SPARQLthon20/TPP-omics

提供：TogoWiki

• ゲノム、トランスクリプトーム、エピゲノムのデータが出てくる
• がんを中心にしたクリニカルオミクスデータ　+　モデル細胞/生物のオミクスデータ
• ゲノム以外を RDF 化する際のオントロジー、細胞株などのメタデータを表現するオントロジーを調査

　

• Technologies
  • NGS ontology (NGSONTO) http://bioportal.bioontology.org/ontologies/NGSONTO http://www.phyloviz.net/NGSonto/index.html
    • The NGSOnto ontology aims at capturing the workflow of all the processes involved, in order to ensure the reproducibility of the entire process, through the use of a controled and specific vocabulary.
      • SRAデータセットのメタデータを記述するオントロジー
    • Instituto de Medicina Molecular - IMM (Portugal)
    • 概念図
    • Data properties
    • 紹介動画
    • 外部オントロジーとしてOntology for Biomedical Investigation - OBI, Software Ontology - SWO, Sequence Typing Method Ontology - TypOnを利用

• Whole genome sequence
  • Variation data (GVF) -> Genomic Feature and Variation Ontology (GFVO) http://www.biointerchange.org/ontologies.html
  • Feature Annotation Location Description Ontology (FALDO) https://github.com/JervenBolleman/FALDO
• RNA-seq
  • Microarray and Gene Expression Data Ontology (MO) http://bioportal.bioontology.org/ontologies/MO
  • Regulation of Gene Expression Ontology (REXO) http://bioportal.bioontology.org/ontologies/REXO
  • (MicroRNA Ontology (MIRNAO) http://bioportal.bioontology.org/ontologies/MIRNAO)?
  • RNA Ontology (RNAO) http://bioportal.bioontology.org/ontologies/RNAO
• Target captured BS-seq
  • Sequence Types and Features Ontology (SO) http://bioportal.bioontology.org/ontologies/SO
  • GFVO?
  • FALDO?
• ChIP-seq
  • SO
  • FALDO?

　

• ENCODEが参考になるかも
  • nanopub

　

• Targets
• cell lines
  • Experimental Factor Ontology (EFO) http://bioportal.bioontology.org/ontologies/EFO
  • Cell Line Ontology (CLO) http://bioportal.bioontology.org/ontologies/CLO
  • BRENDA Tissue and Enzyme Source Ontology (BTO) http://bioportal.bioontology.org/ontologies/BTO
• organs?
  • Vertebrate Homologous Organ Group Ontology (VHOG) http://bioportal.bioontology.org/ontologies/VHOG
• model organisms
  • NCBI Organismal Classification (NCBITAXON) http://bioportal.bioontology.org/ontologies/NCBITAXON
  • BioSample?
• clinical samples
  • International Classification of Diseases, Version 10 (ICD10) http://bioportal.bioontology.org/ontologies/ICD10
  • International Classification of Diseases, Version 10 - Clinical Modification (ICD10CM) http://bioportal.bioontology.org/ontologies/ICD10CM
  • International Classification of Diseases, Version 10 - Procedure Coding Systems (ICD10PCS) http://bioportal.bioontology.org/ontologies/ICD10PCS
  • Human Disease Ontology (DOID) http://bioportal.bioontology.org/ontologies/DOID
  • Disease core ontology applied to Rare Diseases (HRDO) http://bioportal.bioontology.org/ontologies/HRDO
  • Orphanet Rare Disease Ontology (ORDO) http://bioportal.bioontology.org/ontologies/ORDO
  • Ontology for Genetic Disease Investigations (OGDI) http://bioportal.bioontology.org/ontologies/OGDI
  • Disease Ontology (DO) http://disease-ontology.org/

　

• Metadata
• cultures
  • National Drug Data File (NDDF) http://bioportal.bioontology.org/ontologies/NDDF
  • Cell Culture Ontology (CCONT) http://bioportal.bioontology.org/ontologies/CCONT
  • INOH pathway ontology (IEV) http://www.obofoundry.org/cgi-bin/detail.cgi?id=event