EBI-var/RDF

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2014年12月18日 (木) 08:01時点におけるOrenodbcls (トーク | 投稿記録)による版
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ensembl_variant:rs766173 dc:identifier "rs766173" .
ensembl_variant:rs766173 rdfs:label "rs766173" .
  • Class:SO_0001483: SNV (subclass of sequence_alteration) 
ensembl_variant:rs766173 a obo:SO_0001483 .
  • 目的語はOriginal sourceから？
    • DatatypeProperty:has_source: Source information for either data imported into Ensembl Variation or for phenotype associations. 
ensembl_variant:rs766173 ensemblvariation:has_source "dbSNP" .
  • Synonymsから 
ensembl_variant:rs766173 skos:altLabel "NM_000059.3:c.865A>G" .
ensembl_variant:rs766173 skos:altLabel "NM_000059.3:c.865A>C" .
ensembl_variant:rs766173 skos:altLabel "rs52810428" .
ensembl_variant:rs766173 skos:altLabel "rs1801384" .
ensembl_variant:rs766173 skos:altLabel "VAR_005092" .
  • Clinical significanceから
    • has_clinical_significance は ObjectProperty だが、目的語がなぜかリテラル
    • ensembl_variation_ontology.owl には clinical_significance というクラスも存在 
ensembl_variant:rs766173 ensemblvariation:has_clinical_significance "uncertain significance" .
ensembl_variant:rs766173 ensemblvariation:has_clinical_significance "not provided" .
ensembl_variant:rs766173 ensemblvariation:has_clinical_significance "benign" .
  • どこから？
  • has_phenotype_annotation: OWLファイル・スキーマに記述なし 
ensembl_variant:rs766173 ensemblvariation:has_phenotype_annotation "Neoplastic Syndromes, Hereditary" .
ensembl_variant:rs766173 ensemblvariation:has_phenotype_annotation "AllHighlyPenetrant" .
ensembl_variant:rs766173 ensemblvariation:has_phenotype_annotation "Breast-ovarian cancer, familial 2" .
ensembl_variant:rs766173 ensemblvariation:has_phenotype_annotation "Familial cancer of breast" .
ensembl_variant:rs766173 ensemblvariation:has_phenotype_annotation "Breast-ovarian cancer, familial 2" .
  • FALDOによる位置情報
  • Locationから
    • begin-endが同じなのでExactPositionは一組でいいはず（バグ？）ただし、INDEL等でbegin-endが異なることはあり得る 
ensembl_variant:rs766173 faldo:location <http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343-32332343:1> .
<http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343-32332343:1> rdfs:label "chromosome 13:32332343-32332343:1" .
<http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343-32332343:1> rdf:type faldo:Region .
<http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343-32332343:1> faldo:begin <http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343:1> .
<http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343-32332343:1> faldo:end <http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343:1> .
<http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343-32332343:1> faldo:reference <http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13> .
<http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343:1> rdf:type faldo:ExactPosition .
<http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343:1> rdf:type faldo:ForwardStrandPosition .
<http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343:1> faldo:position 32332343 .
<http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343:1> faldo:reference <http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13> .
<http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343:1> rdf:type faldo:ExactPosition .
<http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343:1> rdf:type faldo:ForwardStrandPosition .
<http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343:1> faldo:position 32332343 .
<http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13:32332343:1> faldo:reference <http://rdf.ebi.ac.uk/resource/ensembl/77/chromosome:GRCh38:13> .
  • Allelesから
    • ObjectProperty:has_allele
      • Class:reference_allele: Allele as defined against a reference genome build.
      • Class:ancestral_allele: The allele that was carried by the common ancestor of the taxon you consider.
      • Class:minor_allele: Least frequently observed allele in a given data set.
      • Class:derived_allele: An allele which is not defined as the ancestral allele.
        • メジャーアレル？の型定義（derived_allele?）がない 
ensembl_variant:rs766173 ensemblvariation:has_allele ensembl_variant:rs766173#A .
ensembl_variant:rs766173#A rdfs:label "rs766173 allele A" .
ensembl_variant:rs766173#A a ensemblvariation:reference_allele .
ensembl_variant:rs766173#A a ensemblvariation:ancestral_allele .
ensembl_variant:rs766173 ensemblvariation:has_allele ensembl_variant:rs766173#C .
ensembl_variant:rs766173#C rdfs:label "rs766173 allele C" .
ensembl_variant:rs766173#C a ensemblvariation:minor_allele .
ensembl_variant:rs766173 ensemblvariation:has_allele ensembl_variant:rs766173#G .
ensembl_variant:rs766173#G rdfs:label "rs766173 allele G" .
  • Most severe consequenceのリンク先から
    • ObjectProperty:has_variant_effect 
ensembl_variant:rs766173#C ensemblvariation:has_variant_effect ensembl_variant:ENST00000544455_rs766173#C .
  • Transcriptから
    • so_overlaps: X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y. 
ensembl_variant:ENST00000544455_rs766173#C obo:so_overlaps transcript:ENST00000544455 .
  • Class:SO_0001583: missense_variant (subClass of gene_variant) 
ensembl_variant:ENST00000544455_rs766173#C a obo:SO_0001583 .
  • Showを押すと出てくる HGVS names から
    • DatatypeProperty:has_HGVS_transcript_name (subClass of has_HGVS_name)
    • DatatypeProperty:has_HGVS_protein_name (subClass of has_HGVS_name)
      • ウェブページではTranscriptとProteinは区別されていないが、RDFでは区別している 
ensembl_variant:ENST00000544455_rs766173#C ensemblvariation:has_HGVS_transcript_name "ENST00000544455.3:c.865A>C" .
ensembl_variant:ENST00000544455_rs766173#C ensemblvariation:has_HGVS_protein_name "ENSP00000439902.1:p.Asn289His" .
  • SIFT/PolyPhenから
    • ブランクノードをはさんだほうが良いのでは？
    • OWLにはhas_SIFT_score/has_PolyPhen_scoreがあるのでバグっぽい 
ensembl_variant:ENST00000544455_rs766173#C ensemblvariation:has_SIFT_prediction "tolerated" .
ensembl_variant:ENST00000544455_rs766173#C ensemblvariation:has_SIFT_prediction "0.06"^^xsd:float .
ensembl_variant:ENST00000544455_rs766173#C ensemblvariation:has_PolyPhen_prediction "benign" .
ensembl_variant:ENST00000544455_rs766173#C ensemblvariation:has_PolyPhen_prediction "0.052"^^xsd:float .
  • Amino acidから 
ensembl_variant:ENST00000544455_rs766173#C ensemblvariation:has_reference_peptide_sequence "N" .
ensembl_variant:ENST00000544455_rs766173#C ensemblvariation:has_alternate_peptide_sequence "H" .
  • 以下、繰り返し 
ensembl_variant:rs766173#G ensemblvariation:has_variant_effect ensembl_variant:ENST00000544455_rs766173#G .
ensembl_variant:ENST00000544455_rs766173#G obo:so_overlaps transcript:ENST00000544455 .
ensembl_variant:ENST00000544455_rs766173#G a obo:SO_0001583 .
ensembl_variant:ENST00000544455_rs766173#G ensemblvariation:has_HGVS_transcript_name "ENST00000544455.3:c.865A>G" .
ensembl_variant:ENST00000544455_rs766173#G ensemblvariation:has_HGVS_protein_name "ENSP00000439902.1:p.Asn289Asp" .
ensembl_variant:ENST00000544455_rs766173#G ensemblvariation:has_SIFT_prediction "tolerated" .
ensembl_variant:ENST00000544455_rs766173#G ensemblvariation:has_SIFT_prediction "0.07"^^xsd:float .
ensembl_variant:ENST00000544455_rs766173#G ensemblvariation:has_PolyPhen_prediction "benign" .
ensembl_variant:ENST00000544455_rs766173#G ensemblvariation:has_PolyPhen_prediction "0.022"^^xsd:float .
ensembl_variant:ENST00000544455_rs766173#G ensemblvariation:has_reference_peptide_sequence "N" .
ensembl_variant:ENST00000544455_rs766173#G ensemblvariation:has_alternate_peptide_sequence "D" .
ensembl_variant:rs766173#C ensemblvariation:has_variant_effect ensembl_variant:LRG_293t1_rs766173#C .
ensembl_variant:LRG_293t1_rs766173#C obo:so_overlaps transcript:LRG_293t1 .
ensembl_variant:LRG_293t1_rs766173#C a obo:SO_0001583 .
ensembl_variant:LRG_293t1_rs766173#C ensemblvariation:has_HGVS_transcript_name "LRG_293t1.1:c.865A>C" .
ensembl_variant:LRG_293t1_rs766173#C ensemblvariation:has_HGVS_protein_name "LRG_293p1.1:p.Asn289His" .
ensembl_variant:LRG_293t1_rs766173#C ensemblvariation:has_SIFT_prediction "tolerated" .
ensembl_variant:LRG_293t1_rs766173#C ensemblvariation:has_SIFT_prediction "0.06"^^xsd:float .
ensembl_variant:LRG_293t1_rs766173#C ensemblvariation:has_PolyPhen_prediction "benign" .
ensembl_variant:LRG_293t1_rs766173#C ensemblvariation:has_PolyPhen_prediction "0.052"^^xsd:float .
ensembl_variant:LRG_293t1_rs766173#C ensemblvariation:has_reference_peptide_sequence "N" .
ensembl_variant:LRG_293t1_rs766173#C ensemblvariation:has_alternate_peptide_sequence "H" .
ensembl_variant:rs766173#G ensemblvariation:has_variant_effect ensembl_variant:LRG_293t1_rs766173#G .
ensembl_variant:LRG_293t1_rs766173#G obo:so_overlaps transcript:LRG_293t1 .
ensembl_variant:LRG_293t1_rs766173#G a obo:SO_0001583 .
ensembl_variant:LRG_293t1_rs766173#G ensemblvariation:has_HGVS_transcript_name "LRG_293t1.1:c.865A>G" .
ensembl_variant:LRG_293t1_rs766173#G ensemblvariation:has_HGVS_protein_name "LRG_293p1.1:p.Asn289Asp" .
ensembl_variant:LRG_293t1_rs766173#G ensemblvariation:has_SIFT_prediction "tolerated" .
ensembl_variant:LRG_293t1_rs766173#G ensemblvariation:has_SIFT_prediction "0.07"^^xsd:float .
ensembl_variant:LRG_293t1_rs766173#G ensemblvariation:has_PolyPhen_prediction "benign" .
ensembl_variant:LRG_293t1_rs766173#G ensemblvariation:has_PolyPhen_prediction "0.022"^^xsd:float .
ensembl_variant:LRG_293t1_rs766173#G ensemblvariation:has_reference_peptide_sequence "N" .
ensembl_variant:LRG_293t1_rs766173#G ensemblvariation:has_alternate_peptide_sequence "D" .
ensembl_variant:rs766173#C ensemblvariation:has_variant_effect ensembl_variant:ENST00000530893_rs766173#C .
ensembl_variant:ENST00000530893_rs766173#C obo:so_overlaps transcript:ENST00000530893 .
ensembl_variant:ENST00000530893_rs766173#C a obo:SO_0001619 .
ensembl_variant:ENST00000530893_rs766173#C a obo:SO_0001792 .
ensembl_variant:ENST00000530893_rs766173#C ensemblvariation:has_HGVS_transcript_name "ENST00000530893.4:n.1063A>C" .
ensembl_variant:rs766173#G ensemblvariation:has_variant_effect ensembl_variant:ENST00000530893_rs766173#G .
ensembl_variant:ENST00000530893_rs766173#G obo:so_overlaps transcript:ENST00000530893 .
ensembl_variant:ENST00000530893_rs766173#G a obo:SO_0001619 .
ensembl_variant:ENST00000530893_rs766173#G a obo:SO_0001792 .
ensembl_variant:ENST00000530893_rs766173#G ensemblvariation:has_HGVS_transcript_name "ENST00000530893.4:n.1063A>G" .
ensembl_variant:rs766173#C ensemblvariation:has_variant_effect ensembl_variant:ENST00000380152_rs766173#C .
ensembl_variant:ENST00000380152_rs766173#C obo:so_overlaps transcript:ENST00000380152 .
ensembl_variant:ENST00000380152_rs766173#C a obo:SO_0001583 .
ensembl_variant:ENST00000380152_rs766173#C ensemblvariation:has_HGVS_transcript_name "ENST00000380152.5:c.865A>C" .
ensembl_variant:ENST00000380152_rs766173#C ensemblvariation:has_HGVS_protein_name "ENSP00000369497.3:p.Asn289His" .
ensembl_variant:ENST00000380152_rs766173#C ensemblvariation:has_SIFT_prediction "tolerated" .
ensembl_variant:ENST00000380152_rs766173#C ensemblvariation:has_SIFT_prediction "0.06"^^xsd:float .
ensembl_variant:ENST00000380152_rs766173#C ensemblvariation:has_PolyPhen_prediction "benign" .
ensembl_variant:ENST00000380152_rs766173#C ensemblvariation:has_PolyPhen_prediction "0.052"^^xsd:float .
ensembl_variant:ENST00000380152_rs766173#C ensemblvariation:has_reference_peptide_sequence "N" .
ensembl_variant:ENST00000380152_rs766173#C ensemblvariation:has_alternate_peptide_sequence "H" .
ensembl_variant:rs766173#G ensemblvariation:has_variant_effect ensembl_variant:ENST00000380152_rs766173#G .
ensembl_variant:ENST00000380152_rs766173#G obo:so_overlaps transcript:ENST00000380152 .
ensembl_variant:ENST00000380152_rs766173#G a obo:SO_0001583 .
ensembl_variant:ENST00000380152_rs766173#G ensemblvariation:has_HGVS_transcript_name "ENST00000380152.5:c.865A>G" .
ensembl_variant:ENST00000380152_rs766173#G ensemblvariation:has_HGVS_protein_name "ENSP00000369497.3:p.Asn289Asp" .
ensembl_variant:ENST00000380152_rs766173#G ensemblvariation:has_SIFT_prediction "tolerated" .
ensembl_variant:ENST00000380152_rs766173#G ensemblvariation:has_SIFT_prediction "0.07"^^xsd:float .
ensembl_variant:ENST00000380152_rs766173#G ensemblvariation:has_PolyPhen_prediction "benign" .
ensembl_variant:ENST00000380152_rs766173#G ensemblvariation:has_PolyPhen_prediction "0.022"^^xsd:float .
ensembl_variant:ENST00000380152_rs766173#G ensemblvariation:has_reference_peptide_sequence "N" .
ensembl_variant:ENST00000380152_rs766173#G ensemblvariation:has_alternate_peptide_sequence "D" .
ensembl_variant:rs766173#C ensemblvariation:has_variant_effect ensembl_variant:ENST00000614259_rs766173#C .
ensembl_variant:ENST00000614259_rs766173#C obo:so_overlaps transcript:ENST00000614259 .
ensembl_variant:ENST00000614259_rs766173#C a obo:SO_0001619 .
ensembl_variant:ENST00000614259_rs766173#C a obo:SO_0001792 .
ensembl_variant:ENST00000614259_rs766173#C ensemblvariation:has_HGVS_transcript_name "ENST00000614259.1:n.865A>C" .
ensembl_variant:rs766173#G ensemblvariation:has_variant_effect ensembl_variant:ENST00000614259_rs766173#G .
ensembl_variant:ENST00000614259_rs766173#G obo:so_overlaps transcript:ENST00000614259 .
ensembl_variant:ENST00000614259_rs766173#G a obo:SO_0001619 .
ensembl_variant:ENST00000614259_rs766173#G a obo:SO_0001792 .
ensembl_variant:ENST00000614259_rs766173#G ensemblvariation:has_HGVS_transcript_name "ENST00000614259.1:n.865A>G" .
「/mw/EBI-var/RDF」より作成