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Hirokazu Chiba edited this page Oct 3, 2024 · 29 revisions
  • in taxonをどうするか
  • RDFポータルを使うようにSPARQListを更新するか
    • branchのRDFを使わないようにして書き換えるか
  • humanのgene_infoがあれば、unclassifiedというカテゴリも作れるはず。
    • protein-codingに絞ればよい?
    • HomoloGeneのときにはあったけど、なくなってしまったGene IDはどうする? =>omitでよいか
    • HomoloGeneにあるけど、protein-codingでない遺伝子はどうする? =>omitでよいか
  • TogoDXのメタスタンザとして、オーソログの詳細情報?

README (Last updated: 2024-02-01)

NOTICE:
The HomoloGene website has been retired, replaced by the NCBI Orthologs site.
For more details, see:

The historical data has been retained on FTP for archival purposes only. The last
HomoloGene build (build 68) was produced in 2014, and is no longer aligned with
current data in NCBI RefSeq and Gene, so we recommend using the newer orthologs
dataset. Please send questions to: [email protected]

2023-05-17

Add group properties

  • dct:identifier
  • rdfs:label

Fix URI namespace

  • homologene: http://identifiers.org/homologene/

RDF-config

  • rdf-config/ directory was merged into dbcls/rdf-config repository.

2023-03-31

Use standardized ontologies

  • orth:taxon -> obo:RO_0002162 (in taxon)
  • orth:protein -> sio:SIO_010078 (encodes)

Modify URI namespace

  • homologene: https://identifiers.org/homologene/

Modify URI prefix

  • taxonomy: http://identifiers.org/taxonomy/

metadata.yaml

title: HomoloGene RDF
website: https://www.ncbi.nlm.nih.gov/homologene/
description: HomoloGene RDF is a translation of NCBI HomoloGene data into RDF.
tags: [Genome] [Gene] [Phylogeny/Classification]
provider: National Center for Biotechnology Information
creators:
  - name: Hirokazu Chiba
    affiliation: Database Center for Life Science
version: release_20230301
issued: 2023-03-01
license:
  - name: https://www.ncbi.nlm.nih.gov/home/about/policies/
  - url: https://www.ncbi.nlm.nih.gov/home/about/policies/
  - credit: Source: U.S. National Library of Medicine.

metadata_ja.yaml

title: HomoloGene RDF
website: https://www.ncbi.nlm.nih.gov/homologene/
description: HomoloGene RDFは、NCBI HomoloGeneのデータをRDFに変換したものです。
tags: [Genome] [Gene] [Phylogeny/Classification]
provider: National Center for Biotechnology Information
creators:
  - name: 千葉 啓和
    affiliation: ライフサイエンス統合データベースセンター
version: release_20230301
issued: 2023-03-01
license:
  - name: https://www.ncbi.nlm.nih.gov/home/about/policies/
  - url: https://www.ncbi.nlm.nih.gov/home/about/policies/
  - credit: Source: U.S. National Library of Medicine.

Old URIs

  • orthordf: http://purl.org/net/orthordf/
    • orthordf:taxid
    • orthordf:refseq
  • group: http://purl.org/net/orthordf/homologene/group/
  • group: http://purl.org/orthordf/homologene/group/
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