title: Protein annotation as term categorization in the gene ontology using word proximity networks.
abstract: 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 evidence text for a given annotation in 38% of Task 2.1 queries by building on this method. The term categorization methodology achieved a precision of 16% for annotation within the correct extended family in Task 2.2, though we show through subsequent analysis that this can be improved with a different parameter setting. Our architecture proved not to be very successful on the evidence text component of the task, in the configuration used to generate the submitted results.
  
  
  CONCLUSIONS
  The initial results show promise for both of the methods we explored, and we are planning to integrate the methods more closely to achieve better results overall.
authors.affiliation: Los Alamos National Laboratory, PO Box 1663, MS B256, Los Alamos, NM 87545, USA. verspoor@lanl.gov
authors.forename: Karin
authors.initials: K
authors.lastname: Verspoor
authors.forename: Judith
authors.initials: J
authors.lastname: Cohn
authors.forename: Cliff
authors.initials: C
authors.lastname: Joslyn
authors.forename: Sue
authors.initials: S
authors.lastname: Mniszewski
authors.forename: Andreas
authors.initials: A
authors.lastname: Rechtsteiner
authors.forename: Luis M
authors.initials: LM
authors.lastname: Rocha
authors.forename: Tiago
authors.initials: T
authors.lastname: Simas
mesh_terms: D030541:Databases, Genetic / Q000145:classification*; D005796:Genes; D010363:Pattern Recognition, Automated / Q000379:methods*; D011506:Proteins / Q000145:classification*; D014956:Writing
chemical_list: D011506:Proteins