Display Settings:

Format

Send to:

Choose Destination
AMIA Annu Symp Proc. 2007 Oct 11:538-42.

Interpretation errors related to the GO annotation file format.

Author information

  • 1Stanford University, Stanford, CA, USA. dilvan@gmail.com

Abstract

The Gene Ontology (GO) is the most widely used ontology for creating biomedical annotations. GO annotations are statements associating a biological entity with a GO term. These statements comprise a large dataset of biological knowledge that is used widely in biomedical research. GO Annotations are available as "gene association files" from the GO website in a tab-delimited file format (GO Annotation File Format) composed of rows of 15 tab-delimited fields. This simple format lacks the knowledge representation (KR) capabilities to represent unambiguously semantic relationships between each field. This paper demonstrates that this KR shortcoming leads users to interpret the files in ways that can be erroneous. We propose a complementary format to represent GO annotation files as knowledge bases using the W3C recommended Web Ontology Language (OWL).

PMID:
18693894
[PubMed - indexed for MEDLINE]
PMCID:
PMC2655813
Free PMC Article

Images from this publication.See all images (3)Free text

Figure 1
Figure 2
Figure 3
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

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