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Semi-automatic GO Extension Based on GOA Mappings

Semi-automatic GO Extension Based on GOA Mappings. 2005.10 Bak, Hyeong-u. Contents. Introduction Related Work Our Approach Semantic Expression of GOA Mappings Automatic Expression of GOA Mappings Details Schedule. Introduction(1/2).

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Semi-automatic GO Extension Based on GOA Mappings

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  1. Semi-automatic GO Extension Based on GOA Mappings 2005.10 Bak, Hyeong-u

  2. Contents • Introduction • Related Work • Our Approach • Semantic Expression of GOA Mappings • Automatic Expression of GOA Mappings • Details • Schedule

  3. Introduction(1/2) • Large amounts of data about gene products and its functions have been gathered and being gathered from many research groups e.g. EMBL, UniProt, Ensembl, ... • To fully exploit the potential of vast quantity of bioinformatics data, the SWISS-PROT group integrated biological information from many groups • How to resolve complexities between databases, e.g. the use of different vocabularies?  GO consortium built Gene Ontology, which provides a controlled vocabulary • GO describes gene products in terms of their associated biological processes / cellular components / molecular functions in a species-independent manner

  4. Introduction(2/2) Ontology part-of relationship isa relationship biological process cellular component molecular function antioxidant activity behavior cell ... ... ... Structure of GO

  5. Related Work(1/4) • To easily identify relationships and common properties between gene products from different species, • There should be common vocabulary  GO provides a common vocabulary • Research groups should use GO terms to annotate their gene products  GOA(Gene Ontology Annotation) project is initiated • GOA project has been expanded to cover • Completely sequenced organisms including human • A wide range of organisms where the proteome is not yet complete

  6. Related Work(2/4) • Problems of current GOA mappings • Flat text format • Unclear semantics of mappings

  7. Related Work(3/4) ...(1) • To find sub-terms of acute-phase response, RQL: (2) • To find sub-terms of Acute phase, it is needed to confer (1) and (2)  Better to import (1) into GO ... SP_KW:Acute phase > GO:acute-phase response ; GO:0006953 ... (SELECT X FROM {X} rdfs:subClassOf {<go:GO_0006953>}

  8. Related Work(4/4) • ATP synthesisisaATP biosynthesis • Allosteric enzymehelpscatalytic activity  The semantic relationship between ATP synthesis and ATP biosynthesis is different from that of Allosteric enzyme and catalytic activity ... SP_KW:ATP synthesis > GO:ATP biosynthesis ; GO:0006754 SP_KW:Allosteric enzyme > GO:catalytic activity ; GO:0003824 ...

  9. Contents • Introduction • Related Work • Our Approach • Semantic Expression of GOA Mappings • Automatic Expression of GOA Mappings • Details • Schedule

  10. Semantic Expression of GOA Mappings • To find sub-terms of Acute phase, ※ ‘Issues’ deals with relationships other than “isa” relationship <owl:Class rdf:ID=“GO_0006953"> <go:name>acute-phase response</go:name> <owl:equivalentClass rdf:resource="&uniprot;Acute phase"/> </owl:Class> ... (SELECT X FROM {X} rdfs:subClassOf {<uniprot:acute-phase%20response>}

  11. Automatic Expression of GOA Mappings Automatic Parsing, Conversion, Merging Flat Text Ontology Periodic Checking for Update

  12. Details(1/4) • Equivalence Resolution • (Allosteric enzyme, GO:0003824) is excluded by (1) • Users can add/delete custom rules to include/exclude some pairs satisfying conditions <RULES> [INCLUDE] [EXCLUDE] LEFTHAND ENDWITH ‘enzyme’ AND RIGHTHAND NOT CONTAIN ‘enzyme’ ... SP_KW:ATP synthesis =GO:ATP biosynthesis ; GO:0006754 SP_KW:Allosteric enzyme≠GO:catalytic activity ; GO:0003824 ...

  13. Details(2/4) • Dealing with Many-to-one Relationship • Possible resolutions: association / isa / subclass ... SP_KW:DNA repair > GO:DNA repair ; GO:0006281 SP_KW:SOS response > GO:DNA repair ; GO:0006281 ... <owl:Class rdf:ID=“GO_0006281"> <go:name>DNA repair</go:name> <owl:equivalentClass rdf:resource="&uniprot;DNA repair"/> <owl:equivalentClass rdf:resource="&uniprot;SOS response"/> </owl:Class> ...

  14. Details(3/4) • Dealing with One-to-many Relationship • Possible resolutions: association / superclass / isa ... SP_KW:Detoxification > GO:response to toxin ; GO:0009636 SP_KW:Detoxification > GO:xenobiotic metabolism ; GO:0006805 ... Detoxification xenobiotic metabolism response to toxin

  15. Schedule(1/2) • Modify query conversion(GOGuide triples  SeRQL query) module to enable dealing with equivalent classes e.g. (go:GO_0006277 isSubClassOf_Trans ?X) (uniprot:SOS response isSubClassOf_Trans ?X) ... SELECT X FROM {<go:GO_0006277>} rdfs:subClassOf {?X}, {} owl:equivalentClass {<uniprot:SOS response>}; rdfs:subClassOf {?X} ...

  16. Schedule(2/2) • Support of GO Slim view on GOGuide Abbreviated view Normal view <owl:Class rdf:ID=“GO_0050875"> <go:name>cellular physiological process</go:name> <rdfs:subClassOf rdf:resource=“#GOSlim” /> </owl:Class>

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