PredictingGeneFunctionsfromTextUsingaCross-Species：预测基因功能的文本使用跨物种.pptVIP

April 16, 2004 Supporting Annotation Layers for Natural Language Processing Predicting Gene Functions from Text Using a Cross-Species Approach Emilia Stoica and Marti HearstSchool of InformationUniversity of California, Berkeley Goal Annotate genes with functional information derived from journal articles. Gene Ontology (GO) Gene Ontology (GO) controlled vocabulary for functional annotation ~ 17,600 terms (circa July 2004) Organized into 3 distinct acyclic graphs molecular functions biological processes cellular locations More general terms are “parents” of less general terms: development (GO:0007275) is the parent of embryonic development (GO:0001756) Challenges GO tokens might not appear explicitly Example: PubMed GO:0008285: negative regulation of cell proliferation Occurs as: inhibition of cell proliferation GO tokens might not occur contiguously Example: PubMed GO:0007186: G-protein coupled receptor protein signaling pathway Occurs as: Results indicate that CCR1-mediated responses are regulated …in the signaling pathway, by receptor phosphorylation at the level of receptor G/protein coupling … CCR1 binds MIP-1 alpha. Challenges The simplest strategy (assigning GO codes to genes simply because the GO tokens occur near the gene) yields a large number of false positives. Issues: The text does not contain evidence to support the annotation, The text contains evidence for the annotation, but the curator knows the gene to be involved in a function that is more general or more specific than the GO code matched in text. Challenges GO contains hints about what kinds of evidence are required for annotation, e.g.: The text should mention co-purification, co-immunoprecipitation experiments Requiring these evidence terms does not seem to improve algorithms. Related Work Mainly in the context of BioCreative competition (2004) Chiang and Yu 2003, 2004: Find phrase patterns commonly used in sentences describ