GoPubMed: exploring PubMed with the Gene Ontology

By Andreas Doms, M. Schroeder. Nucleic Acids Res., 2005

593 citations recorded by the source corpus.

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 and 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 . Querying is currently limited to 100 papers per query.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/314a535d298dac6a11a3ba49f1c3ca43e9a07a76

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Citations in the corpus

Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support (2008, methodology): “two ontologies and support searches on either ontology or both [51].”
Ieee/acm Transactions on Computational Biology and Bioinformatics (unknown): “We adopt the techniques proposed in GoPubMed [8] for locating GO terms in abstracts.”
Biomedical text mining and its applications in cancer research (2013, unknown): “GoPubMed [68,69] classifies literature abstracts according to a Gene Ontology and shows the ontology terms that are related to the query words.”
Overview of BioCreative II gene normalization (2008, methodology): “For GO terms, GoPubMed [22] was used to associate each abstract with GO terms.”
PubMed and beyond: a survey of web tools for searching biomedical literature (2011, background): “GOPubMed (34) was originally designed to leverage the hierarchy in Gene Ontology (GO) to organize search results, thus allowing users to quickly navigate results by GO categories.”
Extracting interactions between proteins from the literature (2008, unknown): “After that, researchers in biomedical domain contribute to the curation process by subsequent edits cbioc.eas.asu.edu Chilibot Chilibot [24] is a search software for MEDLINE literature database to rapidly identify relationships between genes, proteins, or any keywords that the user might be interest”