Dear list; I am using package GO and try to extract goterm for some genes. > mget("GO:0008372", GOTERM) >From my record, I would get the following output before > mget("GO:0008372", GOTERM) $"GO:0008372" GOID = GO:0008372 Term = cellular_component unknown Definition = Used for the annotation of gene products whose localization is not known or cannot be inferred. Ontology = CC But I don't know what happened, not it only gives me > mget("GO:0008372", GOTERM) $"GO:0008372" list() attr(,"GOID") [1] "GO:0008372" attr(,"Term") [1] "cellular_component unknown" attr(,"Synonym") [1] NA attr(,"Secondary") character(0) attr(,"Definition") [1] "Used for the annotation of gene products whose localization is not known or cannot be inferred." attr(,"Ontology") [1] "CC" attr(,"class") [1] "GOTerms" attr(,"class")attr(,"package") [1] "annotate" And I wouldn't extract Term information out from this format, anyone can help me to resolve this puzzle? Thanks in advance! fangxin -------------------- Fangxin Hong Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong at salk.edu (Phone): 858-453-4100 ext 1105

On 24 Jun 2005, fhong at salk.edu wrote: > Dear list; > > I am using package GO and try to extract goterm for some genes. >> mget("GO:0008372", GOTERM) > >> From my record, I would get the following output before >> mget("GO:0008372", GOTERM) > > $"GO:0008372" > GOID = GO:0008372 > Term = cellular_component unknown > Definition = Used for the annotation of gene products whose > localization is not known or cannot be inferred. > Ontology = CC > > But I don't know what happened, not it only gives me >> mget("GO:0008372", GOTERM) > $"GO:0008372" list() attr(,"GOID") [1] "GO:0008372" attr(,"Term") > [1] "cellular_component unknown" attr(,"Synonym") [1] NA > attr(,"Secondary") character(0) attr(,"Definition") [1] "Used for > the annotation of gene products whose localization is not known or > cannot be inferred." attr(,"Ontology") [1] "CC" attr(,"class") [1] > "GOTerms" attr(,"class")attr(,"package") [1] "annotate" > > And I wouldn't extract Term information out from this format, anyone > can help me to resolve this puzzle? Try: library(annotate) The last line of the output gives the clue: > "GOTerms" attr(,"class")attr(,"package") [1] "annotate" Basically, what is stored in the GOTERM environment are instances of the GOTerms class and this class is defined in the annotate package. So to get the nice printout, you need annotate loaded. Hmm, perhaps the GO package should depend on annotate? + seth