco",
     "version": "2021-05-03"
   },
+  "PECO": {
+    "contact": {
+      "email": "mohamed-el-amine.boukerfa@inrae.fr",
+      "name": "LOV Migration"
+    },
+    "description": "This ontology defines a vocabulary for describing provenance traces of carbon emission calculations by capturing the quantifiable measurements of carbon emission sources used by some activities (e.g., electricity used by a machinery to produce a product, petrol used to make a car journey, etc.) and emission conversion factors used to estimate the carbon emissions produced by these. In addition, the ontology provides the ability to capture various data transformations that occurred before energy estimates may be used with relevant conversion factors. For example, sensors may provide raw readings about a water flow of an irrigation rig in an agri-food operation which is then used as a proxy to estimate the total volume of fertilisers used.",
+    "license": "CC-BY-4.0",
+    "name": "The Provenance of Emission Calculations Ontology",
+    "prefix": "PECO",
+    "version": "1.0.0"
+  },
   "PHYTOTRAITS": {
     "contact": {
       "email": "elena.stanca@unisalento.it",
@@ -834,6 +868,19 @@
     ],
     "version": "1.5"
   },
+  "PHYTOVRE": {
+    "contact": {
+      "email": "jessica.titocci@cnr.it",
+      "name": "Jessica Titocci"
+    },
+    "description": "The Phytoplankton VRE Thesaurus includes a set of concepts designed to facilitate navigation and use of the Virtual Research Environment (VRE), and to support data harmonisation and interoperability within the VRE, as well as data comparability and reusability across different platforms and research communities. In particular, the thesaurus encompasses concepts related to phytoplankton counting methods, statistical analyses, community indices, and parameters used in the VRE. It also includes standardised terms required to harmonise data templates used as input files for the VRE, the complete list of services available within the VRE, and specific terminology related to phytoplankton. The Phytoplankton VRE Thesaurus is aligned with existing vocabularies and thesauri to ensure semantic consistency and interoperability across research infrastructures, including the Traits Thesaurus, the Biomass VRE Thesaurus, and other relevant domain-specific semantic artefacts.",
+    "example_uri": "https://kos.lifewatch.eu/thesauri/vrephytoplankton/c_b89cdbfb",
+    "homepage": "https://ecoportal.lifewatch.eu/ontologies/PHYTOVRE",
+    "license": "CC-BY-4.0",
+    "name": "Phytoplankton VRE Thesaurus",
+    "prefix": "PHYTOVRE",
+    "version": "1.0.0"
+  },
   "PORO": {
     "contact": {
       "email": "thacker@uab.edu",

bioregistry/external/fairsharing/processed.json

@@ -2114,12 +2114,11 @@
   },
   "FAIRsharing.3e603c": {
     "abbreviation": "PURL",
-    "description": "PURLs are Web addresses or Uniform Resource Locators (URLs) that act as permanent identifiers in the face of a dynamic and changing Web infrastructure. Instead of resolving directly to Web resources (documents, data, services, people, etc.). PURLs allow third party control over both URL resolution and resource metadata provision. A URL is simply an address of a resource on the World Wide Web. A Persistent URL is an address on the World Wide Web that causes a redirection to another Web resource. If a Web resource changes location (and hence URL), a PURL pointing to it can be updated. A user of a PURL always uses the same Web address, even though the resource in question may have moved. PURLs may be used by publishers to manage their own information space or by Web users to manage theirs; a PURL service is independent of the publisher of information. Please note that the referenced homepage contains links to an archived google code site, and may not refer to the current specification location. Please get in touch with us if you have more information.",
+    "description": "PURLs are Web addresses or Uniform Resource Locators (URLs) that act as permanent identifiers in the face of a dynamic and changing Web infrastructure. Instead of resolving directly to Web resources (documents, data, services, people, etc.). PURLs allow third party control over both URL resolution and resource metadata provision. A URL is simply an address of a resource on the World Wide Web. A Persistent URL is an address on the World Wide Web that causes a redirection to another Web resource. If a Web resource changes location (and hence URL), a PURL pointing to it can be updated. A user of a PURL always uses the same Web address, even though the resource in question may have moved. PURLs may be used by publishers to manage their own information space or by Web users to manage theirs; a PURL service is independent of the publisher of information. When a user retrieves a PURL they will be redirected to the current location of the resource. When an author needs to move a page they can update the PURL to point to the new location. PURLs with a common prefix are grouped together into domains. Each domain has a single maintainer who can add new PURLs to the domain and make changes to existing PURLs within the domain. Each PURL has a target and status code or type. The target specifies where the PURL redirects to. The type is a status code from HTTP specification. The default PURL type is \"302 Found\", meaning that the object of the request was found elsewhere. This is the status code that should be used if there is not a reason to use a different one.\n\nA partial PURL is a special type which will match the beginning of a URL. The PURL resolver will match as much of a PURL as it can and append the remainder to the end of the resolved URL. This reduces the need to create multiple PURLs to handle all of the resources that share a common location. For more on partials, see the section below the following table.",
     "domains": [
       "centrally registered identifier"
     ],
-    "homepage": "https://code.google.com/archive/p/persistenturls/",
-    "license": "Apache 2.0 License",
+    "homepage": "https://purl.archive.org/help",
     "name": "Persistent Uniform Resource Locator",
     "subjects": [
       "Subject Agnostic"
@@ -2199,7 +2198,7 @@
   "FAIRsharing.3kcgmr": {
     "abbreviation": "CARO",
     "contact": {
-      "email": "haendel@ohsu.edu",
+      "email": "mhaendel@unc.edu",
       "name": "Melissa Haendel",
       "orcid": "0000-0001-9114-8737"
     },
@@ -2208,6 +2207,7 @@
       "Annotation"
     ],
     "homepage": "http://bioportal.bioontology.org/ontologies/CARO?p=summary",
+    "license": "CC-BY-4.0",
     "name": "Common Anatomy Reference Ontology",
     "publications": [
       {
@@ -2216,6 +2216,7 @@
         "year": 2008
       }
     ],
+    "repository": "https://github.com/obophenotype/caro",
     "subjects": [
       "Life Science",
       "Anatomy"
@@ -5896,11 +5897,11 @@
   },
   "FAIRsharing.9228fv": {
     "abbreviation": "CROPUSAGE",
-    "description": "A thesaurus about crops cultivated in France. The hierarchy is based on the final destination of the crop (human food, animal breeding, food industry) and the cultivated system. The hierachy is not based on scientific agronomic taxon like (species, genus). We are interested on categorize the usage of the crop, not on the plant classification.",
+    "description": "An RDF vocabulary for describing the basic structure and content of concept schemes such as thesauri, classification schemes, subject heading lists, taxonomies, 'folksonomies', other types of controlled vocabulary, and also concept schemes embedded in glossaries and terminologies. The sources used are the parcel register, the agricultural larousse, wikipedia, the official catalogue of species and varieties of plants cultivated in France of GEVES, the \"fodder plants for peerages\" sheets of the GNIS, the Ephy database, the list of crops to be used to fill in the description of the plots and the annual agricultural statistics of the Agreste, the tables of the Acta catalogue published in 2021. Concerning vegetables and their classification, we looked for the common points between several sources: Wikipedia, Bonduelle, FranceAgriMer, Encyclopedia Universalis, AM Nagelseim, the Bec Hellouin farm. To our conclusion, there is no consensus on the classification of vegetables. This classification is used to organize the Plant Health Bulletins (BSV) and the GECO sheets. ",
     "domains": [
       "food"
     ],
-    "homepage": "https://doi.org/10.1016/j.compag.2017.10.022",
+    "homepage": "https://doi.org/10.15454/QHFTMX",
     "license": "CC-BY-4.0",
     "name": "French Crop Usage",
     "publications": [
@@ -6674,7 +6675,7 @@
   },
   "FAIRsharing.FrSPDi": {
     "description": "This thesaurus is based on the vocabulary used in scientific publications for Artificial nutrition and neighbor fields. It contains more than 2500 concepts in two languages (English and French), including various variants (synonyms, acronyms) divided into a number of microthesauri where the terms are grouped around a theme or a semantic field.",
-    "homepage": "https://loterre.istex.fr/BL8/en/",
+    "homepage": "https://dx.doi.org/10.13143/lotr.2136",
     "license": "CC-BY-4.0",
     "name": "Artificial Nutrition Thesaurus",
     "subjects": [
@@ -7973,7 +7974,7 @@
   "FAIRsharing.av8nfd": {
     "abbreviation": "OFSMR",
     "description": "This is the food-matrix ontology for the Open Food Safety Model Repository. Transferring predictive microbial models from research into real world food manufacturing or risk assessment applications is still a challenge for members of the food safety modelling community. This ontology supports the repository where existing predictive models previously published in the scientific literature were re-implemented using Predictive Modelling in Food Markup Language (PMF-ML), which is based on SBML.",
-    "homepage": "https://sites.google.com/site/openfsmr/",
+    "homepage": "https://bioportal.bioontology.org/ontologies/OFSMR",
     "name": "Open Food Safety Model Ontology",
     "publications": [
       {
@@ -12125,6 +12126,7 @@
       "Bioimaging"
     ],
     "homepage": "https://github.com/edamontology/edam-bioimaging",
+    "license": "CC BY-SA 4.0",
     "name": "EDAM Bioimaging Ontology",
     "publications": [
       {
@@ -12134,6 +12136,7 @@
         "year": 2013
       }
     ],
+    "repository": "https://github.com/edamontology/edam-bioimaging",
     "subjects": [
       "Bioinformatics"
     ]
@@ -12431,17 +12434,18 @@
     ]
   },
   "FAIRsharing.hFLKCn": {
-    "abbreviation": "DOI",
+    "abbreviation": "DOI (ISO 26324:2025)",
     "contact": {
       "email": "jonathanmtclark@gmail.com",
       "name": "Jonathan Clark",
       "orcid": "0000-0001-9551-9662"
     },
-    "description": "The digital object identifier (DOI) system originated in a joint initiative of three trade associations in the publishing industry (International Publishers Association; International Association of Scientific, Technical and Medical Publishers; Association of American Publishers). The system was announced at the Frankfurt Book Fair 1997. The International DOI® Foundation (IDF) was created to develop and manage the DOI system, also in 1997. The DOI system was adopted as International Standard ISO 26324 in 2012. The DOI system implements the Handle System and adds a number of new features. The DOI system provides an infrastructure for persistent unique identification of objects of any type. The DOI system is designed to work over the Internet. A DOI name is permanently assigned to an object to provide a resolvable persistent network link to current information about that object, including where the object, or information about it, can be found on the Internet. While information about an object can change over time, its DOI name will not change. A DOI name can be resolved within the DOI system to values of one or more types of data relating to the object identified by that DOI name, such as a URL, an e-mail address, other identifiers and descriptive metadata. The DOI system enables the construction of automated services and transactions. Applications of the DOI system include but are not limited to managing information and documentation location and access; managing metadata; facilitating electronic transactions; persistent unique identification of any form of any data; and commercial and non-commercial transactions. The content of an object associated with a DOI name is described unambiguously by DOI metadata, based on a structured extensible data model that enables the object to be associated with metadata of any desired degree of precision and granularity to support description and services. The data model supports interoperability between DOI applications. The scope of the DOI system is not defined by reference to the type of content (format, etc.) of the referent, but by reference to the functionalities it provides and the context of use. The DOI system provides, within networks of DOI applications, for unique identification, persistence, resolution, metadata and semantic interoperability.",
+    "description": "The digital object identifier (DOI) system originated in a joint initiative of three trade associations in the publishing industry (International Publishers Association; International Association of Scientific, Technical and Medical Publishers; Association of American Publishers). The system was announced at the Frankfurt Book Fair 1997. The International DOI® Foundation (IDF) was created to develop and manage the DOI system, also in 1997. The DOI system was adopted as International Standard ISO 26324 in 2012 and updated in 2025. The DOI system implements the Handle System and adds a number of new features. The DOI system provides an infrastructure for persistent unique identification of objects of any type. The DOI system is designed to work over the Internet. A DOI name is permanently assigned to an object to provide a resolvable persistent network link to current information about that object, including where the object, or information about it, can be found on the Internet. While information about an object can change over time, its DOI name will not change. A DOI name can be resolved within the DOI system to values of one or more types of data relating to the object identified by that DOI name, such as a URL, an e-mail address, other identifiers and descriptive metadata. The DOI system enables the construction of automated services and transactions. Applications of the DOI system include but are not limited to managing information and documentation location and access; managing metadata; facilitating electronic transactions; persistent unique identification of any form of any data; and commercial and non-commercial transactions. The content of an object associated with a DOI name is described unambiguously by DOI metadata, based on a structured extensible data model that enables the object to be associated with metadata of any desired degree of precision and granularity to support description and services. The data model supports interoperability between DOI applications. The scope of the DOI system is not defined by reference to the type of content (format, etc.) of the referent, but by reference to the functionalities it provides and the context of use. The DOI system provides, within networks of DOI applications, for unique identification, persistence, resolution, metadata and semantic interoperability.",
     "domains": [
       "centrally registered identifier"
     ],
-    "homepage": "https://www.doi.org",
+    "homepage": "https://www.doi.org/the-identifier/resources/handbook/",
+    "license": "CC-BY-4.0",
     "name": "Digital Object Identifier",
     "publications": [
       {
@@ -12887,14 +12891,10 @@
   },
   "FAIRsharing.jT49Da": {
     "description": "The Provenance Vocabulary provides classes and properties for describing provenance of Web data. The vocabulary focuses on two main use cases: 1.) It enables consumers of Web data to describe provenance of data retrieved from the Web and of data derived from such Web data. 2.) It enables providers of Web data to publish provenance-related metadata about their data. Notice, the vocabulary is not intended for describing provenance of other kinds of Web content. The Provenance Vocabulary is designed as a Web data specific specialization of the W3C PROV Ontology (PROV-O); classes and properties provided by the vocabulary are domain specific extensions of the more general concepts introduced in PROV-O. As a consequence, any Provenance Vocabulary based description of provenance can be easily interpreted and exchanged according to the W3C PROV family of standards. While this vocabulary is in a stable state, it is not being actively developed at this time.",
-    "domains": [
-      "Resource metadata"
-    ],
     "homepage": "http://purl.org/net/provenance/ns",
     "license": "https://creativecommons.org/licenses/by/1.0",
     "name": "Provenance Vocabulary",
     "subjects": [
-      "Data Management",
       "Computer Science"
     ]
   },
@@ -13842,19 +13842,24 @@
   },
   "FAIRsharing.m0e1s0": {
     "abbreviation": "SOY",
-    "description": "This is a community-curated controlled vocabulary for soybean field growth stages (Soybean Whole Plant Growth Ontology), plant structure names (Soybean Structure Ontology), development (Soybean Development Ontology) and plant traits (Soybean Trait Ontology). Where applicable, soybean specific terms have been associated with their Plant Ontology (PO) and Gramene Plant Trait Ontology (TO) synonyms to facilitate cross species comparisons.  Currently, there are 4 divisions to SOY terms, soybean structural terms (Soybean Structure Ontology), developmental stages (Soybean Developmental Ontology), whole plant development terms (Soybean Whole Plant Growth Stages) and trait terms (Soybean Trait Ontology). For the trait, structure and development terms the old SoyTO and SoyGRO accessions have been added to their records as synonyms for continuity.",
+    "description": "The ontologies below were developed to provide a controlled vocabulary for: field growth stages (Soybean Whole Plant Growth Ontology), plant structure (Soybean Structure Ontology), development (Soybean Development Ontology), and plant traits (Soybean Trait Ontology). Where applicable, soybean specific terms have been associated with their Plant Ontology (PO) synonyms to facilitate cross species comparisons. Since the original release of the SoyBase Ontologies, they have been re-factored at the request of the Plant Ontology Consortium. This change resulted in the elimination of a separate accession system for SoyTO and SoyGRO. These terms were re-accessioned into the SoyWGR namespace and the SoyWGR prefix was changed to SOY. Input from the community is welcomed.",
     "domains": [
       "phenotype",
       "life cycle stage"
     ],
-    "homepage": "https://soybase.org/ontology.php",
-    "name": "SoyOntology",
+    "homepage": "https://www.soybase.org/tools/ontology/",
+    "name": "SoyBase Soybean Ontologies",
     "publications": [
       {
         "doi": "10.1093/nar/gkp798",
         "pubmed": "20008513",
         "title": "SoyBase, the USDA-ARS soybean genetics and genomics database",
         "year": 2009
+      },
+      {
+        "doi": "10.1093/nar/gkaa1107",
+        "title": "A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database",
+        "year": 2021
       }
     ],
     "subjects": [
@@ -13862,8 +13867,7 @@
       "Botany",
       "Anatomy",
       "Developmental Biology"
-    ],
-    "twitter": "SoyBaseDatabase"
+    ]
   },
   "FAIRsharing.m0pprb": {
     "abbreviation": "RCTONT",
@@ -14312,7 +14316,7 @@
       "protein",
       "target"
     ],
-    "homepage": "http://bioassayontology.org",
+    "homepage": "http://bioassayontology.org/bioassayontology/",
     "license": "CC-BY-4.0",
     "name": "BioAssay Ontology",
     "publications": [
@@ -15366,7 +15370,6 @@
     ]
   },
   "FAIRsharing.q47I0t": {
-    "abbreviation": "CryoEM Ontology",
     "contact": {
       "email": "coss@cnb.csic.es",
       "name": "Carlos Oscar S. Sorzano",
@@ -15377,8 +15380,7 @@
       "Bioimaging",
       "electron microscopy"
     ],
-    "homepage": "http://scipion.i2pc.es/ontology/cryoem",
-    "license": "CC-BY-3.0",
+    "homepage": "https://github.com/I2PC/cryoem",
     "name": "CryoEM Ontology",
     "repository": "https://github.com/I2PC/cryoem",
     "subjects": [
@@ -15795,11 +15797,11 @@
   },
   "FAIRsharing.r7Kwy7": {
     "abbreviation": "CAS RN",
-    "description": "Identifier used by the Chemical Abstracts Service Registry. A CAS Registry Number is a numeric identifier that can contain up to 10 digits, divided by hyphens into three parts. The right-most digit is a check digit used to verify the validity and uniqueness of the entire number.",
+    "description": "Chemical compounds are described in many ways, including molecular formulas, chemical structures, generic, systematic, common, and trade names. This lack of clarity can cause frustration, delays, and even safety concerns. A CAS Registry Number (CAS RN®) is a unique and unambiguous identifier for a specific substance that allows clear communication and, with the help of CAS scientists, links together all available data and research about that substance. Governmental agencies rely on CAS Registry Numbers for substance identification in regulatory applications because they are unique, easily validated, and internationally recognised. CAS RNs are used by the Chemical Abstracts Service Registry. A CAS Registry Number is a numeric identifier that can contain up to 10 digits, divided by hyphens into three parts. The right-most digit is a check digit used to verify the validity and uniqueness of the entire number.",
     "domains": [
       "chemical entity"
     ],
-    "homepage": "https://www.cas.org/cas-data/cas-registry",
+    "homepage": "https://www.cas.org/training/documentation/chemical-substances/checkdig",
     "name": "CAS Registry Number",
     "publications": [
       {
@@ -18407,7 +18409,7 @@
       "infection process",
       "pathogen"
     ],
-    "homepage": "http://www.phidias.us/bbp/idobru/index.php",
+    "homepage": "https://hegroup.org/projects.html",
     "name": "Brucellosis Ontology",
     "publications": [
       {
@@ -19310,9 +19312,9 @@
       "pathogen",
       "vaccination"
     ],
-    "homepage": "https://github.com/vaccineontology/VO",
-    "license": "CC-BY-3.0",
-    "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaUFDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--0d3898a5618b34c0bc948bb0d101e906f212f05f/vo_banner.png?disposition=inline",
+    "homepage": "http://www.violinet.org/vaccineontology",
+    "license": "CC-BY-4.0",
+    "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBck1IIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--bcbea6b26f9bd1db48d5f256c3d75bedd6fc2332/Screenshot%20From%202026-01-26%2011-30-20.png?disposition=inline",
     "name": "The Vaccine Ontology",
     "publications": [
       {
@@ -19344,6 +19346,11 @@
         "pubmed": "24209834",
         "title": "Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology",
         "year": 2013
+      },
+      {
+        "doi": "10.1101/2025.08.12.669998",
+        "title": "VO: The Vaccine Ontology",
+        "year": 2025
       }
     ],
     "repository": "https://github.com/vaccineontology",

bioregistry/external/go/processed.json

@@ -3578,6 +3578,7 @@
       {
         "example_id": "SGD_PWY:SERSYN-PWY",
         "example_url": "https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=NIL&object=SERSYN-PWY",
+        "id_syntax": "^[A-Z0-9-]+$",
         "type_id": "BET:0000000",
         "type_name": "entity",
         "url_syntax": "https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=NIL&object=[example_id]"

bioregistry/external/integbio/__init__.py

@@ -131,18 +131,18 @@ def get_integbio(*, force_download: bool = False) -> dict[str, dict[str, Any]]:
         inplace=True,
     )
     for key in SKIP:
-        del df[key]  # type:ignore[operator]
+        del df[key]
 
     df["fairsharing"] = df["fairsharing"].map(_parse_fairsharing_url, na_action="ignore")
     df = df[df["languages"] != "ja"]  # skip only japanese language database for now
-    del df["languages"]  # type:ignore[operator]
+    del df["languages"]
     # df["languages"] = df["languages"].map(_strip_split, na_action="ignore")
     df["target_keywords"] = df["target_keywords"].map(_strip_split, na_action="ignore")
     df["information_keywords"] = df["information_keywords"].map(_strip_split, na_action="ignore")
     df["pubmeds"] = df["references"].map(_parse_references, na_action="ignore")
     df["description"] = df["description"].map(lambda s: s.replace("\r\n", "\n"), na_action="ignore")
 
-    del df["references"]  # type:ignore[operator]
+    del df["references"]
     # TODO ground database maintenance with ROR?
     rv: dict[str, dict[str, Any]] = {}
     for _, row in df.iterrows():

bioregistry/external/integbio/processed.json

@@ -69,7 +69,7 @@
  },
  "nbdc00005": {
   "description": "Animal Search System allows keyword searches to be performed on more than 2000 strains of mice available from the RIKEN BRC, including transgenic, knockout, inbred, wild-derived, ENU mutant and congenic strains. Although the top page is written in Japanese, each search result has a link to the English page. The system also provides detailed information that capture the characteristics of the strain, such as the strain name, description, gene details, references, availability status, images and so on.",
-  "homepage": "http://www2.brc.riken.jp/lab/animal/search.php",
+  "homepage": "https://mus.brc.riken.jp/en/search_for_mouse_strain",
   "information_keywords": [
    "Bioresource",
    "Method",
@@ -386,6 +386,7 @@
   "maintainer": "NCBI (National Center for Biotechnology Information)",
   "name": "Cancer Chromosomes",
   "prefix": "NBDC00021",
+  "status": "Closed",
   "target_keywords": [
    "Genome/Gene",
    "Health/Disease",
@@ -522,7 +523,7 @@
    "14744116",
    "15669238"
   ],
-  "status": "Inactive",
+  "status": "Closed",
   "target_keywords": [
    "cDNA/EST"
   ]
@@ -1795,7 +1796,7 @@
   "maintainer": "University of California",
   "name": "HarvEST",
   "prefix": "NBDC00094",
-  "status": "Active",
+  "status": "Inactive",
   "target_keywords": [
    "cDNA/EST"
   ]
@@ -1822,13 +1823,13 @@
  "nbdc00096": {
   "alt_name": "A navigator of small molecules in Protein Data Bank which is called heterogen atoms or in short hetatoms",
   "description": "Het-PDB Navi is a database of heterogen molecules in the Protein Data Bank (PDB), which act as cofactors for enzymes or stabilizers of proteins. Entries can be surveyed to study their interactions statistically. Searches can be performed based on PDB code, hetero-atom code, protein name or hetero-atom name. Help with the use of the RasMol application is also provided.",
-  "homepage": "http://hetpdbnavi.nagahama-i-bio.ac.jp/index.php?mode=0",
+  "homepage": "https://hetpdbnavi.nagahama-i-bio.ac.jp/",
   "information_keywords": [
    "Interaction/Pathway",
    "3D structure"
   ],
   "maintainer": "Nagahama Institute of Bio-Science and Technology",
-  "name": "Het-PDB Navi",
+  "name": "Het-PDB Navi２",
   "prefix": "NBDC00096",
   "pubmeds": [
    "14999012"
@@ -1900,7 +1901,7 @@
   "maintainer": "NCBI (National Center for Biotechnology Information)",
   "name": "HomoloGene",
   "prefix": "NBDC00101",
-  "status": "Active",
+  "status": "Closed",
   "target_keywords": [
    "Genome/Gene",
    "Protein"
@@ -2144,7 +2145,7 @@
  "nbdc00113": {
   "alt_name": "Japan Mouse/Rat Strain Resources Database",
   "description": "JMSR is constructed by the genetic Informatics Laboratory, National Institute of genetics (NIG) as a database of mouse and rat strains stocked in Japan. JMSR covers almost all the bioresources of mice and rats available in Japan including frozen embryos, frozen sperm, organs and ES cells. This database provides a query form to cross-search databases of 10 stock centers for the strains. A link in each search result shows detailed information on a request for the bioresource.",
-  "homepage": "http://www.shigen.nig.ac.jp/mouse/jmsr/top.jsp",
+  "homepage": "https://shigen.nig.ac.jp/mouse/jmsr/",
   "information_keywords": [
    "Bioresource"
   ],
@@ -2607,7 +2608,7 @@
  "nbdc00139": {
   "alt_name": "Mouse Microsatellite Data Base of Japan",
   "description": "MMDBJ is a database of mouse microsatellite loci to provide information about simple sequence length polymorphisms (SSLPs) among different strains. MMDBJ features SSLP loci obtained from strains derived from Mus musculus molossinus (Japanese wild mouse). Each record contains polymorphism data, PCR condition and a link to Ensembl Genome Browser web page to view primer sequences. This database also provides a search engine and a linkage map of mouse microsatellite loci.",
-  "homepage": "http://www.shigen.nig.ac.jp/mouse/mmdbj/top.jsp",
+  "homepage": "http://shigen.nig.ac.jp/mouse/mmdbj/",
   "information_keywords": [
    "Sequence",
    "Image/Movie"
@@ -2618,7 +2619,7 @@
   "pubmeds": [
    "15153678"
   ],
-  "status": "Active",
+  "status": "Closed",
   "target_keywords": [
    "cDNA/EST",
    "Genetic variation"
@@ -2783,21 +2784,21 @@
   ]
  },
  "nbdc00150": {
-  "alt_name": "Nucleic Acid Database",
-  "description": "The Nucleic Acid Database Project (NDB) aims to collect and distribute information on nucleic acid structures. Each entry contains information on nucleic acid sequences, its structure and the characteristics, the primary citation, experimental information, as well as a link to PDB. Furthermore, structure coordinates and structure factors can be downloaded from the site.",
+  "alt_name": "Nucleic Acid Knowledgebase",
+  "description": "The Nucleic Acid Knowledgebase (NAKB) aims to collect and distribute information on nucleic acid structures. Each entry contains information on nucleic acid sequences, its structure and the characteristics, the primary citation, experimental information, as well as a link to PDB. Furthermore, structure coordinates and structure factors can be downloaded from the site.",
   "fairsharing": "biodbcore-000513",
-  "homepage": "http://ndbserver.rutgers.edu",
+  "homepage": "https://nakb.org/",
   "information_keywords": [
    "Sequence",
    "Bibliography/Documents"
   ],
   "maintainer": "The State University of New Jersey",
-  "name": "NDB",
+  "name": "NAKB",
   "prefix": "NBDC00150",
   "pubmeds": [
    "1384741"
   ],
-  "status": "Inactive",
+  "status": "Active",
   "target_keywords": [
    "DNA",
    "RNA",
@@ -3058,16 +3059,15 @@
   ]
  },
  "nbdc00164": {
-  "alt_name": "Pharmacogenomics Knowledge Base",
-  "description": "PharmGKB is a database of genotype-drug response knowledge. The database contains information about genes, diseases, and drugs independently and information on how the three factors interact. PharmGKB is curated by scientists and engineers with expertise in pharmacogenomics. Bulk data is available for download.",
+  "description": "ClinPGx is a comprehensive database of pharmacogenomics (PGx) resource. It is designed to catalog, curate, annotate, integrate, generate and disseminate PGx knowledge, and advance PGx clinical implementation,  PGx integration with genomic medicine, and PGx education. ClinPGx is constructed from the combination of the NIH-funded PharmGKB, CPIC and PharmCAT projects, with new features and tools. It will also work with ClinGen and ClinVar to improve integration of PGx within broader genomic medicine.",
   "fairsharing": "biodbcore-000525",
-  "homepage": "http://www.pharmgkb.org/",
+  "homepage": "https://www.clinpgx.org/",
   "information_keywords": [
    "Ontology/Terminology/Nomenclature",
    "Interaction/Pathway"
   ],
   "maintainer": "Stanford University",
-  "name": "PharmGKB",
+  "name": "ClinPGx",
   "prefix": "NBDC00164",
   "pubmeds": [
    "11752281",
@@ -3457,7 +3457,7 @@
    "19004872",
    "24288368"
   ],
-  "status": "Inactive",
+  "status": "Closed",
   "target_keywords": [
    "RNA"
   ]
@@ -3608,7 +3608,7 @@
    "15608280",
    "16769687"
   ],
-  "status": "Active",
+  "status": "Closed",
   "target_keywords": [
    "cDNA/EST"
   ]
@@ -3732,7 +3732,7 @@
    "15980577",
    "14681423"
   ],
-  "status": "Active",
+  "status": "Closed",
   "target_keywords": [
    "Cell/Organelle"
   ]
@@ -3978,7 +3978,7 @@
   "pubmeds": [
    "15509851"
   ],
-  "status": "Active",
+  "status": "Closed",
   "target_keywords": [
    "cDNA/EST"
   ]
@@ -4052,7 +4052,7 @@
    "14996221",
    "15840642"
   ],
-  "status": "Active",
+  "status": "Closed",
   "target_keywords": [
    "Genome/Gene",
    "Organism"
@@ -4304,7 +4304,7 @@
   "pubmeds": [
    "12324948"
   ],
-  "status": "Active",
+  "status": "Closed",
   "target_keywords": [
    "Genome/Gene",
    "Organism"
@@ -4811,7 +4811,7 @@
  "nbdc00267": {
   "alt_name": "Four-dimensional Ascidian Body Atlas",
   "description": "FABA is a database of the developmental stages of Ciona intestinalis, with 3D images taken at critical time points, as well as movies of the development process, for standardization of C. intestinalis studies. Images were acquired at zygote, cleavage, gastrula, neurula, tailbud, and larva stages. Downloads are available, as is a companion site (FABA2) with images of organisms post-hatching.",
-  "homepage": "https://www.bpni.bio.keio.ac.jp/chordate/faba/1.4/top.html",
+  "homepage": "https://chordate.bpni.bio.keio.ac.jp/chordate/faba/1.4/top.html",
   "information_keywords": [
    "Image/Movie",
    "3D structure"
@@ -4822,7 +4822,7 @@
   "pubmeds": [
    "17557317"
   ],
-  "status": "Inactive",
+  "status": "Active",
   "target_keywords": [
    "Protein",
    "Organism"
@@ -5260,7 +5260,7 @@
  "nbdc00298": {
   "alt_name": "High Resolution Mass Spectral Database",
   "description": "MassBank is a high-resolution mass spectral database that involves the JST-BIRD project, and was developed by the Institute for Advanced Biosciences, Keio University (IAB) Analytical Chemistry Group, and the RIKEN Plant Science Center (PSC) Metabolomics Research Group. MassBank is used to search chemical compounds that have been detected by mass spectrometry for chemical identification, structure detail, similar spectrum search, etc. MassBank was recognized as the official mass spectral database of the Mass Spectrometry Society of Japan in 2008. It also contains the results of the NEDO project.",
-  "homepage": "http://www.massbank.jp/Index",
+  "homepage": "https://massbank.jp/MassBank/",
   "information_keywords": [
    "Method",
    "Chemical structure"
@@ -10729,6 +10729,7 @@
   "pubmeds": [
    "19032166"
   ],
+  "status": "Closed",
   "target_keywords": [
    "Metabolite"
   ]

bioregistry/external/lov/processed.json

@@ -424,7 +424,7 @@
     "prefix": "era",
     "uri_prefix": "http://data.europa.eu/949/$1",
     "description": "This is the human and machine readable Vocabulary/Ontology governed by the European Union Agency for Railways. It represents the concepts and relationships linked to the sectorial legal framework and the use cases under the Agency\u00b4s remit. Currently, this vocabulary covers the European railway infrastructure and the vehicles authorized to operate over it. It is a semantic/browsable representation of the RINF and ERATV application guides that were built by domain experts in the RINF and ERATV working parties.\nSince version 2.6.0, the ontology includes the routebook concepts described in appendix D2 \\\"Elements the infrastructure manager has to provide to the railway undertaking for the Route Book\\\" (https://eur-lex.europa.eu/eli/reg_impl/2019/773/oj) and the appendix D3 \\\"ERTMS trackside engineering information relevant to operation that the infrastructure manager shall provide to the railway undertaking\\\".",
-    "modified": "2025-09-05",
+    "modified": "2026-01-23",
     "homepage": "https://data-interop.era.europa.eu/era-vocabulary/",
     "keywords": [
       "Transport",
@@ -755,6 +755,18 @@
       "Metadata"
     ]
   },
+  "graphql": {
+    "name": "GraphQL Vocabulary",
+    "prefix": "graphql",
+    "uri_prefix": "http://datashapes.org/graphql#$1",
+    "description": "A vocabulary to annotate RDF schemas (in particular SHACL shapes) with metadata to define mappings to GraphQL.",
+    "modified": "2026-01-21",
+    "keywords": [
+      "API",
+      "Methods"
+    ],
+    "homepage": "http://datashapes.org/graphql"
+  },
   "cis": {
     "name": "Cultural-ON (Cultural ONtology): Ontologia dei Luoghi della Cultura e degli Eventi Culturali",
     "prefix": "cis",
@@ -7939,7 +7951,7 @@
     "prefix": "dpp",
     "uri_prefix": "https://ns.verisav.fr/dpp#$1",
     "description": "Vocabulary for Digital Product Passports (DPP) managing product lifecycle, warranties, repairs, and compliance with EU regulations (ESPR EU 2024/1781). Aligned with GS1 Digital Link standards, including GTIN, GLN, granularity (model/batch/serial) and compound identifier support.",
-    "modified": "2025-12-28",
+    "modified": "2026-01-23",
     "keywords": [
       "Food",
       "Industry"
@@ -8637,6 +8649,18 @@
     ],
     "homepage": "https://w3id.org/dco"
   },
+  "dtw": {
+    "name": "WoTDT: The WoT Digital Twin Ontology.",
+    "prefix": "dtw",
+    "uri_prefix": "https://w3id.org/def/dtw#$1",
+    "description": "Digital Twin ontology used to define Digital Twins and Semantic Digital Twins and aggregations by dimensions using Web of Things.",
+    "modified": "2025-06-15",
+    "keywords": [
+      "Industry",
+      "IoT"
+    ],
+    "homepage": "https://w3id.org/def/dtw#"
+  },
   "foo": {
     "name": "Forest Observatory Ontology (FOO)",
     "prefix": "foo",