SPARQLthon25/DDBJ
提供:TogoWiki
(版間での差分)
(→DDBJリソースからOWL変換) |
(→OWL形式) |
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=== OWL形式 === | === OWL形式 === | ||
+ | ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division | ||
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+ | :Division rdf:type owl:Class ; | ||
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+ | rdfs:subClassOf owl:Thing . | ||
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+ | ### http://ddbj.nig.ac.jp/ontologies/nucleotide/DDBJ_Division | ||
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+ | :DDBJ_Division rdf:type owl:Class ; | ||
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+ | rdfs:subClassOf :Division . | ||
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+ | ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Taxonomic_division | ||
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+ | :Taxonomic_division rdf:type owl:Class ; | ||
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+ | rdfs:subClassOf :DDBJ_Division . | ||
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+ | ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Other_Division | ||
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+ | :Other_Division rdf:type owl:Class ; | ||
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+ | rdfs:subClassOf :DDBJ_Division . | ||
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+ | |||
### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#HUM | ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#HUM | ||
2014年10月28日 (火) 09:00時点における最新版
目次 |
DDBJリソースからOWL変換
- DDBJ HPの情報をgoogle spreadsheetで取得、編集
- Google Visualization APIを用いてデータ取得
- html形式 https://docs.google.com/spreadsheets/d/1lcquFaRHHUs6weBd6_C6kgz6jBZ_HHYtnfgZx6vOeKA/gviz/tq?tqx=out:html&headers=1&tq=SELECT%20A,B,C,D,F,G,H,I%20WHERE%20C%20IS%20NOT%20NULL
- json形式 https://docs.google.com/spreadsheets/d/1lcquFaRHHUs6weBd6_C6kgz6jBZ_HHYtnfgZx6vOeKA/gviz/tq?tqx=out:json&headers=1&tq=SELECT%20A,B,C,D,F,G,H,I%20WHERE%20C%20IS%20NOT%20NULL
- csv形式 https://docs.google.com/spreadsheets/d/1lcquFaRHHUs6weBd6_C6kgz6jBZ_HHYtnfgZx6vOeKA/gviz/tq?tqx=out:csv&headers=1&tq=SELECT%20A,B,C,D,F,G,H,I%20WHERE%20C%20IS%20NOT%20NULL
- ftdoc2ttl.rbでjsonを利用してOWL形式に変換
- Divisionを更新
- Division > DDBJ_Division > Taxonomic division, Other divisionをクラスで定義
- HUM, PRIのリソースはIndividiual で定義
- Divisionを更新
例)DDBJ Division
json形式
{"cols"=> [{"id"=>"A", "label"=>"feature", "type"=>"string"}, {"id"=>"B", "label"=>"qualifier", "type"=>"string"}, {"id"=>"C", "label"=>"value", "type"=>"string"}, {"id"=>"D", "label"=>"label_en", "type"=>"string"}, {"id"=>"F", "label"=>"label_ja", "type"=>"string"}, {"id"=>"G", "label"=>"type_en", "type"=>"string"}, {"id"=>"H", "label"=>"type_ja", "type"=>"string"}, {"id"=>"I", "label"=>"uri", "type"=>"string"}], "rows"=> [{"c"=> [{"v"=>"DIVISION"}, {"v"=>"division"}, {"v"=>"HUM"}, {"v"=>"human"}, {"v"=>"ヒト"}, {"v"=>"taxonomic division"}, {"v"=>"由来生物種に基づく分類"}, {"v"=>"http://ddbj.nig.ac.jp/ontologies/nucleotide/division.HUM"}]}, {"c"=> [{"v"=>"DIVISION"}, {"v"=>"division"}, {"v"=>"PRI"}, {"v"=>"primates (other than human)"}, {"v"=>"霊長類 (ヒトを除く)"}, {"v"=>"taxonomic division"}, {"v"=>"由来生物種に基づく分類"}, {"v"=>"http://ddbj.nig.ac.jp/ontologies/nucleotide/division.PRI"}]}, {"c"=> [{"v"=>"DIVISION"}, {"v"=>"division"}, {"v"=>"ROD"}, {"v"=>"rodents"}, {"v"=>"齧歯類"}, {"v"=>"taxonomic division"}, {"v"=>"由来生物種に基づく分類"}, {"v"=>"http://ddbj.nig.ac.jp/ontologies/nucleotide/division.ROD"}]}, {"c"=> [{"v"=>"DIVISION"}, {"v"=>"division"}, {"v"=>"MAM"}, {"v"=>"mammals (other than primates and rodents)"}, {"v"=>"哺乳類 (ヒト,霊長類,齧歯類を除く)"}, {"v"=>"taxonomic division"}, {"v"=>"由来生物種に基づく分類"}, {"v"=>"http://ddbj.nig.ac.jp/ontologies/nucleotide/division.MAM"}]}, . . . ( 略)
OWL形式
### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division :Division rdf:type owl:Class ; rdfs:subClassOf owl:Thing . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/DDBJ_Division :DDBJ_Division rdf:type owl:Class ; rdfs:subClassOf :Division . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Taxonomic_division :Taxonomic_division rdf:type owl:Class ; rdfs:subClassOf :DDBJ_Division . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Other_Division :Other_Division rdf:type owl:Class ; rdfs:subClassOf :DDBJ_Division .
### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#HUM :Division#HUM rdf:type :Taxonomic_Division , owl:NamedIndividual ; rdfs:label "human"@en , "ヒト"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#PRI :Division#PRI rdf:type :Taxonomic_Division , owl:NamedIndividual ; rdfs:label "primates (other than human)"@en , "霊長類 (ヒトを除く)"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#ROD :Division#ROD rdf:type :Taxonomic_Division , owl:NamedIndividual ; rdfs:label "rodents"@en , "齧歯類"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#MAM :Division#MAM rdf:type :Taxonomic_Division , owl:NamedIndividual ; rdfs:label "mammals (other than primates and rodents)"@en , "哺乳類 (ヒト,霊長類,齧歯類を除く)"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#VRT :Division#VRT rdf:type :Taxonomic_Division , owl:NamedIndividual ; rdfs:label "vertebrates (other than mammals)"@en , "脊椎動物 (ヒト,霊長類,齧歯類,哺乳類を除く)"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#INV :Division#INV rdf:type :Taxonomic_Division , owl:NamedIndividual ; rdfs:label "invertebrates (animals other than vertebrates)"@en , "無脊椎動物"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#PLN :Division#PLN rdf:type :Taxonomic_Division , owl:NamedIndividual ; rdfs:label "plants, fungi, plastids (eukaryotes other than animals)"@en , "植物・真菌類 など"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#BCT :Division#BCT rdf:type :Taxonomic_Division , owl:NamedIndividual ; rdfs:label "bacteria (including both Eubacteria and Archaea)"@en , "バクテリア"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#VRL :Division#VRL rdf:type :Taxonomic_Division , owl:NamedIndividual ; rdfs:label "viruses"@en , "ウイルス"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#PHG :Division#PHG rdf:type :Taxonomic_Division , owl:NamedIndividual ; rdfs:label "bacteriophages"@en , "バクテリオファージ"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#PAT :Division#PAT rdf:type :Other_Division , owl:NamedIndividual ; rdfs:label "sequence data related to patent application The data those which Japan Patent Office (JPO), United States Patent and Trademark Office (USPTO), European Patent Office (EPO), and Korean Intellectual Property Office (KIPO) collected, processed and released."@en , "特許出願に含まれる塩基配列データ Japan Patent Office (JPO), European Patent Office (EPO), United States Patent and Trademark Office (USPTO), Korean Intellectual Property Office (KIPO) が収集・処理したデータ"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#ENV :Division#ENV rdf:type :Other_Division , owl:NamedIndividual ; rdfs:label "sequences obtained via environmental sampling methods"@en , "PCR, DGGE、あるいは、その他の方法で直接、分子を単離した環境上のサンプルに由来した配列"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#SYN :Division#SYN rdf:type :Other_Division , owl:NamedIndividual ; rdfs:label "synthetic constructs; artificially constructed sequences"@en , "synthetic constructs 人為的に構成された配列"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#EST :Division#EST rdf:type :Other_Division , owl:NamedIndividual ; rdfs:label "expressed sequence tags; short single pass cDNA sequences"@en , "expressed sequence tags short single pass の cDNA 配列"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#TSA :Division#TSA rdf:type :Other_Division , owl:NamedIndividual ; rdfs:label "transcriptome shotgun assemblies; assembled mRNA sequences"@en , "transcriptome shotgun assemblies 再構成された (assembled) mRNA 配列"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#GSS :Division#GSS rdf:type :Other_Division , owl:NamedIndividual ; rdfs:label "genome survey sequences; short single pass genomic sequences"@en , "genome survey sequences short single pass のゲノム配列"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#HTC :Division#HTC rdf:type :Other_Division , owl:NamedIndividual ; rdfs:label "high throughput cDNA sequences; The sequence submitted from cDNA sequencing projects except for EST. This division is to include unfinished high throughput cDNA sequences, each of which has 5'UTR and 3'UTR at both ends and part of a coding region. The sequence may also include introns. When the sequence becomes finished later, it moves to the corresponding taxonomic division."@en , "high throughput cDNA sequences EST 以外の大規模 cDNA 配列プロジェクトに由来し,更新が期待されるデータ。 配列が finish した後,生物種による division に移される場合があります。"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#HTG :Division#HTG rdf:type :Other_Division , owl:NamedIndividual ; rdfs:label "high throughput genomic sequences The sequence submitted mainly from genome sequencing projects which regarded a clone as a sequencing unit."@en , "high throughput genomic sequences ゲノムプロジェクトに由来し,頻繁に update されることが期待されるデータで,段階に応じて以下の 3 phase に分類されます。その配列がいずれの phase であるかは KEYWORD 行に記載されます。配列が更新されると phase が上がり,finish した後は生物種による division に移されます。 - phase0; piece contig が構築される以前の配列 - phase1; 構築された piece contig の向きや順序が未確定の配列 - phase2; piece contig の向きや順序が確定した unfinished の配列"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#STS :Division#STS rdf:type :Other_Division , owl:NamedIndividual ; rdfs:label "sequence tagged sites The tag site for genome sequencing. The information of chromosome, map, PCR_condition is necessary for this division."@en , "sequence tagged sites Genome sequencing の tag となる配列。 chromosome, map, PCR_condition 等の情報が必要です。"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#UNA :Division#UNA rdf:type :Other_Division , owl:NamedIndividual ; rdfs:label "the data not annotated The UNA division is not used recently."@en , "未注釈データ 最近は UNA division は使用していません。"@ja . ### http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#CON :Division#CON rdf:type :Other_Division , owl:NamedIndividual ; rdfs:label "Contig / Constructed To conjugate a series of entries, such as those submitted from a genome project, each of the three data banks constructs an entry and assign an accession number to a large scale sequence dataset. Such entries are classified into the CON division. The entry in the CON division has the information of joined accession numbers instead of the sequence data. The corresponding entries of the CON entry have been submitted to other divisions."@en , "Contig / Constructed ゲノムプロジェクトのように個々に登録された一連の配列データをデータバンク側が結合し,1つのアクセッション番号を付与した長大なデータ。CON division に格納されるエントリには長大な配列を構成する配列のアクセッション番号が記載され,塩基配列は記載されません。また,すでに登録されている個々のデータのエントリは、他の division に保存されています。 CON division への直接のデータ登録は受け付けていません。まず、CON エントリを構成する個々の配列データを登録して頂きます。その上で CON エントリの構築が適当と判断された場合に、データバンク側で CON エントリを構築します。CON エントリを構成する個々の配列データが更新された場合には、CON エントリもバンク側で更新します。"@ja .
参考
- Google Spreadsheets を簡易 SQL DB に!「Google Visualization API」 http://webos-goodies.jp/archives/51310352.html
- スプレッドシートからJavaScriptで値を取得する(Google Visualization APIと旧スプレッドシートを使用) http://basato.no-blog.jp/a2/2014/07/post-3.html