Annotating Genes Using Textual Patterns

Cakmak A, Ozsoyoglu G

Department of Electrical Engineering and Computer Science Case Western Reserve University Cleveland, OH 44106, USA
E-mail: {ali.cakmak, tekin} @

Pac Symp Biocomput. 2007;:221-232.


Annotating genes with Gene Ontology (GO) terms is crucial for biologists to characterize the traits of genes in a standardized way. However, manual curation of textual data, the most reliable form of gene annotation by GO terms, requires significant amounts of human effort, is very costly, and cannot catch up with the rate of increase in biomedical publications. In this paper, we present GEANN, a system to automatically infer new GO annotations for genes from biomedical papers based on the evidence support linked to PubMed, a biological literature database of 14 million papers. GEANN (i) extracts from text significant terms and phrases associated with a GO term, (ii) based on the extracted terms, constructs textual extraction patterns with reliability scores for GO terms, (iii) expands the pattern set through “pattern crosswalks”, (iv) employs semantic pattern matching, rather than syntactic pattern matching, which allows for the recognition of phrases with close meanings, and (iv) annotates genes based on the “quality” of the matched pattern to the genomic entity occurring in the text. On the average, in our experiments, GEANN has reached to the precision level of 78% at the 57% recall level.

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