Providing named entity based search with a common biological database naming scheme

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Bio2RDF

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Providing named entity based search with a common biological database naming scheme

  1. 1. Bio2RDF Providing named entity based search with a common biological database naming scheme BioSearch08 Peter Ansell real world 1 R a university for the CRICOS No. 00213J
  2. 2. Introduction • Bio2RDF is a set of query services and RDF versions of biological databases that provide query resolution based on URI's and common formats for URI's so that a reference to a given database can always be recognised based on the URI real world 2 R a university for the CRICOS No. 00213J
  3. 3. real world 3 R a university for the CRICOS No. 00213J
  4. 4. Entity based link detection • Reverse links o http://bio2rdf.org/links/namespace:identifier o Example: http://bio2rdf.org/links/geneid:12345 o Finds all of the items which have linked back to the Entrez Geneid for “capping protein (actin filament) muscle Z-line, beta” • Namespace specific reverse links – http://bio2rdf.org/linksns/targetNamespace/names pace:identifier o http://bio2rdf.org/linksns/uniprot/geneid:12345 o Only finds items linked from the UniProt database real world 4 R a university for the CRICOS No. 00213J
  5. 5. Complete full text search • Overall RDF database search – http://bio2rdf.org/search/searchTerm • Provides an efficient multi database full text search functionality real world 5 R a university for the CRICOS No. 00213J
  6. 6. Namespace specific search • Namespace specific RDF database search – http://bio2rdf.org/searchns/namespace:searchTer m • Live search, converted to RDF using Bio2RDF URI's – This method is preferred to RDF database search for a small number of very large databases such as Swoogle and Pubmed which have their own search engines implemented real world 6 R a university for the CRICOS No. 00213J
  7. 7. Integration with text mining • The live search option could be one place to provide an interchange point between Text Mining tools and the Biological databases that are provided by Bio2RDF • Results from text mining recognition tools can be provided in RDF form, or can be rdfised in some way to contain Bio2RDF URI's that link to the rest of the Bio2RDF databases • Alternatively, some basic text mining can be performed using fulltext search real world 7 R a university for the CRICOS No. 00213J
  8. 8. Cross-database queries • Cross-database queries with SPARQL currently require both of the databases to exist within the same SPARQL endpoint • While this is not available on the public endpoints, a user can setup their own database relatively quickly and load in their desired databases and setup a new query type to execute on that endpoint only real world 8 R a university for the CRICOS No. 00213J
  9. 9. Example cross database query • An example of this might be resolving the Pubmed articles relating to a GO term. Endpoint http://localhost:8890/sparql loaded with PubMed, Entrez Geneid, and GO • If abstracts were loaded into the endpoint they could also be used • SPARQL = CONSTRUCT ... WHERE ... ?geneid geneid:xGo ?myGoTerm . ?geneid geneid:xPubMed ?pubmed . real world 9 R a university for the CRICOS No. 00213J

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