In the light of C: Create object "Go3AnnDbBimap" and include it in a org.Xx.eg.db package to use wi

I explain here in more detail my problems with the creation of an organism package.

I tried to create my orgnaism package using the function makeOrgPackage() of the AnnotationForge package.These are my original data.frames

​
​> head(genes.goID)
       GID         GO EVIDENCE
4 11593683 GO:0005524      IEA
5 11593683 GO:0005737      IEA
6 11593683 GO:0017111      IEA
7 11593683 GO:0016485      IEA
8 11593683 GO:0009408      IEA
9 11593684 GO:0003824      IEA

> head(gene.names)
       GID    Locus EnsemblNames
1 11593568 PSE_0001     AEV34513
2 11593570 PSE_0002     AEV34514
3 11593572 PSE_0003     AEV34515
4 11593683 PSE_0004     AEV34516
5 11593684 PSE_0005     AEV34517
6 11593685 PSE_0006     AEV34518

I created the package as follow:

makeOrgPackageFromNCBI(gene_info=gene.names,  go=genes.goID,

                      version = "0.1",
                       author = "Some One <so@someplace.org>",
                       maintainer = "Some One <so@someplace.org>",
                       outputDir = ".",
                       tax_id = "911045",
                       genus = "Pseudovibrio",
                       species = "sp.FOBEG1"

                       goTable=go)

The creation was succesfull and I have the following organism package now:

> ls("package:org.Psp.FOBEG1.eg.db")
[1] "org.Psp.FOBEG1.eg"          "org.Psp.FOBEG1.eg.db"       "org.Psp.FOBEG1.eg_dbconn"   "org.Psp.FOBEG1.eg_dbfile"   "org.Psp.FOBEG1.eg_dbInfo"  
[6] "org.Psp.FOBEG1.eg_dbschema" "org.Psp.FOBEG1.egORGANISM" 

> keytypes(org.Psp.FOBEG1.eg.db)
[1] "Locus"        "EnsemblNames" "GID"          "GO"           "EVIDENCE"     "ONTOLOGY"     "GOALL"        "EVIDENCEALL"  "ONTOLOGYALL" 

> head(keys(org.Psp.FOBEG1.eg.db, keytypes="GID"))->ids

 >select(org.Psp.FOBEG1.eg.db, keys=ids, columns=c("GO", "ONTOLOGY"), keytype="GID")
        GID         GO ONTOLOGY
1  11588526       <NA>     <NA>
2  11588527 GO:0003735       MF
3  11588527 GO:0005840       CC
4  11588527 GO:0006412       BP
5  11588528 GO:0005737       CC
6  11588528 GO:0052906       MF
7  11588529 GO:0005840       CC
8  11588529 GO:0006364       BP
9  11588529 GO:0042274       BP
10 11588529 GO:0043022       MF
11 11588530 GO:0003735       MF
12 11588530 GO:0005840       CC
13 11588530 GO:0006412       BP
14 11588531 GO:0046417       BP
Warning message:
In .generateExtraRows(tab, keys, jointype) :
  'select' resulted in 1:many mapping between keys and return rows

So basically I have all information concerning the GO IDs and the relative ONTOLOGY.

However, when I use the package in programs as goProfile, I got the following error:

> basicProfile (test1, onto="ALL", level=1, orgPackage="org.Psp.FOBEG1.eg.db")

Error in eval(expr, envir, enclos) : 

  object 'org.Psp.FOBEG1.egGO' not found

Can someone help me to understand what I did wrong in the creation my organism's package? The information are there si jsut that goProfiles does not find the object it is looking for. Does someone know how to add this object?

Thanks again for your support and your help.

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] org.Psp.FOBEG1.eg.db_0.1 AnnotationForge_1.6.1    org.Hs.eg.db_2.14.0      RSQLite_0.11.4           DBI_0.3.0                AnnotationDbi_1.26.0    
[7] GenomeInfoDb_1.0.2       Biobase_2.24.0           BiocGenerics_0.10.0     

loaded via a namespace (and not attached):
[1] IRanges_1.22.10 stats4_3.1.1    tools_3.1.1  

Hi Stefano,

The issue here is that the creation function creates an organism package for you but not the older bimaps objects that were in some of the oldest annotation packages.  So the object

org.Psp.FOBEG1.egGO

is actually a name for of these much older style of 'bimap' objects and goProfiles is apparently still requiring those do it's work.  It turns out that it is not a very scalable plan to create custom bimaps for the broadening set of organisms that people need to study these days. 

But there is no reason that this has to happen however as the same data is much more straightforward to make available via the much more generic select() method.  I would be very happy to help the authors of goProfile to upgrade their package to the newer approach so that this will work with the newer annotation packages in addition to the older classic ones.

Going forward, the modernizing of software that depends on these annotations (and improving the annotation infrastructure as needed) are things that we aim to work on.