Colil RDF Data Portal

Contents

1. Colil is a search service for citation contexts of a cited paper along with its relevant ones.
   • Search Top
   
   
2. You can access the Colil database in RDF.
   • SPARQL Endpoint: http://colil.dbcls.jp/sparql
   • SPARQL Explorer
   • Faceted Search
   • Colil Vocabulary
   • RDF Data (Citation data) (Co-citaion data) (Linked data)
   
   
3. You can obtain the entire database in RDF.
   • Download site
   
   
4. Related Publication
   • Please refer the following publication:
     T. Fujiwara and Y. Yamamoto, "Colil: a database and search service for citation contexts in the life sciences domain.", Journal of Biomedical Semantics, 6:38 (19 October 2015)
     PubMed Entry | Full text paper available

Examples

• SPARQL Queries
  1. Retrieve citation contexts where a paper (Pubmed ID: 11237011) is cited in the papers.
     PREFIX bibo: <http://purl.org/ontology/bibo/> PREFIX colil: <http://purl.jp/bio/10/colil/ontology/201303#> PREFIX doco: <http://purl.org/spar/doco/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX togows: <http://togows.dbcls.jp/ontology/ncbi-pubmed#> select ?CitationPaper ?Context where { ?CitationPaper bibo:cites ?ReferencePaper . ?CitationPaper doco:contains [ doco:contains [ rdf:value ?Context ; colil:mentions ?ReferencePaper ] ] . ?ReferencePaper rdfs:seeAlso [ rdf:type colil:PubMed ; togows:pmid '23831647' ] . } Issue Query
     
     
  2. Retrieve a PMC ID list of papers which a paper (Pubmed ID: 17049089) cites.
     PREFIX bibo: <http://purl.org/ontology/bibo/> PREFIX colil: <http://purl.jp/bio/10/colil/ontology/201303#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX togows: <http://togows.dbcls.jp/ontology/ncbi-pubmed#> select ?CitationPaper ?PMCID where { ?CitationPaper bibo:cites ?ReferencePaper ; colil:pmcid ?PMCID . ?ReferencePaper rdfs:seeAlso [ rdf:type colil:PubMed ; togows:pmid '23831647' ] . } Issue Query
     
     
  3. Retrieve a title list of papers relevant to a paper (DOI: 10.1186/1748-7188-1-18).
     PREFIX bibo: <http://purl.org/ontology/bibo/> PREFIX colil: <http://purl.jp/bio/10/colil/ontology/201303#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX togows: <http://togows.dbcls.jp/ontology/ncbi-pubmed#> select ?RelevantPaper ?RelevantPaperTitle where { [] bibo:doi '10.1186/1748-7188-1-18' ; colil:hasRelevantBibliographicResourceOf [ colil:hasRelevantPaperId ?RelevantPaper ] . ?RelevantPaper rdfs:seeAlso [ rdf:type colil:PubMed ; togows:ti ?RelevantPaperTitle ] . } order by ?RelevantPaperTitle Issue Query
     
     
  4. Retrieve a DOI list of papers mentioned in the Background section of a paper (PMC ID: PMC1630425).
     PREFIX bibo: <http://purl.org/ontology/bibo/> PREFIX colil: <http://purl.jp/bio/10/colil/ontology/201303#> PREFIX dcterms: <http://purl.org/dc/elements/1.1/> PREFIX doco: <http://purl.org/spar/doco/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> select distinct ?ReferencePaper ?DOI where { ?CitationPaper rdf:type colil:CitationPaper ; colil:pmcid 'PMC1630425' ; doco:contains [ dcterms:title 'background' ; doco:contains [ colil:mentions ?ReferencePaper ] ] . ?ReferencePaper bibo:doi ?DOI . } Issue Query

Colil by Database Center for Life Science (DBCLS) is licensed under a Creative Commons Attribution 2.1 Japan License.