Semi-automatic GO Extension Based on GOA Mappings

2005.10Bak, Hyeong-u

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Contents Introduction Related Work Our Approach

Semantic Expression of GOA Mappings Automatic Expression of GOA Mappings Details

Schedule

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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

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Introduction(2/2)

Structure of GO

molecular function

antioxidant activity

Ontology

...

part-of relationship

isa relationship

biological process

behavior

...

cellular component

cell

...

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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

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Related Work(2/4)

Problems of current GOA mappings Flat text format Unclear semantics of mappings

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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>}

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Related Work(4/4)

ATP synthesis isa ATP biosynthesis Allosteric enzyme helps catalytic 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:0006754SP_KW:Allosteric enzyme > GO:catalytic activity ; GO:0003824...

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Contents Introduction Related Work Our Approach

Semantic Expression of GOA Mappings Automatic Expression of GOA Mappings Details

Schedule

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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>}

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Automatic Expression of GOA Mappings

AutomaticParsing,

Conversion,Merging

Periodic Checking for Update

Flat Text Ontology

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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

SP_KW:ATP synthesis = GO:ATP biosynthesis ; GO:0006754SP_KW:Allosteric enzyme ≠ GO:catalytic activity ; GO:0003824...

<RULES>[INCLUDE][EXCLUDE]LEFTHAND ENDWITH ‘enzyme’ AND RIGHTHAND NOT CONTAIN ‘enzyme’...

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Details(2/4)

Dealing with Many-to-one Relationship

Possible resolutions: association / isa / subclass

...SP_KW:DNA repair > GO:DNA repair ; GO:0006281SP_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>...

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Details(3/4)

Dealing with One-to-many Relationship

Possible resolutions: association / superclass / isa

...SP_KW:Detoxification > GO:response to toxin ; GO:0009636SP_KW:Detoxification > GO:xenobiotic metabolism ; GO:0006805...

response to toxin

xenobioticmetabolism

Detoxification

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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}...

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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>