Interpretation errors related to the GO annotation file format

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...

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Bibliographic Details
Published inAMIA ... Annual Symposium proceedings Vol. 2007; pp. 538 - 542
Main Authors Moreira, Dilvan A, Shah, Nigam H, Musen, Mark A
Format Journal Article
LanguageEnglish
Published United States American Medical Informatics Association 11.10.2007
Subjects
Animals
Databases, Genetic
Databases, Protein
Genes
Humans
Proteins
Vocabulary, Controlled
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Summary: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).
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ISSN:1559-4076