The list below covers ontologies mentioned during the workshop that may be of use to BioMedBridges members for infrastructure development.
GENES AND GENE PRODUCTS
- Gene Ontology (GO) - large and widely accepted for describing genes and their products across many species
BIOLOGICAL ENTITIES
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CL (cell ontology) - ontology for representation of cell types
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PRO (protein ontology) - ontology for protein entities and the relationships between them
SMALL MOLECULES
- ChEBI - 'dictionary' of chemicals, includes information on their role as drugs or pesticides
PATHWAYS
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BioPax - standard language for integration and exchange of pathway data
PHENOTYPES
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PaTO (phenotype ontology) - OBO ontology of phenotypic qualities
DISEASE
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ICD-10 - used for describing disease and billing in healthcare practice; ICD-10 is closed, ICD-9 is an open version, ICD-11 in development
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Human Disease Ontology - maps to SNOMED, more research focused, biomolecular view on disease
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NCI Thesaurus - National Cancer Institute; terms across clinical care, research, adiminstration and public information
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SNOMED CT (Clinical Terms) - disease ontology mandated for use in >60 countries, BUT not open in some countries; for example, EBI can use it as it as they are based in UK, but it can’t redistribute it in pan-European and international projects; built for clinical practice
- UMLS (Unified Medical Language System) - resource for biomedical information and electronic health records
SOFTWARE / SERVICES
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SWO (Software Ontology) - resource for describing software
- EDAM - bioinformatics operations, data types and tools [BMB project member Jon Ison ([email protected]) worked on EDAM]
TAXONOMY
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NCBI taxonomy - nomenclature for species in sequence databases
PROVENANCE
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ECO (Evidence Code Ontology) - ontology of codes representing experimental evidence
- PROV-O - generic evidence ontology
REPRODUCIBILITY
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OBI - ontology for biomedical and clinical investigations
- BMB software registry - uses SWO-EDAM
- myGRID ontology - now part of EDAM
RELATIONSHIPS
RO (Relation Ontology) - standardisation ontology for OBO Foundry
MICE
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Mammalian Phenotype Ontology - developed by International Mouse Phenotyping Consortium
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Adult Mouse Anatomical Dictionary - annotation of adult mice anatomy
- Uberon - cross species anatomy ontology