Open Biomedical Ontologies

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    These are ontologies derived from the Open Biomedical Ontologies (OBO) , and used under the terms of the OBO license: " (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed under the original name or with the same identifiers."

    The files were converted to OWL on April 27, 2007 by Syed Hamid Ali Tirmizi - hamid@cs.utexas.edu http://www.cs.utexas.edu/~hamid/research/obo2owl.cgi A future alternative may be to use http://www.berkeleybop.org/ontologies/

    The files were semi-automatically merged with SUMO by Adam Pease, using the Sigma knowledge engineering environment's ontology mapping tool and OWL to SUO-KIF translator.

    It must be mentioned that these are "best guess" mappings. In nearly all cases, the original sources are simple taxonomies, with little formal definition, and often even lacking documentation strings. More effort would be needed to turn them into formal ontologies. In some cases, SUMO does not have much content in the particular topic, so there are few mappings. For example, since SUMO has the concept of DNA, but not of genomes or the many types of genomes, there won't be many mappings for OBO's gene ontology. However that ontology could be more fully integrated by hand, and benefit from using SUMO's rich ontology of spatial relations etc.

    Note also that this is just a first cut semi-automatic matching. A full manual mapping would certainly find more connections. For example, these ontologies make little or no use of the part-of relation that many of them contain, so many things like special anatomical parts wind up not being linked simply because there is no direct equivalent in SUMO. A manual mapping however could use the part-of relation (or more properly SUMO's typicalPart and typicallyContainsPart), to state for example that a OBO:metatarsal is part of a SUMO:Hand even though the automatic mapper won't find a link for metatarsal since there's no direct equivalent in SUMO.

    This is a work in progress, and new ontologies will be posted as they are mapped.

    NameMapping fileMerged with SUMONotes
    adult_mouse_anatomy .kif .kif
    arabidopsis_development .kif .kif
    caro .kif .kif
    cell .kif .kif
    cereals_development no mappings
    chebi .kif
    dictyostelium_anatomy no mappings
    EMAP no mappings
    environment .kif .kif
    evidence_code no mappings
    fix
    fly_anatomy .kif .kif
    flybase_controlled_vocabulary .kif .kif
    fly_development .kif .kif
    fma .kif .kif
    fungal_anatomy .kif .kif
    gene_ontology .kif .kif
    human-dev-anat-abstract .kif .kif
    human-dev-anat-staged .kif .kif
    mammalian_phenotype .kif .kif
    medaka no mappings
    mesh no mappings
    molecule no mappings
    mosquito_anatomy .kif .kif
    mouse_pathology .kif .kif
    pathway .kif .kif
    plant_trait no mappings
    po_anatomy .kif .kif
    po_temporal no mappings
    psi-mi .kif .kif
    psi-mod not mapped (file format issue)
    quality .kif .kif
    rex .kif .kif
    ro .kif .kif
    sep .kif .kif Note that SEP already has included a number of terms from SUMO
    so not mapped (file format issue)
    worm_development no mappings
    zea_mays_anatomy .kif .kif
    zebrafish_anatomy .kif .kif

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