UniProt & Ontologies How ontologies are used in the context of a  large life sciences database  Eric Jain Swiss Institute ...
<ul><li>What is UniProt? </li></ul>
+ +
UniMES UniRef UniParc ... UniProtKB
UniParc 8.9M sequences
50% 1.5M 90% 2.9M 100% 4.5M UniRef 8.9M clusters
UniProtKB 4.5M entries reviewed 0.3M Species & organelles Description of function etc Keywords & GO Description of sequenc...
<ul><li>What is an Ontology? </li></ul>
unique identifier names  and synonyms relationships within the ontology stable! mapped to other ontologies human-readable ...
<ul><li>Why? </li></ul>
Practical. Navigation, auto-completion etc
 
Consistency! More than one way to say one thing...
Aggregate. i.e. set-oriented views
Automate?
What
Keywords Taxonomy Enzyme Pathways Tissues Subcellular Locations Cellular Components Gene Ontology
 
 
 
 
 
 
Summary Increased use of ontologies is  inevitable  as data volumes grow. UniProt has (or is in the process of introducing...
beta.uniprot.org login: guest/amazing
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UniProt & Ontologies

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

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  • UniProt & Ontologies

    1. 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. 2. <ul><li>What is UniProt? </li></ul>
    3. 3. + +
    4. 4. UniMES UniRef UniParc ... UniProtKB
    5. 5. UniParc 8.9M sequences
    6. 6. 50% 1.5M 90% 2.9M 100% 4.5M UniRef 8.9M clusters
    7. 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. 8. <ul><li>What is an Ontology? </li></ul>
    9. 9. unique identifier names and synonyms relationships within the ontology stable! mapped to other ontologies human-readable definitions machine-readable definitions
    10. 10. <ul><li>Why? </li></ul>
    11. 11. Practical. Navigation, auto-completion etc
    12. 13. Consistency! More than one way to say one thing...
    13. 14. Aggregate. i.e. set-oriented views
    14. 15. Automate?
    15. 16. What
    16. 17. Keywords Taxonomy Enzyme Pathways Tissues Subcellular Locations Cellular Components Gene Ontology
    17. 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]
    18. 25. beta.uniprot.org login: guest/amazing

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