Map between Gene Ontology (GO) Identifiers and all TAIR Identifiers in the subtree

Description

org.At.tairGO2ALLTAIRS is an R object that provides mappings between a given GO identifier and all TAIR identifiers annotated at that GO term or one of its children in the GO ontology.

Details

GO consists of three ontologies—molecular function (MF), biological process (BP), and cellular component (CC). All ontologies are structured as directed acyclic graphs (DAGs). Each node in each DAG (tree) is a GO term (id) associated with a named vector of manufacturer identifiers. The name associated with each manufacturer id corresponds to the evidence code for that GO identifier. This object org.At.tairGO2ALLTAIRS maps between a given GO identifier and all TAIR identifiers annotated at that GO term or one of its children in the GO ontology.

The evidence code indicates what kind of evidence supports the association between the GO and Entrez Gene identifiers. Evidence codes currently in use include:

IMP - inferred from mutant phenotype

IGI - inferred from genetic interaction

IPI - inferred from physical interaction

ISS - inferred from sequence similarity

IDA - inferred from direct assay

IEP - inferred from expression pattern

IEA - inferred from electronic annotation

TAS - traceable author statement

NAS - non-traceable author statement

ND - no biological data available

IC - inferred by curator

A GO identifier may be mapped to the same TAIR identifier more than once but the evidence code can be different. Mappings between Gene Ontology identifiers and Gene Ontology terms and other information are available in a separate data package named GO.

Mappings were based on data provided by:

Gene Ontology ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ With a date stamp from the source of: 20130907

For GO2ALL style mappings, the intention is to return all the genes that are the same kind of term as the parent term (based on the idea that they are more specific descriptions of the general term). However because of this intent, not all relationship types will be counted as offspring for this mapping. Only "is a" and "has a" style relationships indicate that the genes from the child terms would be the same kind of thing.

References

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

Examples

    # Convert to a list
    xx <- as.list(org.At.tairGO2ALLTAIRS)
    if(length(xx) > 0){
        # Gets the tair identifiers for the top 2nd and 3nd GO identifiers
        goids <- xx[2:3]
        # Gets all the tair identifiers for the first element of goids
        goids[[1]]
        # Evidence code for the mappings
        names(goids[[1]])
    }