May 4-6, 2015 Department of Energy Joint Genome Institute, Walnut Creek, California
Standards for the Microbial Dark Matter (uncultured microbial life)
Charles Parker will be presenting a poster at the GSC Workshop on May 5th.
Despite significant improvements in genome annotation, many assertions are hypothetical and may lack experimental support. The taxonomic literature for prokaryotes contains a wealth of experimental phenotypic data, but that knowledge is currently in a form that does not lend itself to integration with databases or ontologies.
Our knowledge base is designed to address these problems by providing reference phenotypic data for nearly all type strains of Bacteria and Archaea, based on concepts and observational data drawn from the primary taxonomic literature (the corpus of literature that supports our up-to-date taxonomy and strain database).
We developed software (Semantic Desktop) to extract putative feature domain vocabularies from this corpus, we have since developed this vocabulary into a precise thesaurus of phenotypic terms, which will ultimately conform to W3C SKOS-XL semantics, providing a link between the language of microbial phenotype, the semantic web and existing NamesforLife services.
[permalink] Posted May 1, 2015.