Hi, I'm a little confused about the location of the environments GOmolecularfunction, GObiologicalprocess, and GOcellularcomponent in release 1.1.1 of the GO data package. I know they used to be there (1.1.0), but a few days ago I updated to 1.1.1 and now they seem to be missing. Have they been replaced with other objects that I can use to translate GOID to the path of ontologies? For example (using 1.1.0), xx <- ls(env = GOMFID2TERM) get(xx[12], env=GOmolecularfunction) $ontology [1] "alpha-1,3-mannosyltransferase" $ontology [1] "mannosyltransferase" $ontology [1] "transferase, transferring hexosyl groups" $ontology [1] "transferase, transferring glycosyl groups" $ontology [1] "transferase" $ontology [1] "enzyme" Thanks, Mark Wilkinson Informatics Analyst St. Jude Children's Research Hospital Department of Pharmaceutical Sciences The opinions expressed here are my own and do not necessarily represent those of St. Jude Children's Research Hospital.

The structure of the package has changed. To get the previous behavior you can use a function like trace2root <- function(tag,env=GOMFID2TERM,parenv=GOMFPARENTS) { line <- get(tag,env) thistag <- tag tmp <- thistag while( !is.na(tmp <- get(thistag,parenv)) ) { # # following needs to be made a bigger OR clause with elements # for BP and CC root tags # if (tmp == "GO:0003674") break line <- c(line,get(tmp,env)) # ok because depth not so great thistag <- tmp } line } > trace2root( xx[12] ) [1] "alpha-1,3-mannosyltransferase" [2] "mannosyltransferase" [3] "transferase, transferring hexosyl groups" [4] "transferase, transferring glycosyl groups" [5] "transferase" [6] "enzyme" Jianhua Zhang who maintains this system is away but can comment more fully on his return > Hi, > > I'm a little confused about the location of the environments > GOmolecularfunction, GObiologicalprocess, and GOcellularcomponent in release > 1.1.1 of the GO data package. I know they used to be there (1.1.0), but a > few days ago I updated to 1.1.1 and now they seem to be missing. Have they > been replaced with other objects that I can use to translate GOID to the > path of ontologies? > > For example (using 1.1.0), > xx <- ls(env = GOMFID2TERM) > get(xx[12], env=GOmolecularfunction) > $ontology > [1] "alpha-1,3-mannosyltransferase" > > $ontology > [1] "mannosyltransferase" > > $ontology > [1] "transferase, transferring hexosyl groups" > > $ontology > [1] "transferase, transferring glycosyl groups" > > $ontology > [1] "transferase" > > $ontology > [1] "enzyme" > > > > Thanks, > > > Mark Wilkinson > Informatics Analyst > St. Jude Children's Research Hospital > Department of Pharmaceutical Sciences > > The opinions expressed here are my own and do not necessarily represent > those of St. Jude Children's Research Hospital. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >