\name{hguatlas13kGO2ALLPROBES} \alias{hguatlas13kGO2ALLPROBES} \title{Map between Gene Ontology (GO) Identifiers and all Manufacturer Identifiers in the subtree} \description{ hguatlas13kGO2ALLPROBES is an R object that provides mappings between a given GO identifier and all manufactuerer 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 hguatlas13kGO2ALLPROBES maps between a given GO identifier and all manufactuerer 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 manufacturer 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: 20120303 and Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA With a date stamp from the source of: 2012-Mar7 } \references{ \url{ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/} } \examples{ # Convert to a list xx <- as.list(hguatlas13kGO2ALLPROBES) if(length(xx) > 0){ # Get the probe identifiers for the top 2nd and 3nd GO identifiers goids <- xx[2:3] # Get all the probe identifiers for the first element of goids goids[[1]] # Evidence code for the mappings names(goids[[1]]) } } \keyword{datasets}