title: STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation.
abstract: BACKGROUND
  Gene Ontology (GO) enrichment analysis remains one of the most common methods for hypothesis generation from high throughput datasets. However, we believe that researchers strive to test other hypotheses that fall outside of GO. Here, we developed and evaluated a tool for hypothesis generation from gene or protein lists using ontological concepts present in manually curated text that describes those genes and proteins.
  
  
  RESULTS
  As a consequence we have developed the method Statistical Tracking of Ontological Phrases (STOP) that expands the realm of testable hypotheses in gene set enrichment analyses by integrating automated annotations of genes to terms from over 200 biomedical ontologies. While not as precise as manually curated terms, we find that the additional enriched concepts have value when coupled with traditional enrichment analyses using curated terms.
  
  
  CONCLUSIONS
  Multiple ontologies have been developed for gene and protein annotation, by using a dataset of both manually curated GO terms and automatically recognized concepts from curated text we can expand the realm of hypotheses that can be discovered. The web application STOP is available at http://mooneygroup.org/stop/.
authors: Buck Institute for Research on Aging, Novato, CA, USA.
authors: Tobias
authors: T
authors: Wittkop
authors: Emily
authors: E
authors: TerAvest
authors: Uday S
authors: US
authors: Evani
authors: K Mathew
authors: KM
authors: Fleisch
authors: Ari E
authors: AE
authors: Berman
authors: Corey
authors: C
authors: Powell
authors: Nigam H
authors: NH
authors: Shah
authors: Sean D
authors: SD
authors: Mooney
mesh_terms: D005796:Genes; D006801:Humans; D006816:Huntington Disease / Q000235:genetics / Q000378:metabolism; D020407:Internet; D058977:Molecular Sequence Annotation; D010300:Parkinson Disease / Q000235:genetics / Q000378:metabolism; D025941:Protein Interaction Mapping; D011506:Proteins; D012984:Software; D018875:Vocabulary, Controlled
chemical_list: D011506:Proteins