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UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
UniProt & Ontologies
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UniProt & Ontologies

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Brief overview of the different "ontologies" used by the UniProt protein sequence database.

Brief overview of the different "ontologies" used by the UniProt protein sequence database.

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  • Transcript

    • 1. UniProt & Ontologies How ontologies are used in the context of a large life sciences database Eric Jain Swiss Institute of Bioinformatics, Geneva April 2007
    • 2. <ul><li>What is UniProt? </li></ul>
    • 3. + +
    • 4. UniMES UniRef UniParc ... UniProtKB
    • 5. UniParc 8.9M sequences
    • 6. 50% 1.5M 90% 2.9M 100% 4.5M UniRef 8.9M clusters
    • 7. UniProtKB 4.5M entries reviewed 0.3M Species & organelles Description of function etc Keywords & GO Description of sequence features Sequence(s) Literature Citations Cross-References Protein & gene names
    • 8. <ul><li>What is an Ontology? </li></ul>
    • 9. unique identifier names and synonyms relationships within the ontology stable! mapped to other ontologies human-readable definitions machine-readable definitions
    • 10. <ul><li>Why? </li></ul>
    • 11. Practical. Navigation, auto-completion etc
    • 12.  
    • 13. Consistency! More than one way to say one thing...
    • 14. Aggregate. i.e. set-oriented views
    • 15. Automate?
    • 16. What
    • 17. Keywords Taxonomy Enzyme Pathways Tissues Subcellular Locations Cellular Components Gene Ontology
    • 18.  
    • 19.  
    • 20.  
    • 21.  
    • 22.  
    • 23.  
    • 24. Summary Increased use of ontologies is inevitable as data volumes grow. UniProt has (or is in the process of introducing) several ontologies. What data will be &quot;ontologized&quot; and how detailed the ontologies are depends on your feedback ! [email_address]
    • 25. beta.uniprot.org login: guest/amazing

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