SPARQLthon25/DDBJ

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目次

DDBJリソースからOWL変換

  1. DDBJ HPの情報をgoogle spreadsheetで取得、編集
  2. Google Visualization APIを用いてデータ取得
  3. 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

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

個人用ツール