org.Sc.sgdGO {org.Sc.sgd.db} | R Documentation

## Map between ORF IDs and Gene Ontology (GO)

### Description

org.Sc.sgdGO is an R object that provides mappings between ORF identifiers and the GO identifiers that they are directly associated with. This mapping and its reverse mapping do NOT associate the child terms from the GO ontology with the gene. Only the directly evidenced terms are represented here.

### Details

Each ORF identifier is mapped to a list of lists. The names on the outer list are GO identifiers. Each inner list consists of three named elements: GOID, Ontology, and Evidence.

The GOID element matches the GO identifier named in the outer list and is included for convenience when processing the data using 'lapply'.

The Ontology element indicates which of the three Gene Ontology categories this identifier belongs to. The categories are biological process (BP), cellular component (CC), and molecular function (MF).

The Evidence element contains a code indicating what kind of evidence supports the association of the GO identifier to the Entrez Gene id. The evidence codes 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

Mappings between ORF identifiers and GO information were obtained through their mappings to ORF identifiers. NAs are assigned to ORF identifiers that can not be mapped to any Gene Ontology information. Mappings between Gene Ontology identifiers an Gene Ontology terms and other information are available in a separate data package named GO.

Mappings were based on data provided by: Yeast Genome ( ftp://genome-ftp.stanford.edu/pub/yeast/data_download ) on 2008-Sep06

For the reverse map org.Sc.sgdGO2ORF, each GO term maps to a named vector of ORF identifiers. A GO identifier may be mapped to the same ORF 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.

### References

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

### See Also

`org.Sc.sgdGO2ALLORFS`.

### Examples

        x <- org.Sc.sgdGO
        # Get the ORF identifiers that are mapped to a GO ID
        mapped_genes <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_genes])
        if(length(xx) > 0) {
            # Try the first one
            got <- xx[[1]]
            got[[1]][["GOID"]]
            got[[1]][["Ontology"]]
            got[[1]][["Evidence"]]
        }
        # For the reverse map:
        # Convert to a list
        xx <- as.list(org.Sc.sgdGO2ORF)
        if(length(xx) > 0){
            # Gets the ORF ids for the top 2nd and 3nd GO identifiers
            goids <- xx[2:3]
            # Gets the ORF ids for the first element of goids
            goids[[1]]
            # Evidence code for the mappings
            names(goids[[1]])
        }

[Package org.Sc.sgd.db version 2.2.6 Index]