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Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies

Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies,10.1101/gr.580102,Genome Research,D. P. Hill

Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies   (Citations: 32)
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Structured vocabulary development enhances the management of information in biological databases. As information grows, handling the complexity of vocabularies becomes difficult. Defined methods are needed to manipulate, expand and integrate complex vocabularies. The Gene Ontology (GO) project provides the scientific community with a set of structured vocabularies to describe domains of molecular biology. The vocabularies are used for annotation of gene products and for computational annotation of sequence data sets. The vocabularies focus on three concepts universal to living systems, biological process, molecular function and cellular component. As the vocabularies expand to incorporate terms needed by diverse annotation communities, species-specific terms become problematic. In particular, the use of species-specific anatomical concepts remains unresolved. We present a method for expansion of GO into areas outside of the three original universal concept domains. We combine concepts from two orthogonal vocabularies to generate a larger, more specific vocabulary. The example of mammalian heart development is presented because it addresses two issues that challenge GO; inclusion of organism-specific anatomical terms, and proliferation of terms and relationships. The combination of concepts from orthogonal vocabularies provides a robust representation of relevant terms and an opportunity for evaluation of hypothetical concepts.
Journal: Genome Research - GENOME RES , vol. 12, no. 12, pp. 1982-1991, 2002
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    • ...In this project, a mouse heart anatomical ontology is combined with a developmental process ontology using cross products to describe all of the processes involved in the development of all anatomical parts of the heart [16]...
    • ...In a biological context, orthogonal vocabularies are those vocabularies whose terms are unrelated [16]...
    • ...Combining ontologies is more advantageous than constructing an ontology of, for example, heart development, using conventional methods of GO expansion, given the fact that domain experts can create new vocabularies in their own field without attempting to describe domains outside their area of expertise [16]...
    • ...The resulting cross product represents a new vocabulary that includes aspects derived from each of the two base ontologies [16]...

    Kathleen Stewart Hornsbyet al. Combining ontologies to automatically generate temporal perspectives o...

    • ...The automated enrichment of biomedical ontologies is still in its early steps, with few works in existence: [17] propose a method based on verb patterns to enrich a molecular interaction knowledge base;[10] propose a method to expand GO outside its 3 areas by combining two orthogonal vocabularies; and [13] uses the syntactic relations between existing GO terms to propose new ones...

    Catia Pesquitaet al. Identifying Gene Ontology Areas for Automated Enrichment

    • ...to link molecular functions and biological processes from the Gene Ontology to small molecule participants from the Chemical Entities of Biomedical Interest (ChEBI) ontology. For example, this process creates relationships between the GO molecular function terms “Calcium Signaling” and “Calcium Transport” and the ChEBI term “Calcium(2+).” Additional semantic relationships between genes are inferred if such enrichment results in two genes sharing a small molecule participant in a molecular function or biological process (co-ChEBI). For example, this inference adds a semantic relationship between pairs of genes that have functions each of which in turn has calcium as a participant. Similar inference is made over the GO cross-products (see ...

    Sonia M. Leachet al. Biomedical Discovery Acceleration, with Applications to Craniofacial D...

    • ... This methodology of cross-products is being applied, in one of the biological projects driving the NCBO, to the annotation of Drosophila, zebrafish and human alleles for genes implicated in diseas...

    Barry Smithet al. The OBO Foundry: coordinated evolution of ontologies to support biomed...

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