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Interpretation errors related to the GO annotation file format.

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).

SUBMITTER: Moreira DA

PROVIDER: S-EPMC2655813 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature

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Interpretation errors related to the GO annotation file format.

Moreira Dilvan A DA Shah Nigam H NH Musen Mark A MA

AMIA ... Annual Symposium proceedings. AMIA Symposium 20071011

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 ...[more]

PMID: 18693894

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Project description:BackgroundIndividuals with attention-deficit/hyperactivity disorder and other externalizing psychopathologies tend to display poor behavioral performance on the go/no-go task, which is thought to reflect deficits in inhibitory control. However, clinical neuroimaging studies using this task have yielded conflicting results, raising basic questions about what the task measures and which aspects of the task relate to clinical outcomes. We used computational modeling to provide a clearer understanding of how neural activations from this task relate to the cognitive mechanisms that underlie performance and to probe the implications of these relationships for clinical research.MethodsA total of 143 young adults (8-21 years of age) performed the go/no-go task during functional magnetic resonance imaging scanning. We used the diffusion decision model (DDM), a cognitive modeling approach, to quantify distinct neurocognitive processes that underlie go/no-go performance. We then assessed correlations between DDM parameters and brain activation from standard go/no-go contrasts and assessed relationships of DDM parameters and associated neural measures with clinical ratings.ResultsRight-lateralized prefrontal activations on correct inhibition trials, which are generally assumed to isolate neural processes involved in inhibition, were unrelated to DDM parameters (and other performance indices). However, responses to failed inhibitions in brain regions associated with error monitoring were strongly related to more efficient task performance and correlated with externalizing behavior and attention-deficit/hyperactivity disorder symptoms.ConclusionsOur findings cast doubt on conventional interpretations of go/no-go task-related activations as reflecting the neural basis of inhibitory functioning. We instead found evidence that error-related contrasts provide clinically relevant information about neural systems involved in monitoring and optimizing the efficiency of cognitive performance.

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Interpretation errors related to the GO annotation file format.

Publications

Interpretation errors related to the GO annotation file format.

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