Bundles/ncbi/goa
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Under construction
Graph: http://purl.org/science/graph/ncbi/goa
GO annotations are represented as classes. In order to understand what these classes are, we need to first see what the source material for the annotoations is. This image from Amigo shows the basic information. A gene is named, with the underlying identifier from Entrez Gene, a gene ontology term is named, from one of Cellular Component, Biological Process, or Molecular function, there is an "evidence code" that gives some indication of the manner in which the annotation was inferred, and citation of one or more papers.
We need to interpret this information in a manner that is consistent with the rest of the Neurocommons representation. The source files for the annotations are obtained from the EBI and their format is documented. We've converted human, mouse, and rat annotation - the files we use are:
- gene_association.goa_human
- human.xrefs
- gene_association.goa_mouse
- mouse.xrefs
- gene_association.goa_rat
- rat.xrefs
(CORRECTION: Currently we only have GO annotations from NCBI - not from EBI.)
The following illustration shows how the annotation is to be interpreted.
To what does the annotation refer?
A query for processes annotated to a gene view query
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix ro: <http://www.obofoundry.org/ro/ro.owl#>
select distinct ?process ?processname
where
{ graph <http://purl.org/commons/hcls/goa>
{ ?protein rdfs:subClassOf ?restriction1.
?restriction1 owl:onProperty ro:has_function.
?restriction1 owl:someValuesFrom ?restriction2.
?restriction2 owl:onProperty ro:realized_as.
?restriction2 owl:someValuesFrom ?process.
?protein rdfs:subClassOf ?parent.
?parent owl:equivalentClass ?res3.
?restriction3 owl:hasValue <http://purl.org/commons/record/ncbi_gene/24898>.
}
graph <http://purl.org/commons/hcls/20070416>
{ ?process rdfs:label ?processname}
}
Some classes:
http://www.w3.org/2002/07/owl#Ontology http://www.w3.org/2002/07/owl#Thing http://www.w3.org/2002/07/owl#Class http://www.w3.org/2002/07/owl#AnnotationProperty http://www.w3.org/2002/07/owl#ObjectProperty http://www.w3.org/2002/07/owl#Restriction http://purl.org/obo/owl/ECO#ECO_0000001 http://purl.org/obo/owl/ECO#ECO_0000002 http://purl.org/obo/owl/ECO#ECO_0000033 http://purl.org/obo/owl/ECO#ECO_0000008 http://purl.org/obo/owl/ECO#ECO_0000011 http://purl.org/obo/owl/ECO#ECO_0000014 http://purl.org/obo/owl/ECO#ECO_0000021 http://purl.org/obo/owl/ECO#ECO_0000044 http://purl.org/obo/owl/ECO#ECO_0000034 http://purl.org/obo/owl/ECO#ECO_0000035 http://purl.org/obo/owl/ECO#ECO_0000036 http://purl.org/obo/owl/ECO#ECO_0000037 http://purl.org/obo/owl/ECO#ECO_0000053 http://purl.org/science/owl/sciencecommons/domain_record http://purl.org/science/owl/sciencecommons/protein_record http://purl.org/science/owl/sciencecommons/gene_record http://purl.org/science/owl/sciencecommons/journal_article http://purl.org/science/owl/sciencecommons/pubmed_record http://purl.org/science/owl/sciencecommons/term http://purl.org/science/owl/sciencecommons/enzyme_record
