MIREOT
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MIREOT: The Minimal Information to Reference an External Ontology Term
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MIREOT
- 1. MIREOT Minimal information to reference external ontology terms Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman and Alan Ruttenberg ICBO: International Conference on Biomedical Ontology University at Buffalo, NY ▪ July 24-26, 2009 Session 4: Creating ontologies that work together
- 3. Modeling experimental processes See the OBI poster for more information
- 4. Some material entities in OBI anatomical entity (FMA, CARO) protein complex (Gene Ontology) molecular entity (ChEBI) organism (NCBI taxonomy) processed material material entity chemical entities in solution device cell culture organization cell (Cell Ontology) PCR product
- 18. Step 3: Plug it in external.owl externalDerived.owl Pre-release update obi.owl IMPORTS
Editor's Notes
- Terms necessary for describing biomedical investigations as well as defining necessary cross-product terms are already available in a number of OBO ontologies.
- For example, OBI's scope include materials made and produced for investigations, many of which are derived from natural entities described in the GO cellular component Ontology, Cell Ontology, and ChEBI, qualities of which can be described by terms in PATO OBI is committed to using existing terms from other ontologies - OBI follows OBO Foundry principles
- ChEBI encompasses molecular entities, with focus on 'small" chemical coumpounds, PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. The Cell Ontology is designed as a structured controlled vocabulary for cell types. The NCBI Taxonomy database is a curated set of names and classifications for all of the organisms that are represented in GenBank
- First, some OWL tools ( e.g., Protégé, SWOOP) can neither load or reason over very large ontologies, such as the NCBI Taxonomy 2 or the Foundational Model of Anatomy 3 , making direct OWL imports of such ontologies impractical. Second, different resources may have been constructed using different design principles, which may not align. Importing such ontologies as a whole could lead to inconsistencies or unintended inferences.
- Script uses external.owl to create sparql queries based on templates for each resource.
- Keeping files separated from the “main” ontology allows us to destroy externalDerived.owl, containing the additional information more prone to change, before each release, and we can easily regenerate it in order to distribute up to date information. Also we hope that in the future we would be able to import whole ontologies, and the replacement would then be easy.