public class GafToLegoTranslator extends Object
Given a set of gene associations, this procedure will generate LEGO individuals. The set of associations can be specified by a user query. Includes: grepping a GAF and feeding results selecting all associations for all genes that are involved with some process # STEP 0 - map GeneAssociation in GAF model GeneAssociation( bioentity:class: ext: reference: evidence: # TODO ) ==> # STEP 1 - calculate class expression IF THEN let = IntersectionOf( ) ELSE let = # STEP 2 - map to protein ID IF .IRI startsWith "uniProtKB" THEN let = ELSE let = SELECT WHERE SubClassOf encoded_by some ### requires Omeo # STEP 3 - create instance: IF SubClassOf MF THEN: NamedIndividual( Types: , enabled_by SOME Facts: source ELSE IF SubClassOf CC THEN: NamedIndividual( Types: 'molecular_function', occurs_in some enabled_by SOME Facts: source ELSE IF SubClassOf BP THEN: # note we create two individuals here NamedIndividual( Types: Facts: source NamedIndividual( Types: 'molecular_function' enabled_by SOME Facts: part_of , source # VARIANT OF ABOVE STEP (optional) keep a map of Refs -> generated Ids when performing , first check map. If an individual Id has already been generated for this , then re-use the existing id from the map. Note this may result in multiple classification of individuals (MCI). The user can rectify these in Protege. One variant of this strategy may be to retain the original Id, generate new Ids for the collapsed aggregate MF individual, and include evidence links back to the atomic MF individuals.
Constructor and Description |
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GafToLegoTranslator(OWLGraphWrapper graph,
Map<String,String> gp2protein) |
Modifier and Type | Method and Description |
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org.semanticweb.owlapi.model.OWLOntology |
minimizedTranslate(GafDocument gaf)
Translate the given
GafDocument into an OWL representation of the LEGO model. |
protected void |
reportError(String error,
GeneAnnotation annotation) |
protected void |
reportWarn(String warning,
GeneAnnotation annotation) |
org.semanticweb.owlapi.model.OWLOntology |
translate(Collection<GeneAnnotation> annotations)
Translate the given annotations (
GeneAnnotation ) into an OWL representation of the LEGO model. |
org.semanticweb.owlapi.model.OWLOntology |
translate(GafDocument gaf)
Translate the given
GafDocument into an OWL representation of the LEGO model. |
public GafToLegoTranslator(OWLGraphWrapper graph, Map<String,String> gp2protein)
protected void reportError(String error, GeneAnnotation annotation)
protected void reportWarn(String warning, GeneAnnotation annotation)
public org.semanticweb.owlapi.model.OWLOntology translate(GafDocument gaf)
GafDocument
into an OWL representation of the LEGO model.gaf
- public org.semanticweb.owlapi.model.OWLOntology translate(Collection<GeneAnnotation> annotations)
GeneAnnotation
) into an OWL representation of the LEGO model.annotations
- public org.semanticweb.owlapi.model.OWLOntology minimizedTranslate(GafDocument gaf)
GafDocument
into an OWL representation of the LEGO model.
Additionally minimize the lego model and imports into one ontology module.gaf
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