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Hirokazu Chiba edited this page Jun 14, 2023 · 4 revisions

gene2go (simple version)

$ gunzip gene2go.gz
$ cat gene2go | grep -P '^9606' | ./gene2go.pl > gene2go.human.ttl

@prefix : <http://purl.org/net/orthordf/hOP/ontology#> .
@prefix ncbigene: <http://identifiers.org/ncbigene/> .
@prefix obo: <http://purl.obolibrary.org/obo/> .

ncbigene:1 :hasGO obo:GO_0005576, obo:GO_0005615, obo:GO_0031093, obo:GO_0034774, obo:GO_0062023, obo:GO_0070062, obo:GO_0072562, obo:GO_1904813 .

gene2go (full version)

$ gunzip gene2go.gz
$ ./gene2go.pl gene2go > gene2go.ttl

@prefix ncbigene: <http://identifiers.org/ncbigene/> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix pmid: <http://identifiers.org/pubmed/> .
@prefix taxid: <http://identifiers.org/taxonomy/> .
@prefix : <http://purl.org/orthordf/ontology#> .

...

ncbigene:10 :hasGOAnnotation
    [
        :hasGO obo:GO_0004060 ;
        :category :Function ;
        :evidence :IBA ;
        :qualifier :enables ;
        rdfs:label "arylamine N-acetyltransferase activity" ;
        dct:references pmid:21873635
    ],
    [
        :hasGO obo:GO_0004060 ;
        :category :Function ;
        :evidence :TAS ;
        :qualifier :enables ;
        rdfs:label "arylamine N-acetyltransferase activity" ;
        dct:references :NA
    ],
    [
        :hasGO obo:GO_0005515 ;
        :category :Function ;
        :evidence :IPI ;
        :qualifier :enables ;
        rdfs:label "protein binding" ;
        dct:references pmid:25640309, pmid:32296183
    ],
    [
        :hasGO obo:GO_0005829 ;
        :category :Component ;
        :evidence :TAS ;
        :qualifier :located_in ;
        rdfs:label "cytosol" ;
        dct:references :NA
    ],
    [
        :hasGO obo:GO_0006805 ;
        :category :Process ;
        :evidence :TAS ;
        :qualifier :involved_in ;
        rdfs:label "xenobiotic metabolic process" ;
        dct:references :NA
    ];
    :gene2go obo:GO_0004060, obo:GO_0005515, obo:GO_0005829, obo:GO_0006805 ;
    :taxid taxid:9606 .

ncbigene:12 :hasGOAnnotation
    [
        :hasGO obo:GO_0003677 ;
        :category :Function ;
        :evidence :TAS ;
        :qualifier :enables ;
        rdfs:label "DNA binding" ;
        dct:references pmid:14668352
    ],
    [
...
    [
        :hasGO obo:GO_0045540 ;
        :category :Process ;
        :evidence :IDA ;
        :qualifierNOT :involved_in ;
        rdfs:label "regulation of cholesterol biosynthetic process" ;
        dct:references pmid:21810484
    ],
...
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