Abstract
BackgroundThe Clinical Measurement Ontology (CMO), Measurement Method Ontology (MMO), and Experimental Condition Ontology (XCO) were originally developed at the Rat Genome Database (RGD) to standardize quantitative rat phenotype data in order to integrate results from multiple studies into the PhenoMiner database and data mining tool. These ontologies provide the framework for presenting what was measured, how it was measured, and under what conditions it was measured.ResultsThere has been a continuing expansion of subdomains in each ontology with a parallel 2–3 fold increase in the total number of terms, substantially increasing the size and improving the scope of the ontologies. The proportion of terms with textual definitions has increased from ~60% to over 80% with greater synchronization of format and content throughout the three ontologies. Representation of definition source Uniform Resource Identifiers (URI) has been standardized, including the removal of all non-URI characters, and systematic versioning of all ontology files has been implemented. The continued expansion and success of these ontologies has facilitated the integration of more than 60,000 records into the RGD PhenoMiner database. In addition, new applications of these ontologies, such as annotation of Quantitative Trait Loci (QTL), have been added at the sites actively using them, including RGD and the Animal QTL Database.ConclusionsThe improvements to these three ontologies have been substantial, and development is ongoing. New terms and expansions to the ontologies continue to be added as a result of active curation efforts at RGD and the Animal QTL database. Use of these vocabularies to standardize data representation for quantitative phenotypes and quantitative trait loci across databases for multiple species has demonstrated their utility for integrating diverse data types from multiple sources. These ontologies are freely available for download and use from the NCBO BioPortal website at http://bioportal.bioontology.org/ontologies/1583 (CMO), http://bioportal.bioontology.org/ontologies/1584 (MMO), and http://bioportal.bioontology.org/ontologies/1585 (XCO), or from the RGD ftp site at ftp://rgd.mcw.edu/pub/ontology/.
Highlights
Introduction to theRat Genome Database (RGD) phenotypes and models portal video tutorial page. [http://rgd.mcw.edu/wg/home/rgd_rat_community_videos/ introduction-to-the-rgd-phenotypes-and-models-portal]37
Increases in the size and scope of the clinical measurement ontology As stated when this ontology was originally released, the Clinical Measurement Ontology was “...primarily organized on the highest level according to the body system in which the measurement is made” [4]
It is a common practice to limit the number of asserted parents to a single one for each ontology term, the applications for which these ontologies were designed are largely geared toward physiological and clinical researchers
Summary
Introduction to theRGD phenotypes and models portal video tutorial page. [http://rgd.mcw.edu/wg/home/rgd_rat_community_videos/ introduction-to-the-rgd-phenotypes-and-models-portal]37. The Clinical Measurement Ontology (CMO), Measurement Method Ontology (MMO), and Experimental Condition Ontology (XCO) were originally developed at the Rat Genome Database (RGD) to standardize quantitative rat phenotype data in order to integrate results from multiple studies into the PhenoMiner database and data mining tool. These ontologies provide the framework for presenting what was measured, how it was measured, and under what conditions it was measured. This paper will present details regarding these improvements to the ontologies and information about applications of the ontologies which have recently been implemented
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