Hi list, I have a question about the difference between org.Hs.eg.dbGO2EG and org.Hs.eg.dbGO2ALLEGS. The user manual of org.Hs.eg.db says that GO2EG does not associate the child terms from the GO ontology with the gene. Only the directly evidenced terms are represented in GO2EG. But, for example, ?GO:0000435?, which is in GO2EG, has three parents: GO:0000431, GO:0000411, GO:0000436. None of the three parents is in GO2EG (they are all included in GO2ALLEGS). So this is conflicted with the description given in the manual? I want to know exactly how GO2EG choose terms. Thank you. Kind regards, Zhishi Wang

Hi Zhishi, GO2EG doesn't choose terms. It is the starting annotation. Somewhere someone decided that certain GO terms describes certain gene products and GO2EG is the direct result of that. GO2ALLEGs is derived from GO2EG. It starts with GO2EG and then appends all the implicit GO terms (based on relationships in the GO DAG hierarchy). Does that clarify things? Marc On 04/09/2014 01:01 PM, Zhishi Wang wrote: > Hi list, > > I have a question about the difference between org.Hs.eg.dbGO2EG and org.Hs.eg.dbGO2ALLEGS. The user manual of org.Hs.eg.db says that GO2EG does not associate the child terms from the GO ontology with the gene. Only the directly evidenced terms are represented in GO2EG. But, for example, ?GO:0000435?, which is in GO2EG, has three parents: GO:0000431, GO:0000411, GO:0000436. None of the three parents is in GO2EG (they are all included in GO2ALLEGS). So this is conflicted with the description given in the manual? > > I want to know exactly how GO2EG choose terms. Thank you. > > Kind regards, > Zhishi Wang > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor