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.

Image:Go_Annotation_in_Amigo.png

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:

(CORRECTION: Currently we only have GO annotations from NCBI - not from EBI.)

The following illustration shows how the annotation is to be interpreted.

Image:Go_annotation_illustration.png

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
{     ?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>.
      ?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