Journal article

A categorization approach to automated ontological function annotation

Karin Verspoor, Judith Cohn, Susan Mniszewski, Cliff Joslyn

PROTEIN SCIENCE | COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT | Published : 2006

Abstract

Automated function prediction (AFP) methods increasingly use knowledge discovery algorithms to map sequence, structure, literature, and/or pathway information about proteins whose functions are unknown into functional ontologies, typically (a portion of) the Gene Ontology (GO). While there are a growing number of methods within this paradigm, the general problem of assessing the accuracy of such prediction algorithms has not been seriously addressed. We present first an application for function prediction from protein sequences using the POSet Ontology Categorizer (POSOC) to produce new annotations by analyzing collections of GO nodes derived from annotations of protein BLAST neighborhoods. ..

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