GO2PUB: Querying PubMed with Semantic Expansion of Gene Ontology Terms

Charles Bettembourg (1, 2) , Christian Diot (1) , Anita Burgun (2) , Olivier Dameron (2)

1 PEGASE - Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes]
2 UMR 936

As PubMed grows, literature searches become more complex and time-consuming. Automated search tools with good precision and recall are thus necessary. We developed GO2PUB to address this demand. Our goal was to use the knowledge from Gene Ontology (GO), its annotations and following the true path rule for semantic expansion. GO2PUB enriches PubMed queries based on selected GO terms and keywords. It processes the result and displays the PMID, title, authors, abstract and bibliographic references of the articles. Gene names, symbols and synonyms that have been generated as extra keywords from the GO terms are also highlighted. Two experts manually assessed the relevance of GO2PUB, GoPubMed and PubMed on three queries about lipid metabolism. Experts agreement was high (kappa=0.83). GO2PUB returned 76 % of the relevant articles, GoPubMed: 45 % and PubMed: 21 %. 39 % of the relevant articles were returned only by GO2PUB, and 18 % only by GoPubMed. We also generated 20 queries based on random GO terms with a granularity similar to those of the first three queries and compared the proportions of GO2PUB and GoPubMed results. These were respectively of 70 % and 38 %. The comparison of GO2PUB, based on semantic expansion, with GoPubMed, based on text-mining techniques, showed that both tools are complementary. GO2PUB is available at http://go2pub.genouest.org

Domaines: Sciences du Vivant [q-bio]

Charles Bettembourg, Christian Diot, Anita Burgun, Olivier Dameron. GO2PUB: Querying PubMed with Semantic Expansion of Gene Ontology Terms. Journées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM 2012, Jul 2012, Rennes, France. LIRMM UMR CNRS/UM2 5506, 2012, Journées Ouvertes de Biologie, Informatique et Mathématiques. ⟨hal-01210643⟩