The compositional structure of Gene Ontology terms.
Ontology highlight
ABSTRACT:
SUBMITTER: Ogren PV
PROVIDER: S-EPMC2490823 | biostudies-literature | 2004
REPOSITORIES: biostudies-literature
Publications
The compositional structure of Gene Ontology terms.
Ogren P V PV Cohen K B KB Acquaah-Mensah G K GK Eberlein J J Hunter L L
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 20040101
An analysis of the term names in the Gene Ontology reveals the prevalence of substring relations between terms: 65.3% of all GO terms contain another GO term as a proper substring. This substring relation often coincides with a derivational relationship between the terms. For example, the term regulation of cell proliferation (GO:0042127) is derived from the term cell proliferation (GO:0008283) by addition of the phrase regulation of. Further, we note that particular substrings which are not the ...[more]
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Project description:BackgroundVast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however, either apply to specific subsets, or their predictions are not formalised, or they do not provide precise confidence values for their predictions.DescriptionWe recently established a learning system for automated annotation, trained with a broad variety of different organisms to predict the standardised annotation terms from Gene Ontology (GO). Now, this method has been made available to the public via our web-service GOPET (Gene Ontology term Prediction and Evaluation Tool). It supplies annotation for sequences of any organism. For each predicted term an appropriate confidence value is provided. The basic method had been developed for predicting molecular function GO-terms. It is now expanded to predict biological process terms. This web service is available via http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husarConclusionOur web service gives experimental researchers as well as the bioinformatics community a valuable sequence annotation device. Additionally, GOPET also provides less significant annotation data which may serve as an extended discovery platform for the user.
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