GOENTREZID2GO               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 identifiers to a list of GO
     identifiers that are associated with it.  In addition to the GO
     identifier. 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 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 identifier. 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 identifiers 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 Tue
     Sep  5 18:42:30 2006

     Package built: Tue Sep  5 18:42:30 2006

_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 <- GOENTREZID2GO[[egId]]

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

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

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