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DDBJ BioSample OWL

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Takatomo Fujisawa edited this page Jun 14, 2017 · 14 revisions

コンバーター

Excelファイルを入力して、OWLに変換

ソースコード

https://gist.github.com/tfuji/f552f942c11538ac2cdb

履歴

  • 2017-06-12 DDBJ現行ルール v0.9版 OWL生成
    • 入力: ddbj_validator/ykodama/ddbj_packages/ddbj_biosample_definition_table_0.9.xlsx
ruby create_owl_for_ddbj_biosample.rb ../ddbj_biosample_definition_table_0.9.xlsx  >../ddbj_biosample_v0.9_owl_20170612.ttl
  • 2016-06-28 #入力ファイル統合
    • 入力: ddbj_validator/ykodama/ddbj_packages/ddbj_biosample_definition_table.xlsx のシートpackage-attribute, attribute
ruby create_owl_for_ddbj_biosample.rb ../ddbj_biosample_definition_table.xlsx > ../ddbj_biosample_owl_2016-06-28.ttl
  • ver. 2016-06-02
    • 入力
      • ddbj_validator/ykodama/definition_by_xml/attributes.xlsx
      • ddbj_validator/ykodama/ddbj_packages/ddbj_biosample_definition_table.xlsx
ruby create_owl_for_ddbj_biosample_20160602.rb attributes.xlsx ddbj_biosample_definition_table.xlsx > ddbj_biosample_owl_2016-06-09.ttl
  • ver. 2016-02-22
    • 入力: ddbj_validator/ykodama/definition_by_xml/attributes.xlsx
ruby create_owl_for_ddbj_biosample.rb attributes.xlsx

OWL配置先

scp ../ddbj_biosample_v0.9_owl_20170612.ttl  [email protected]:/tga/services/virtuoso/var/lib/virtuoso/db/projects/sw/biosample/
scp ../ddbj_biosample_v0.9_owl_20170612.ttl  [email protected]:/home/w3sw/ddbj/DDBJValidator/biosample/

テスト環境

以下のSPARQL ep.のグラフにインポート

サンプルSPARQL

DDBJ Defined Packageリストを取得

PREFIX dbs: <http://ddbj.nig.ac.jp/ontologies/biosample/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
select *
#FROM <http://ddbj.nig.ac.jp/ontologies/biosample>
FROM <http://ddbj.nig.ac.jp/ontologies/2017/06/12/biosample>
WHERE
{
?package rdfs:subClassOf dbs:DDBJ_Defined_Package.
?package dc:identifier ?id.
?package rdfs:label ?label.
?package owl:versioninfo ?version.
#?package ?p ?o.
}
ORDER BY ?package
#limit 100

v1.0

v0.9

BioSample attibuteのリストを取得

PREFIX dbs: <http://ddbj.nig.ac.jp/ontologies/biosample/>
PREFIX dct: <http://purl.org/dc/elements/1.1/>
select *
#FROM <http://ddbj.nig.ac.jp/ontologies/biosample>
FROM <http://ddbj.nig.ac.jp/ontologies/2017/06/12/biosample>
WHERE
{
?attribute rdfs:subClassOf dbs:Attribute.
?attribute dct:identifier ?id.
?attribute rdfs:label ?label.
?attribute dbs:format ?format.
#?attribute dbs:value ?value.
#?attribute ?p ?o.
}
ORDER BY ?attribute
#limit 100

v1.0

v0.9

Generic packageのattributeリストを取得

PREFIX dct: <http://purl.org/dc/elements/1.1/>
PREFIX dbs: <http://ddbj.nig.ac.jp/ontologies/biosample/>

select *
#FROM <http://ddbj.nig.ac.jp/ontologies/biosample>
FROM <http://ddbj.nig.ac.jp/ontologies/2017/06/12/biosample>
WHERE
{
?package rdfs:subClassOf dbs:DDBJ_Defined_Package.
?package rdfs:label ?label.
?package owl:versioninfo ?version.
#?package ?p ?o.
?package ?attribute_type ?attribute.
?attribute rdfs:subClassOf dbs:Attribute.
FILTER(?package = dbs:Generic_Package)
}

ORDER BY ?package, ?attribute_type
#limit 100

v1.0

v0.9

Package毎のAttribute_Group情報を取得

PREFIX dbs: <http://ddbj.nig.ac.jp/ontologies/biosample/>
PREFIX dct: <http://purl.org/dc/elements/1.1/>

select
# *
?package, ?group_attribute, ?label, ?attribute_id

#FROM <http://ddbj.nig.ac.jp/ontologies/biosample>
FROM <http://ddbj.nig.ac.jp/ontologies/2017/06/12/biosample>
WHERE
{

?axiom a owl:Axiom .
?axiom owl:annotatedSource ?source.
?axiom owl:annotatedTarget ?group_attribute.
?source owl:domain ?package.
?source rdfs:range ?range.
?source rdfs:label ?label.
#?range owl:oneOf* ?x.
#?x ?y ?attribute.
?range owl:oneOf/rdf:rest*/rdf:first ?attribute.
?attribute rdfs:subClassOf dbs:Attribute.
?attribute dct:identifier ?attribute_id.

#FILTER(?package = dbs:Microbe_Package)
}

ORDER BY ?package, ?group_attribute

#limit 100

v1.0

v0.9

submission/validation api

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