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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (49) hide show
  1. bioregistry/.DS_Store +0 -0
  2. bioregistry/__init__.py +1 -1
  3. bioregistry/analysis/paper_ranking.py +6 -2
  4. bioregistry/app/.DS_Store +0 -0
  5. bioregistry/app/api.py +1 -2
  6. bioregistry/app/templates/.DS_Store +0 -0
  7. bioregistry/app/ui.py +3 -3
  8. bioregistry/bibliometrics.py +1 -1
  9. bioregistry/cli.py +1 -1
  10. bioregistry/curation/.DS_Store +0 -0
  11. bioregistry/curation/add_cessda.py +1 -1
  12. bioregistry/curation/add_provider_status_curations.py +1 -1
  13. bioregistry/curation/add_sweet.py +146 -0
  14. bioregistry/curation/clean_publications.py +1 -1
  15. bioregistry/curation/enrich_publications.py +1 -1
  16. bioregistry/data/bioregistry.json +6849 -619
  17. bioregistry/data/collections.json +24 -1
  18. bioregistry/data/curated_papers.tsv +9 -0
  19. bioregistry/data/metaregistry.json +1 -1
  20. bioregistry/export/rdf_export.py +1 -1
  21. bioregistry/export/tables_export.py +1 -1
  22. bioregistry/external/.DS_Store +0 -0
  23. bioregistry/external/aberowl/processed.json +23 -19
  24. bioregistry/external/bartoc/processed.json +5 -5
  25. bioregistry/external/biolink/processed.json +3 -0
  26. bioregistry/external/bioportal/agroportal.json +3 -3
  27. bioregistry/external/bioportal/bioportal.json +45 -17
  28. bioregistry/external/cellosaurus/processed.json +3 -3
  29. bioregistry/external/fairsharing/processed.json +6 -5
  30. bioregistry/external/integbio/processed.json +56 -55
  31. bioregistry/external/lov/processed.json +59 -0
  32. bioregistry/external/miriam/.DS_Store +0 -0
  33. bioregistry/external/obofoundry/processed.json +4 -4
  34. bioregistry/external/ols/__init__.py +13 -5
  35. bioregistry/external/ols/processed.json +6 -6
  36. bioregistry/external/ols/tib-processed.json +0 -1
  37. bioregistry/external/ols/tib.py +1 -0
  38. bioregistry/external/re3data/processed.json +24 -2
  39. bioregistry/record_accumulator.py +1 -1
  40. bioregistry/resolve.py +1 -2
  41. bioregistry/resource_manager.py +1 -1
  42. bioregistry/schema/.DS_Store +0 -0
  43. bioregistry/schema/__init__.py +24 -0
  44. bioregistry/schema/struct.py +10 -3
  45. bioregistry/version.py +1 -1
  46. {bioregistry-0.13.8.dist-info → bioregistry-0.13.10.dist-info}/METADATA +1 -1
  47. {bioregistry-0.13.8.dist-info → bioregistry-0.13.10.dist-info}/RECORD +49 -41
  48. {bioregistry-0.13.8.dist-info → bioregistry-0.13.10.dist-info}/WHEEL +1 -1
  49. {bioregistry-0.13.8.dist-info → bioregistry-0.13.10.dist-info}/entry_points.txt +0 -0
@@ -11,11 +11,12 @@
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  ]
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  },
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  "FAIRsharing.01e983": {
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- "description": "Controlled, standardized and multilingual vocabulary for archaeology, from prehistory to the contemporary period and for the sciences of antiquity in all their aspects.\nIts name cames from its first version ",
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+ "abbreviation": "Pactols",
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+ "description": "Created between 1985 and 1987 to index the CNRS-Frantiq network library catalogue, the Pactols thesaurus is a controlled, standardised and multilingual vocabulary, freely accessible and interoperable. Its name comes from its first version : Peuples et Cultures, Anthroponymes, Chronologie relative, Toponymes, Oeuvres, Lieux, Sujets. It is managed with the Opentheso free software. It has evolved to gradually meet the needs of enriching archaeological research data. It is updated regularly.\nIt is organised into two micro-thesauruses:\n- Subjects (approx. 13,000 concepts) relating to archaeology and the Classics;\n- Places (+50,000 concepts) for locating archaeological sites and their natural environment.\nUsed by libraries, archives, scientific journals and scientific resources to enrich thematic metadata, it is now a reference system included in the web of data. It is part of the controlled vocabulary aligned on the linked data cloud.\n",
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  "homepage": "https://pactols.frantiq.fr",
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  "license": "ODBL",
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  "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbmNGIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--9746b8b9da5996f8a86c1fa80e520eb096950ec4/pactols-17x8-300dpi.png?disposition=inline",
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- "name": "PACTOLS: Peuples et Cultures, Anthroponymes, Chronologie relative, Toponymes, Oeuvres, Lieux, Sujets",
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+ "name": "Thésaurus Pactols",
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  "repository": "https://github.com/frantiq/PACTOLS",
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  "subjects": [
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  "Archaeology",
@@ -5841,7 +5842,7 @@
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  "domains": [
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  "food"
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  ],
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- "homepage": "http://ontology.inrae.fr/cropusage",
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+ "homepage": "https://doi.org/10.1016/j.compag.2017.10.022",
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  "license": "CC-BY-4.0",
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  "name": "French Crop Usage",
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  "publications": [
@@ -6188,7 +6189,7 @@
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  "domains": [
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  "centrally registered identifier"
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  ],
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- "homepage": "https://tools.ietf.org/html/rfc1630",
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+ "homepage": "https://url.spec.whatwg.org/",
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  "name": "Uniform Resource Locator",
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  "subjects": [
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  "Knowledge and Information Systems",
@@ -9653,7 +9654,7 @@
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  "domains": [
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  "web service"
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  ],
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- "homepage": "https://www.rfc-editor.org/rfc/rfc3986",
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+ "homepage": "https://datatracker.ietf.org/doc/html/rfc1630",
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  "name": "Uniform Resource Identifier",
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  "publications": [
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  {
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  "pubmeds": [
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  "15608194"
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  ],
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- "status": "Active",
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+ "status": "Inactive",
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  "target_keywords": [
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  "Protein",
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  "Metabolite"
@@ -24513,7 +24513,7 @@
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  ],
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  "name": "Buruli ulcer bacillus Database",
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  "prefix": "NBDC01803",
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- "status": "Active",
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+ "status": "Closed",
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  "target_keywords": [
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  "Genome/Gene",
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  "Protein"
@@ -24528,7 +24528,7 @@
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  ],
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  "name": "Colibri",
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  "prefix": "NBDC01804",
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- "status": "Active",
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+ "status": "Closed",
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  "target_keywords": [
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  "Genome/Gene",
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  "Protein"
@@ -24544,7 +24544,7 @@
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  ],
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  "name": "Legionella pneumophila genome database",
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  "prefix": "NBDC01805",
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- "status": "Active",
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+ "status": "Closed",
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  "target_keywords": [
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  "Genome/Gene",
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  "Organism"
@@ -24560,7 +24560,7 @@
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  ],
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  "name": "Listeria innocua and Listeria monocytogenes genomes database",
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  "prefix": "NBDC01806",
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- "status": "Active",
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+ "status": "Closed",
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  "target_keywords": [
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  "Genome/Gene",
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  "Health/Disease"
@@ -24576,7 +24576,7 @@
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  ],
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  "name": "Mycoplasma pulmonis genome database",
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  "prefix": "NBDC01807",
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- "status": "Active",
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+ "status": "Closed",
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  "target_keywords": [
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  "DNA",
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  "Genome/Gene",
@@ -24593,7 +24593,7 @@
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  ],
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  "name": "Photorhabdus luminescens genome database",
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  "prefix": "NBDC01808",
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- "status": "Active",
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+ "status": "Closed",
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  "target_keywords": [
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  "Genome/Gene",
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  "Health/Disease"
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  ],
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  "name": "Streptococcus agalactiae NEM316 / Serotype III genome database",
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  "prefix": "NBDC01809",
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- "status": "Active",
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+ "status": "Closed",
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  "target_keywords": [
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  "DNA",
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  "Genome/Gene",
@@ -24968,7 +24968,7 @@
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  "nbdc01828": {
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  "description": "caNanoLab is a data sharing portal designed to facilitate information sharing across the international biomedical nanotechnology research community to expedite and validate the use of nanotechnology in biomedicine. caNanoLab provides support for the annotation of nanomaterials with characterizations resulting from physico-chemical, in vitro and in vivo assays and the sharing of these characterizations and associated nanotechnology protocols in a secure fashion.",
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  "fairsharing": "FAIRsharing.y1qpdm",
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- "homepage": "http://cananolab.nci.nih.gov/caNanoLab/",
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+ "homepage": "https://cananolab.cancer.gov/#/",
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  "information_keywords": [
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  "Method",
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  "Portal",
@@ -25036,6 +25036,7 @@
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  ],
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  "name": "dbMHC",
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  "prefix": "NBDC01831",
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+ "status": "Closed",
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  "target_keywords": [
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  "Genome/Gene",
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  "Health/Disease",
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  "nbdc01838": {
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  "description": "This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data.",
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  "fairsharing": "FAIRsharing.qrw6b7",
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- "homepage": "http://rice.plantbiology.msu.edu/",
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+ "homepage": "http://rice.uga.edu/",
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  "information_keywords": [
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  "Sequence",
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  "Expression"
@@ -25644,7 +25645,7 @@
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  "maintainer": "VSNU (Association of Universities in the Netherlands)||DANS(Data Archiving and Networked Services)",
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  "name": "NARCIS",
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  "prefix": "NBDC01862",
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- "status": "Active"
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+ "status": "Closed"
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  },
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  "nbdc01863": {
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  "description": "ChemSpider is a freely available collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.",
@@ -25729,7 +25730,7 @@
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  "18003653",
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  "24316575"
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  ],
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- "status": "Active",
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+ "status": "Closed",
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  "target_keywords": [
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  "Genome/Gene"
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  ]
@@ -26333,7 +26334,7 @@
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  "nbdc01901": {
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  "description": "This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map of Saccharomyces cerevisiae S288c that is periodically updated by a team of collaborators from various research groups.",
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  "fairsharing": "FAIRsharing.cm6j6r",
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- "homepage": "http://yeast.sourceforge.net/",
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+ "homepage": "https://github.com/SysBioChalmers/yeast-GEM",
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  "information_keywords": [
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  "Interaction/Pathway"
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  ],
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  "pubmeds": [
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  "24214957"
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  ],
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- "status": "Active",
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+ "status": "Inactive",
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  "target_keywords": [
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  "Protein"
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  ]
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  ],
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  "name": "iSpyBio",
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  "prefix": "NBDC01933",
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- "status": "Active",
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+ "status": "Inactive",
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  "target_keywords": [
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  "cDNA/EST",
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  "Protein",
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  "pubmeds": [
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  "24220210"
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  ],
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- "status": "Active",
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+ "status": "Inactive",
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  "target_keywords": [
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  "Cell/Organelle",
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  "Health/Disease"
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  "maintainer": "SMHI (Swedish Meterological and Hydrological Institute)",
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  "name": "Swedish Ocean Archive",
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  "prefix": "NBDC01969",
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- "status": "Active"
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+ "status": "Inactive"
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  },
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  "nbdc01970": {
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  "description": "speciesLink (also known as the Distributed Information System for Biological Collections: Integrating Species Analyst and SinBiota (FAPESP)) implements a distributed information system to retrieve primary biodiversity data from collections within the state of São Paulo (Brazil) as well as data integrated from other networks and observation data registered in the SinBiota database.",
@@ -28102,7 +28103,7 @@
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  "pubmeds": [
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  "24647222"
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  ],
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- "status": "Active",
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+ "status": "Closed",
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  "target_keywords": [
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  "Genetic variation",
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  "Genome/Gene"
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  "pubmeds": [
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  "26481352"
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  ],
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- "status": "Active",
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+ "status": "Closed",
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  "target_keywords": [
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  "Genome/Gene",
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  "Genetic variation",
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  "pubmeds": [
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  "25231498"
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  ],
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- "status": "Active",
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+ "status": "Inactive",
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  "target_keywords": [
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  "Genome/Gene",
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  "RNA",
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  "pubmeds": [
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  "25902408"
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  ],
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- "status": "Active",
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+ "status": "Inactive",
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  "target_keywords": [
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  "Organism",
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  "Health/Disease"
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  "19930558",
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  "17445256"
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  ],
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- "status": "Active",
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+ "status": "Inactive",
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  "target_keywords": [
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  "Protein"
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  ]
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  "17090585",
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  "20711478"
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  ],
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- "status": "Active",
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+ "status": "Inactive",
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  "target_keywords": [
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  "Genome/Gene"
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  ]
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  "23205526",
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  "27899619"
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  ],
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- "status": "Active",
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+ "status": "Closed",
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  "target_keywords": [
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  "Genetic variation",
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  "Protein",
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  "pubmeds": [
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  "23175606"
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  ],
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- "status": "Active",
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  "target_keywords": [
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  "Genome/Gene",
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  "RNA",
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  "pubmeds": [
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  "26635394"
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  ],
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+ "status": "Inactive",
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  "target_keywords": [
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  "Protein",
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  "Genome/Gene",
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  "pubmeds": [
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  "23800225"
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  ],
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- "status": "Active",
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+ "status": "Inactive",
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  "target_keywords": [
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  "DNA"
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  ]
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  "pubmeds": [
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  "27799474"
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  ],
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- "status": "Active",
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+ "status": "Inactive",
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  "target_keywords": [
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  "Genome/Gene",
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  "Genetic variation",
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  "pubmeds": [
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  "27903890"
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  ],
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- "status": "Active",
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+ "status": "Closed",
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  "target_keywords": [
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  "Drug",
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  "Protein"
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  "maintainer": "IOCB (Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences)",
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  "name": "The Benchmark Energy & Geometry Database",
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  "prefix": "NBDC02194",
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+ "status": "Inactive",
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  "target_keywords": [
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  "Metabolite"
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  ]
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  "pubmeds": [
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  "27651835"
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  ],
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- "status": "Active",
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+ "status": "Inactive",
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  "target_keywords": [
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  "Drug"
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  ]
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  "maintainer": "RECOLNAT (Réseau national des collections naturalistes )",
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  "name": "e-ReColNat",
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  "prefix": "NBDC02286",
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- "status": "Active",
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+ "status": "Inactive",
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  "target_keywords": [
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  "Organism"
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  ]
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  "maintainer": "NIH (National Institutes of Health)",
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  "name": "caArray",
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  "prefix": "NBDC02331",
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- "status": "Active",
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+ "status": "Closed",
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  "target_keywords": [
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  "Genome/Gene"
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  ]
@@ -35059,7 +35060,7 @@
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  "alt_name": "GCMD/IDN",
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  "description": "This resource provides support to scientific community by providing access to Earth science data and services.",
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  "fairsharing": "FAIRsharing.3aabq1",
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- "homepage": "https://idn.ceos.org",
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+ "homepage": "https://www.earthdata.nasa.gov/learn/find-data/idn",
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  "information_keywords": [
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  "Environment",
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  "Geographic Distribution",
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  "Interaction/Pathway",
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  "Portal"
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  ],
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- "name": "NASA Global Change Master Directory",
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+ "name": "NASA Global Change Master Directory / CEOS International Directory Network",
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  "prefix": "NBDC02342",
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  "status": "Active",
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  "target_keywords": [
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  "pubmeds": [
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  "26774245"
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  ],
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- "status": "Active",
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+ "status": "Inactive",
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  "target_keywords": [
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  "Genome/Gene",
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  "Drug",
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  },
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  "nbdc02422": {
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  "description": "The Marmoset Gene Atlas provides a whole brain, high-resolution gene expression atlas in the common marmoset (Callithrix jacchus). It provides in situ hybridization (ISH) data over the course of postnatal brain development to adult stage. Users can search for gene expression data by gene name or disease. This is a part of the Brain/MINDS project.",
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- "homepage": "https://gene-atlas.brainminds.riken.jp/",
36316
+ "homepage": "https://gene-atlas.brainminds.jp/",
36316
36317
  "information_keywords": [
36317
36318
  "Expression",
36318
36319
  "Localization",
@@ -36537,7 +36538,7 @@
36537
36538
  "pubmeds": [
36538
36539
  "30152011"
36539
36540
  ],
36540
- "status": "Active",
36541
+ "status": "Inactive",
36541
36542
  "target_keywords": [
36542
36543
  "Organism"
36543
36544
  ]
@@ -36845,7 +36846,7 @@
36845
36846
  "pubmeds": [
36846
36847
  "30329086"
36847
36848
  ],
36848
- "status": "Active",
36849
+ "status": "Inactive",
36849
36850
  "target_keywords": [
36850
36851
  "Genome/Gene",
36851
36852
  "Genetic variation",
@@ -36901,7 +36902,7 @@
36901
36902
  },
36902
36903
  "nbdc02459": {
36903
36904
  "description": "CellMarker database provides a manually curated, comprehensive and accurate resource of cell markers for various cell types in tissues of human and mouse. Users can search for cell markers by clicking on hyperlinks embedded in the web anatomical images, selecting tissue and cell type from the hierarchical trees, or entering gene symbol, gene ID or protein name. In addition, users can download all data and submit new data via the 'Download' and 'Submit' page, respectively.",
36904
- "homepage": "http://biocc.hrbmu.edu.cn/CellMarker/",
36905
+ "homepage": "http://xteam.xbio.top/CellMarker/",
36905
36906
  "information_keywords": [
36906
36907
  "Method",
36907
36908
  "Classification"
@@ -36979,7 +36980,7 @@
36979
36980
  "pubmeds": [
36980
36981
  "30202990"
36981
36982
  ],
36982
- "status": "Active",
36983
+ "status": "Inactive",
36983
36984
  "target_keywords": [
36984
36985
  "Genome/Gene",
36985
36986
  "DNA",
@@ -37054,7 +37055,7 @@
37054
37055
  "nbdc02466": {
37055
37056
  "alt_name": "Database of somatic mutations in normal cells",
37056
37057
  "description": "DSMNC is a comprehensive catalogue of somatic single nucleotide variations (SNVs) occurring in a normal cell from various human and mouse normal tissues. Each entry contains chromosome position, reference allele, variant allele, VAF, gene name, amino acid substitution, species, gender, tissue/cell type, single-cell genomics biotechnology/method, control sample/tissue, etc. Users can browse using SNVs table or chromosome browsers.",
37057
- "homepage": "http://dsmnc.big.ac.cn",
37058
+ "homepage": "https://dsmnc.ngdc.cncb.ac.cn/",
37058
37059
  "information_keywords": [
37059
37060
  "Sequence",
37060
37061
  "Method"
@@ -37202,7 +37203,7 @@
37202
37203
  "nbdc02473": {
37203
37204
  "alt_name": "Extracellular vesicle miRNA database",
37204
37205
  "description": "EVmiRNA is a comprehensive database of miRNA in extracellular vesicles. It provides miRNA expression profiles, miRNA related drug, miRNA regulated pathways, miRNA function and related publications. Those data originally come from NCBI SRA. This database allows users to browse data at three aspects; 1) Samples: Users can browse sample cancer types, heatmap, expressed miRNAs, SRA sample information. 2) miRNAs: This list contains miRNA basic information and the expression histogram. Click the miRNA ID link, users can browse comprehensive miRNA information, contain miRNA basic information, miRNA expression profiles, miRNA related drug, miRNA regulated pathways, miRNA function, and related publications. 3) Specific miRNA: specific miRNAs in each source and cancer.",
37205
- "homepage": "http://bioinfo.life.hust.edu.cn/EVmiRNA",
37206
+ "homepage": "https://guolab.wchscu.cn/EVmiRNA/#!/",
37206
37207
  "information_keywords": [
37207
37208
  "Sequence",
37208
37209
  "Expression"
@@ -37500,7 +37501,7 @@
37500
37501
  "pubmeds": [
37501
37502
  "30445567"
37502
37503
  ],
37503
- "status": "Active",
37504
+ "status": "Inactive",
37504
37505
  "target_keywords": [
37505
37506
  "Genome/Gene",
37506
37507
  "Genetic variation",
@@ -37528,9 +37529,9 @@
37528
37529
  ]
37529
37530
  },
37530
37531
  "nbdc02489": {
37531
- "alt_name": "Methylation quantitative trait loci in cancer",
37532
+ "alt_name": "Pan-cancer methylation quantitative trait loci",
37532
37533
  "description": "Pancan-meQTL is a database for systematically prediction about the effects of SNPs on methylation levels of human genome. It provides cis-meQTLs (SNPs affect local methylation levels of CpG sties) and trans-meQTLs (SNPs affect distant methylation levels of CpG sites) across cancer types by using thousands of genotype and methylation data from The Cancer Genome Atlas (TCGA). Users can browse or search following information;\n1) cis-meQTLs and trans-meQTLs across different cancer types\n2) meQTLs associated with patient overall survival across different cancer types\n3) meQTLs in GWAS linkage disequilibrium (LD) regions.",
37533
- "homepage": "http://bioinfo.life.hust.edu.cn/Pancan-meQTL",
37534
+ "homepage": "https://gong_lab.hzau.edu.cn/Pancan-meQTL/",
37534
37535
  "information_keywords": [
37535
37536
  "Sequence",
37536
37537
  "Phenotype",
@@ -37901,7 +37902,7 @@
37901
37902
  "pubmeds": [
37902
37903
  "29425804"
37903
37904
  ],
37904
- "status": "Active",
37905
+ "status": "Inactive",
37905
37906
  "target_keywords": [
37906
37907
  "DNA",
37907
37908
  "RNA"
@@ -38380,7 +38381,7 @@
38380
38381
  },
38381
38382
  "nbdc02536": {
38382
38383
  "description": "OrthoInspector is a catalog of orthologs predicted across three domains of life, Eukaryota, Bacteria, and Archaea. Each entry provides a fully searchable list of orthologs and inparalogs across multiple species, and tools to investigate function and evolutionary history of the protein. Users can query this site using a Uniprot identifier or access, or using a BLAST similarity search with a protein sequence.",
38383
- "homepage": "https://lbgi.fr/orthoinspectorv3/",
38384
+ "homepage": "https://lbgi.fr/orthoinspector/",
38384
38385
  "information_keywords": [
38385
38386
  "Sequence",
38386
38387
  "Classification"
@@ -38527,7 +38528,7 @@
38527
38528
  "pubmeds": [
38528
38529
  "30535239"
38529
38530
  ],
38530
- "status": "Active",
38531
+ "status": "Inactive",
38531
38532
  "target_keywords": [
38532
38533
  "Cell/Organelle",
38533
38534
  "Health/Disease"
@@ -38615,7 +38616,7 @@
38615
38616
  "nbdc02549": {
38616
38617
  "alt_name": "Crowd Extracted Expression of Differential Signatures",
38617
38618
  "description": "CREEDS is a knowledgebase for associations between drugs, genes and diseases based on the data from a crowdsourcing microtask project implemented to annotate and reanalyze gene expression profiles from GEO. Signatures of these data are unique and are manually validated for quality. This database visualizes all of the signatures in a packed circles layout in which similar signatures are closer to each other. Furthermore, it has interactive heatmaps of hierarchically clustered matrices of all signatures.",
38618
- "homepage": "http://amp.pharm.mssm.edu/CREEDS/",
38619
+ "homepage": "https://maayanlab.cloud/CREEDS/",
38619
38620
  "information_keywords": [
38620
38621
  "Sequence",
38621
38622
  "Expression",
@@ -39067,7 +39068,7 @@
39067
39068
  "nbdc02574": {
39068
39069
  "alt_name": "Japanese aquatic macroinvertebrate reference",
39069
39070
  "description": "J-amir is a collection of digital data about aquatic macroinvertebrates inhabiting Japan. It contains photo-images and analyzed DNA sequences (partial coding regions of 18S rRNA, histone H3, and mitochondrial cytochrome c oxidase subunit I genes) of each specimen.",
39070
- "homepage": "http://www.b.s.osakafu-u.ac.jp/~mkato/J-amir_home.htm",
39071
+ "homepage": "https://jamir.stars.ne.jp/",
39071
39072
  "information_keywords": [
39072
39073
  "Sequence",
39073
39074
  "Taxonomy",
@@ -39111,14 +39112,14 @@
39111
39112
  "maintainer": "Hiroshima University Faculty of Pharmaceutical Sciences",
39112
39113
  "name": "Phos-tag SDS-PAGE database",
39113
39114
  "prefix": "NBDC02576",
39114
- "status": "Active",
39115
+ "status": "Inactive",
39115
39116
  "target_keywords": [
39116
39117
  "Protein"
39117
39118
  ]
39118
39119
  },
39119
39120
  "nbdc02577": {
39120
39121
  "description": "KNApSAcK Biomarker is a database for human biomarkers that provide indication of diseases. The biomarker information, which are biomarker name, related diseases, marker type (metabolite or protein), and references, is collected from reliable articles. The data can be searched by keywords.",
39121
- "homepage": "http://www.knapsackfamily.com/Biomarker/top.php",
39122
+ "homepage": "https://www.knapsackfamily.com/Biomarker/top.php",
39122
39123
  "information_keywords": [
39123
39124
  "Interaction/Pathway",
39124
39125
  "Bibliography/Documents",
@@ -39401,7 +39402,7 @@
39401
39402
  "31602478",
39402
39403
  "30521000"
39403
39404
  ],
39404
- "status": "Active",
39405
+ "status": "Inactive",
39405
39406
  "target_keywords": [
39406
39407
  "Genome/Gene",
39407
39408
  "RNA",
@@ -39464,7 +39465,7 @@
39464
39465
  "maintainer": "Pathogen Genomics Center, National Institute of Infectious Diseases",
39465
39466
  "name": "gGENEPID",
39466
39467
  "prefix": "NBDC02594",
39467
- "status": "Active",
39468
+ "status": "Inactive",
39468
39469
  "target_keywords": [
39469
39470
  "Genome/Gene",
39470
39471
  "Organism",
@@ -5819,6 +5819,17 @@
5819
5819
  ],
5820
5820
  "homepage": "http://w3id.org/rsp/vocals#"
5821
5821
  },
5822
+ "attack": {
5823
+ "name": "MITRE ATT&CK Ontology",
5824
+ "prefix": "attack",
5825
+ "uri_prefix": "http://w3id.org/sepses/vocab/ref/attack#$1",
5826
+ "description": "An ontology to represent MITRE ATT & CK.\nThis ontology is developed based on the MITRE ATT & CK (https://attack.mitre.org/)",
5827
+ "modified": "2025-11-22",
5828
+ "keywords": [
5829
+ "Security"
5830
+ ],
5831
+ "homepage": "http://w3id.org/sepses/vocab/ref/attack"
5832
+ },
5822
5833
  "cbcm": {
5823
5834
  "name": "The European Union Company Mobility Ontology (EUCM ontology)",
5824
5835
  "prefix": "cbcm",
@@ -7968,6 +7979,18 @@
7968
7979
  ],
7969
7980
  "homepage": "https://privatealpha.com/ontology/transformation/1#"
7970
7981
  },
7982
+ "ce": {
7983
+ "name": "CityExplorer Ontology",
7984
+ "prefix": "ce",
7985
+ "uri_prefix": "https://purl.org/cityexplorer#$1",
7986
+ "description": "This ontology models personalized tourist experiences by representing cities, points of interest, events, accommodations, restaurants, transportation, and their relationships. This ontology is part of a university project.",
7987
+ "modified": "2025-11-22",
7988
+ "keywords": [
7989
+ "Events",
7990
+ "Society"
7991
+ ],
7992
+ "homepage": "https://purl.org/cityexplorer"
7993
+ },
7971
7994
  "apco": {
7972
7995
  "name": "African Public Contract Ontology",
7973
7996
  "prefix": "apco",
@@ -8779,6 +8802,18 @@
8779
8802
  ],
8780
8803
  "homepage": "https://w3id.org/fog"
8781
8804
  },
8805
+ "fwo": {
8806
+ "name": "Food Wastage Ontology",
8807
+ "prefix": "fwo",
8808
+ "uri_prefix": "https://w3id.org/foodwaste/ontology#$1",
8809
+ "description": "An ontology to model food donation logistics.",
8810
+ "modified": "2025-11-22",
8811
+ "keywords": [
8812
+ "Food",
8813
+ "Industry"
8814
+ ],
8815
+ "homepage": "https://w3id.org/foodwaste/ontology"
8816
+ },
8782
8817
  "gom": {
8783
8818
  "name": "GOM: Geometry Metadata Ontology",
8784
8819
  "prefix": "gom",
@@ -9196,6 +9231,18 @@
9196
9231
  ],
9197
9232
  "homepage": "https://w3id.org/opm"
9198
9233
  },
9234
+ "opti": {
9235
+ "name": "Offshore Wind Power Platform Ontology for OPTiMAR",
9236
+ "prefix": "opti",
9237
+ "uri_prefix": "https://w3id.org/optimar#$1",
9238
+ "description": "This ontology describes the components, failures, sensors, and events related to offshore wind platforms.",
9239
+ "modified": "2025-10-06",
9240
+ "keywords": [
9241
+ "Environment",
9242
+ "IoT"
9243
+ ],
9244
+ "homepage": "https://w3id.org/optimar"
9245
+ },
9199
9246
  "okh": {
9200
9247
  "name": "Open Know How (OKH) ontology",
9201
9248
  "prefix": "okh",
@@ -9843,6 +9890,18 @@
9843
9890
  ],
9844
9891
  "homepage": "https://w3id.org/vocab/xbrll"
9845
9892
  },
9893
+ "vpa": {
9894
+ "name": "ERA ontology for verified permissions",
9895
+ "prefix": "vpa",
9896
+ "uri_prefix": "https://w3id.org/vpa#$1",
9897
+ "description": "ERA ontology for verified permissions, as applied in vehicle(type) authorisations, registrations and approvals",
9898
+ "modified": "2025-05-23",
9899
+ "keywords": [
9900
+ "Methods",
9901
+ "Transport"
9902
+ ],
9903
+ "homepage": "https://w3id.org/vpa"
9904
+ },
9846
9905
  "wfont": {
9847
9906
  "name": "Wind Farm Ontology (wfont)",
9848
9907
  "prefix": "wfont",
Binary file
@@ -691,10 +691,10 @@
691
691
  "xpo",
692
692
  "ehdaa2"
693
693
  ],
694
- "contact": "addiehl@buffalo.edu",
695
- "contact.github": "addiehl",
696
- "contact.label": "Alexander Diehl",
697
- "contact.orcid": "0000-0001-9990-8331",
694
+ "contact": "do12@sanger.ac.uk",
695
+ "contact.github": "dosumis",
696
+ "contact.label": "David Osumi-Sutherland",
697
+ "contact.orcid": "0000-0002-7073-9172",
698
698
  "depends_on": [
699
699
  "go",
700
700
  "ncbitaxon",