Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
BMC Bioinformatics. 2005;6 Suppl 1:S20. Epub 2005 May 24.

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

Author information

  • 1Los Alamos National Laboratory, PO Box 1663, MS B256, Los Alamos, NM 87545, USA. verspoor@lanl.gov

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.

CONCLUSION:

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.

PMID:
15960833
[PubMed - indexed for MEDLINE]
PMCID:
PMC1869013
Free PMC Article

Images from this publication.See all images (7)Free text

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for BioMed Central Icon for PubMed Central
    Loading ...
    Write to the Help Desk