Journal article

Protein annotation as term categorization in the gene ontology using word proximity networks

K Verspoor, J Cohn, C Joslyn, S Mniszewski, A Rechtsteiner, LM Rocha, T Simas

BMC Bioinformatics | BMC | Published : 2005


BACKGROUND: We participated in the BioCreAtIvE Task 2, which addressed the annotation of proteins into the Gene Ontology (GO) based on the text of a given document and the selection of evidence text from the document justifying that annotation. We approached the task utilizing several combinations of two distinct methods: an unsupervised algorithm for expanding words associated with GO nodes, and an annotation methodology which treats annotation as categorization of terms from a protein's document neighborhood into the GO. RESULTS: The evaluation results indicate that the method for expanding words associated with GO nodes is quite powerful; we were able to successfully select appropriate ev..

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