Dataset Information

The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.

ABSTRACT: 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.There 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.The 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/.

SUBMITTER: Smith JR

PROVIDER: S-EPMC3882879 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.

Smith Jennifer R JR Park Carissa A CA Nigam Rajni R Laulederkind Stanley Jf SJ Hayman G Thomas GT Wang Shur-Jen SJ Lowry Timothy F TF Petri Victoria V Pons Jeff De JD Tutaj Marek M Liu Weisong W Worthey Elizabeth A EA Shimoyama Mary M Dwinell Melinda R MR

Journal of biomedical semantics 20131008 1

<h4>Background</h4>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.<h4>Results</h4>Th ...[more]

PMID: 24103152

Similar Datasets

Project description:An evaluation of human osteoblast metabolism usually involves measurements of the by-products of bone matrix elaboration. The assessment of glycolytic activity of osteoblasts is not a standard tool in most of the reports, but might be of value by providing a direct indicator of cellular metabolism. Measurement of the incorporation of [(18)F]-fluorodeoxyglucose, which is not further degradable following its conversion into glycose-6-phosphate during glycolysis and is trapped in this form within the cells, can be used as an effective research tool for estimation of osteoblast metabolism. In order to estimate the [(18)F]-fluorodeoxyglucose incorporation we used cultured human osteoblast-like cells. Following incubation of the culture samples in a glucose free medium with 5 mu Ci [(18)F]-fluorodeoxyglucose we measured the radioactivity of the cell fraction, as a percent from the initial dose, and compared to the incorporation values in cells treated by protoporphyrine IX (10(-5) M), an endogenous pro-apoptotic agent. To compare the response of [(18)F]-fluorodeoxyglucose incorporation studies, following treatment of cells with the protoporphyrine IX, to other experimental cell metabolism evaluation methods, we performed a parallel comparison of alkaline phospatase activity, which is a standard measurement tool of osteoblast metabolism, in the control and treatment groups. A narrow range of 0.22-1.36% of [(18)F]-fluorodeoxyglucose incorporation per million cells was found. Additionally in the protoporphyrine IX treated cells a significant 62% decrease of [(18)F]-fluorodeoxyglucose incorporation was observed (p < .05). A parallel significant decrease in alkaline phosphatase activity (p < .001) was found in the cells treated by the protoporphyrine IX. Therefore we suggest that the presented method of [(18)F]-fluorodeoxyglucose incorporation measurement can be utilized as an effective research tool for estimation of the cellular glycolitic activity in human osteoblast-like cells in vitro.

Dataset Information

The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.

Publications

The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets