The Experimental Factor Ontology (EFO) available from http://www.ebi.ac.uk/efo is an application focused ontology modeling the experimental factors in ArrayExpress and constructing mappings to multiple existing domain specific ontologies.
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covers a lot of omics terms, useful
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Open Biomedical Ontologies
obo An umbrella organization for ontologies and structured shared controlled vocabularies for use across all biological and biomedical domains
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