Cross-product extensions of the Gene Ontology
| Autor: | Michael Bada, Tanya Z. Berardini, Jane Lomax, Midori A. Harris, Jennifer I. Deegan, Amelia Ireland, Christopher J. Mungall, David P. Hill |
|---|---|
| Jazyk: | angličtina |
| Předmět: |
Computer science
Process ontology Cross product Ontology (information science) computer.software_genre Mutually exclusive events Genetics & Genomics Gene 0302 clinical medicine Ontology components Databases Genetic General Materials Science 030212 general & internal medicine 0303 health sciences Hierarchy (mathematics) Gene ontology Ontology Ontology-based data integration Computer Science Applications Vocabulary Controlled GO Data mining Term enrichment Anatomy Data integration Bioinformatics Logic Cells Data_MISCELLANEOUS Health Informatics Article Open Biomedical Ontologies Cross-products 03 medical and health sciences OBO Foundry Controlled vocabulary Genetics Upper ontology Animals Humans Pathways Molecular Biology CHEBI 030304 developmental biology OWL Information retrieval Cell Biology Reasoning Genes Database Management Systems ComputingMethodologies_GENERAL Gene expression computer 030217 neurology & neurosurgery |
| Zdroj: | Nature Precedings |
| ISSN: | 1532-0464 |
| DOI: | 10.1016/j.jbi.2010.02.002 |
| Popis: | The Gene Ontology (GO) consists of nearly 30,000 classes for describing the activities and locations of gene products. Manual maintenance of ontology of this size is a considerable effort, and errors and inconsistencies inevitably arise. Reasoners can be used to assist with ontology development, automatically placing classes in a subsumption hierarchy based on their properties. However, the historic lack of computable definitions within the GO has prevented the user of these tools.In this paper, we present preliminary results of an ongoing effort to normalize the GO by explicitly stating the definitions of compositional classes in a form that can be used by reasoners. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry candidate ontologies for chemical entities, proteins, biological qualities and anatomical entities. Using these logical definitions we are gradually beginning to automate many aspects of ontology development, detecting errors and filling in missing relationships. These definitions also enhance the GO by weaving it into the fabric of a wider collection of interoperating ontologies, increasing opportunities for data integration and enhancing genomic analyses. |
| Databáze: | OpenAIRE |
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