GOLOCUSID2GO               package:GO               R Documentation

_E_n_t_r_e_z _G_e_n_e _t_o _G_e_n_e _O_n_t_o_l_o_g_y (_G_O) _m_a_p_p_i_n_g

_D_e_s_c_r_i_p_t_i_o_n:

     This data set describes associations between Entrez Gene
     identifiers and GO identifiers as reported by NCBI.  The format is
     an R environment mapping Entrez Gene ids to a list of GO ids that
     are associated with it.  In addition to the GO id, the GO ontology
     category and the evidence code (the reason for the association) is
     given.

_D_e_t_a_i_l_s:

     Each Entrez Gene id is mapped to a list of lists.  The names on
     the outer list are GO ids.  Each inner list consists of three
     named elements: GOID, Ontology, and Evidence.

     The GOID element matches the GO id 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 id 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

     Entrez Gene ids for which no GO associations exist are left out of
     the environment.

     Mappings were based on data provided by:

     Entrez Gene:<URL:
     http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/g
     ene/DATA/>. Built: Source data downloaded from Entrez Gene on Fri
     Sep 30 02:51:32 2005

     Package built: Fri Sep 30 02:51:32 2005

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene>

_E_x_a_m_p_l_e_s:

     library("GO")
     ## Select an Entrez Gene id
     egId <- "10043"
     egIdGoData <- GOLOCUSID2GO[[egId]]

     ## Display GO ids associated with the Entrez Gene id
     sapply(egIdGoData, function(x) x$GOID)

     ## The ontology categories of the GO ids
     sapply(egIdGoData, function(x) x$Ontology)

     ## The evidence codes for the GO ids
     sapply(egIdGoData, function(x) x$Evidence)

