title: Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.
abstract: The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.
authors.affiliation: Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands.
authors.forename: Andra
authors.initials: A
authors.lastname: Waagmeester
authors.affiliation: Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands.|Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands.
authors.forename: Martina
authors.identifier: 0000-0002-7699-8191
authors.initials: M
authors.lastname: Kutmon
authors.affiliation: Gladstone Institutes, San Francisco, California, United States of America.
authors.forename: Anders
authors.identifier: 0000-0002-4693-0591
authors.initials: A
authors.lastname: Riutta
authors.affiliation: Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands.
authors.forename: Ryan
authors.identifier: 0000-0003-3477-7443
authors.initials: R
authors.lastname: Miller
authors.affiliation: Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands.
authors.forename: Egon L
authors.identifier: 0000-0001-7542-0286
authors.initials: EL
authors.lastname: Willighagen
authors.affiliation: Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands.|Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands.
authors.forename: Chris T
authors.identifier: 0000-0002-5301-3142
authors.initials: CT
authors.lastname: Evelo
authors.affiliation: Gladstone Institutes, San Francisco, California, United States of America.
authors.forename: Alexander R
authors.initials: AR
authors.lastname: Pico
mesh_terms: D064229:Biological Ontologies; D035843:Biomedical Research; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D012660:Semantics