Event

March 6-9, 2016 Tysons, Virginia

Genomic Science Program (GSP) 2016

Contractors-Grantees Meeting XIV

An early working version of our faceted search for strains by phenotype. Using our novel method of Semantic Equivalence, we may construct representations of an environment as a set of environmental constraints.

Charles Parker and George Garrity will be presenting poster 147 (“Semantic Index of Phenotypic and Genotypic Data”, Abstract Book, pages 256-257) highlighting their team’s recent work during the Monday evening mixer (5:00pm-7:00pm) in Tyson’s Ballroom.

During the course of this project we developed many software components that overcome specific technical barriers in terminology management, text mining, information extraction, knowledge transformation, entity recognition, document classification and annotation. The individual tools (N4L::Guide, N4L::Scribe, the Taxonomic Abstracts, Taxomatic, the KWIC Index and the Semantic Desktop) were implemented using W3C standards and recommendations (SPARQL, RDFS, RDF, OWL2, SKOS, SKOS-XL, XML, XSL, XSD, SPIN, OWL RL, DOI/CrossRef, CORS) and commercially-compatible FOS frameworks (Java, Apache, PostgreSQL, Virtuoso OSE, Jena/ARQ, SPIN Reasoner). We are integrating these components into a single software suite that can support a variety of document analysis needs.

Backed by the Fairview Research Alexandria platform (CLAIMS Global Patent Database), this analysis suite has access to the full text of the worldwide patent literature. We have demonstrated the ability to reverse-engineer the diagnostic phrases that human indexers use to classify large corpora of technical documents, and to measure both the quality of previously annotated documents and the cohesion of individual document classifications. Our software provides a novel way to navigate and bridge multiple classification systems.

Our continued collaborations with the Joint Genome Institute, Fairview Research/IFI Claims and Oak Ridge National Laboratories provide excellent opportunities to test and refine the capabilities of this analysis suite while raising the visibility of other federal funded projects by completing the semantic linking between projects, entities and publications.

Parker et al., Semantic Index of Phenotypic and Genotypic Data

Download Abstract (46kB PDF) Download Poster (7.4MB PDF)

[permalink] Posted March 1, 2016.