Hi Fabian, If the data for GO is not available at NCBI, makeOrgPackageFromNCBI will try to use blast2GO instead (for GO at least). Marc On 10/23/2012 01:20 PM, Fabian Grammes wrote: > Hi Herv? > > Thanks a lot, that was exactly the information that I've been > looking for ! > > After updating BioConductor today, I am struggling a bit with > getting the code to work again, but that should be fixed tomorrow > I hope :) > > @ Marc > > I've checked the function: makeOrgPackageFromNCBI, > however since I have most of my annotation information stored locally > (GO etc. - obtained via Blast2GO) and not yet available at NCBI, > I do not think the function helps in my case. > > cheers, F > > On Oct 23, 2012, at 12:04 AM, Hervé Pagès wrote: > >> Hi Fabian, >> >> On 10/22/2012 05:57 AM, Fabian Grammes wrote: >>> Dear List >>> >>> I am working with Atlantic salmon and am highly interested to make a >>> custom annotation package for the >>> microarray that I am using. >>> >>> I've worked through the tutorial from Gabor Csardi ("Creating an >>> annotation package with a new database >>> schema" ), which was very helpful. However, I am struggling to >>> implement >>> the bimap objects to access >>> the GO annotations that I have in the DB. >>> >>> The GO data is stored in 6 tables (BP, BP_all, MF, MF_all, CC, CC_all) >>> looking like the format that I found for >>> the organism packages in BioC: >>> ID GOID evi >>> 6092 GO:0000910 IEA >>> 6092 GO:0040035 IEA >>> 6092 GO:0000398 IEA >>> >>> So if someone could help me/ point me to the correct way how to >>> implement the GO mappings >>> in an annotation package that would be great. >> >> If you look for example at the hgu95av2.db package, it provides 3 >> predefined Bimaps for accessing the GO data: hgu95av2GO (GO map), >> hgu95av2GO2PROBE (GO2PROBE map), and hgu95av2GO2ALLPROBES (GO2ALLPROBES >> map). The 1st is a direct map, the 2nd and 3rd are reverse maps: >> >> > direction(hgu95av2GO) >> [1] 1 >> > direction(hgu95av2GO2PROBE) >> [1] -1 >> > direction(hgu95av2GO2ALLPROBES) >> [1] -1 >> >> All of them are of class "ProbeGo3AnnDbBimap". >> >> The predefined Bimaps are created at load-time. The direct maps >> with a call to AnnotationDbi:::createAnnDbBimaps() and the reverse >> maps by "manually" reversing some of the direct maps returned by >> createAnnDbBimaps(). >> >> So you need to add an entry for the GO map to the list of "seeds" >> passed to createAnnDbBimaps(). In your case this entry needs to look >> something like (assuming ID is your internal id for genes): >> >> seeds <- list( >> ... >> list( >> objName="GO", >> Class="ProbeGo3AnnDbBimap", >> L2Rchain=list( >> list( >> tablename="probes", >> Lcolname="probe_id", >> Rcolname="gene_id", >> filter="{is_multiple}='0'" >> ), >> list( >> tablename="genes", >> Lcolname="gene_id", >> Rcolname="ID" >> ), >> list( >> Lcolname="ID", >> tagname=c(Evidence="{evi}"), >> Rcolname="GOID", >> Rattribnames=c(Ontology="NULL") >> ) >> ), >> rightTables=c(BP="BP", CC="CC", MF="MF") >> ) >> ... >> ) >> >> Then: >> >> ann_objs <- createAnnDbBimaps(seeds, seed0) >> >> where 'seed0' is defined by something like: >> >> seed0 <- list(objTarget="chip <name_of_your_chip>", >> datacache=datacache) >> >> and 'datacache' is the environment that will be used for package- level >> caching of the data loaded from the DB (use NULL for no caching, I'm >> assuming those extra details, which are not GO-specific, are covered >> in Gabor's document, but I don't know). >> >> Then you can append the reverse maps to 'ann_objs' with something like: >> >> ## Append GO2PROBE map: >> map <- ann_objs$GO >> map <- revmap(map) >> map at objName <- "GO2PROBE" >> ann_objs$GO2PROBE <- map >> >> ## Append GO2ALLPROBES map: >> map <- ann_objs$GO2PROBE >> map at rightTables <- c(BP="BP_all", CC="CC_all", MF="MF_all") >> map at objName <- "GO2ALLPROBES" >> ann_objs$GO2ALLPROBES <- map >> >> All this needs to happen at load-time (via the .onLoad hook). Again I'm >> focusing on the GO-specific part of the story here, assuming that you've >> already managed to create the non-GO specific maps (thanks to Gabor's >> document). >> >> Hope this helps, >> >> H. >> >>> >>> kind regards, Fabian >>> >>> _______________________________________________ >>> 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 >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M1-B514 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpages at fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 > > _______________________________________________ > 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