BH12.12/SPARQLthon8/INSDCオントロジー
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refseq2ttl.rbによる変換
2013.05.23最新版 v6 https://gist.github.com/ktym/5547403
ruby refseq2ttl.rb genome_conf/datasets/cyanobase/data_sources/Synechocystis/genbank/NC_000911.gb
スクリプト実行結果のエントリーメタデータ＋source feature部分
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix faldo: <http://biohackathon.org/resource/faldo#> . @prefix idorg: <http://rdf.identifiers.org/database/> . @prefix insdc: <http://insdc.org/owl/> . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> rdf:type obo:SO_0000340 . # SO:chromosome <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> rdfs:label "Synechocystis sp. PCC 6803 chromosome, complete genome." . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> insdc:sequence_version "NC_000911.1" . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> insdc:sequence_length 3573470 . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> insdc:sequence_fasta <http://togows.dbcls.jp/entry/nucleotide/NC_000911.1.fasta> . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> rdf:type obo:SO_0000988 . # SO:circular <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> insdc:sequence_date "2012-01-19"^^xsd:date . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> rdfs:seeAlso <http://identifiers.org/ncbigi/16329170> . <http://identifiers.org/ncbigi/16329170> rdfs:label "GI:16329170" . <http://identifiers.org/ncbigi/16329170> rdf:type idorg:GI . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> rdfs:seeAlso <http://identifiers.org/refseq/NC_000911.1> . <http://identifiers.org/refseq/NC_000911.1> rdfs:label "RefSeq:NC_000911.1" . <http://identifiers.org/refseq/NC_000911.1> rdf:type idorg:RefSeq . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> rdfs:seeAlso <http://identifiers.org/bioproject/57659> . <http://identifiers.org/bioproject/57659> rdfs:label "BioProject:57659" . <http://identifiers.org/bioproject/57659> rdf:type idorg:BioProject . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> rdfs:seeAlso <http://identifiers.org/pubmed/9724772> . <http://identifiers.org/pubmed/9724772> rdfs:label "PubMed:9724772" . <http://identifiers.org/pubmed/9724772> rdf:type idorg:PubMed . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> rdfs:seeAlso <http://identifiers.org/pubmed/8905231> . <http://identifiers.org/pubmed/8905231> rdfs:label "PubMed:8905231" . <http://identifiers.org/pubmed/8905231> rdf:type idorg:PubMed . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> rdfs:seeAlso <http://identifiers.org/pubmed/8590279> . <http://identifiers.org/pubmed/8590279> rdfs:label "PubMed:8590279" . <http://identifiers.org/pubmed/8590279> rdf:type idorg:PubMed . <urn:uuid:69ff7bb6-54cb-47f7-81ce-fc0fb95d246d> insdc:location "1..3573470" . <urn:uuid:69ff7bb6-54cb-47f7-81ce-fc0fb95d246d> rdf:type faldo:Region . <urn:uuid:69ff7bb6-54cb-47f7-81ce-fc0fb95d246d> faldo:begin <urn:uuid:ce08fa48-a23b-40f8-aa50-553f90a7c177> . <urn:uuid:69ff7bb6-54cb-47f7-81ce-fc0fb95d246d> faldo:end <urn:uuid:326eba1a-590e-4a56-b5fb-addc30a6983d> . <urn:uuid:ce08fa48-a23b-40f8-aa50-553f90a7c177> faldo:position 1 . <urn:uuid:ce08fa48-a23b-40f8-aa50-553f90a7c177> faldo:reference <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> . <urn:uuid:ce08fa48-a23b-40f8-aa50-553f90a7c177> rdf:type faldo:ExactPosition . <urn:uuid:ce08fa48-a23b-40f8-aa50-553f90a7c177> rdf:type faldo:ForwardStrandPosition . <urn:uuid:326eba1a-590e-4a56-b5fb-addc30a6983d> faldo:position 3573470 . <urn:uuid:326eba1a-590e-4a56-b5fb-addc30a6983d> faldo:reference <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> . <urn:uuid:326eba1a-590e-4a56-b5fb-addc30a6983d> rdf:type faldo:ExactPosition . <urn:uuid:326eba1a-590e-4a56-b5fb-addc30a6983d> rdf:type faldo:ForwardStrandPosition . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> faldo:location <urn:uuid:69ff7bb6-54cb-47f7-81ce-fc0fb95d246d> . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> rdfs:seeAlso <http://identifiers.org/taxonomy/1148> . <http://identifiers.org/taxonomy/1148> rdfs:label "taxon:1148" . <http://identifiers.org/taxonomy/1148> rdf:type idorg:Taxonomy . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> insdc:source_organism "Synechocystis sp. PCC 6803" . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> insdc:source_mol_type "genomic DNA" . <urn:uuid:05b20629-fb41-4fd0-8e41-1011fd4375a4> insdc:source_strain "PCC 6803" .
NC000911エントリーで現在利用しているinsdc
insdc: insdc:feature_EC_number insdc:feature_codon_start insdc:feature_function insdc:feature_gene insdc:feature_gene_synonym insdc:feature_locus_tag insdc:feature_note insdc:feature_product insdc:feature_transl_table insdc:feature_translation insdc:location insdc:sequence_date insdc:sequence_fasta → insdc:sequence insdc:sequence_length insdc:sequence_version insdc:source_mol_type insdc:source_organism insdc:source_strain
refseq2ttl.rbとINSDCオントロジーの差異
- feature_はついていない
- source_はつけていない
- sequence_ はつけなくてもよさそう メタデータのSOURCE, ORGANISMを除いて
- insdseq.dtdを確認する【Todo】
SPARQL
gene attributes
例）gene-id＝slr0473
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>
prefix obo: <http://purl.obolibrary.org/obo/>
prefix faldo: <http://biohackathon.org/resource/faldo#>
prefix idorg: <http://rdf.identifiers.org/database/>
prefix insdc: <http://insdc.org/owl/>
SELECT *
from <http://togogenome.org/refseq/>
from <http://togogenome.org/so/>
where{
#?gene a obo:SO_0000704 .
?gene a ?gene_type.
?gene_type rdfs:label ?gene_type_label.
?gene insdc:feature_locus_tag ?locus_tag.
?gene rdfs:label ?label.
?gene rdfs:seeAlso ?seeAlso.
?gene obo:so_part_of ?parent_so.
#?gene ?v ?o.
?parent_so rdfs:label ?parent_so_label.
#?parent_so ?v ?o.
?gene faldo:location ?faldo.
#?faldo ?faldo_v ?faldo_o.
?faldo insdc:location ?faldo_location.
?faldo faldo:begin ?faldo_begin.
#?faldo_begin ?faldo_begin_v ?faldo_begin_o.
?faldo_begin faldo:position ?faldo_begin_position.
?faldo_begin rdf:type ?faldo_begin_type.
?faldo faldo:end ?faldo_end.
#?faldo_end ?faldo_end_v ?faldo_end_o.
?faldo_end faldo:position ?faldo_end_position.
?faldo_end rdf:type ?faldo_end_type.
?faldo rdf:type ?faldo_type.
FILTER(?gene_type = obo:SO_0000704 || ?gene_type = obo:SO_0000252 || ?gene_type = obo:SO_0000253)
FILTER(?locus_tag = "slr0473")
}
