GoPubMed: exploring PubMed with the Gene Ontology

A. Doms, M. Schroeder
2005 Nucleic Acids Research  
The biomedical literature grows at a tremendous rate and PubMed comprises already over 15 000 000 abstracts. Finding relevant literature is an important and difficult problem. We introduce GoPubMed, a web server which allows users to explore PubMed search results with the Gene Ontology (GO), a hierarchically structured vocabulary for molecular biology. GoPubMed provides the following benefits: first, it gives an overview of the literature abstracts by categorizing abstracts according to the GO
more » ... nd thus allowing users to quickly navigate through the abstracts by category. Second, it automatically shows general ontology terms related to the original query, which often do not even appear directly in the abstract. Third, it enables users to verify its classification because GO terms are highlighted in the abstracts and as each term is labelled with an accuracy percentage. Fourth, exploring PubMed abstracts with GoPubMed is useful as it shows definitions of GO terms without the need for further look up. GoPubMed is online at www.gopubmed.org. Querying is currently limited to 100 papers per query. BACKGROUND Limits of classical literature search The biomedical literature grows at a tremendous pace. PubMed, the main biomedical literature database references over 15 000 000 abstracts. Owing to this size, simple web-style text search of the literature is often not yielding the best results and a lot of important information remains buried in the masses of text. Consider the following example: a researcher wants to know the enzymes that are inhibited by levamisole. A keyword search for 'levamisole inhibitor' produces well over 100 hits in the PubMed. To find out about specific functions, the
doi:10.1093/nar/gki470 pmid:15980585 pmcid:PMC1160231 fatcat:dvwi7cnzvfeyffosvz7gax5zxa