[Bioc-devel] PANTHER.db GOSLIM_ID hosed?

[Julius Müller]

Dear Steve,

thanks a lot for pointing out the error! The problem Martin described is 
exactly the problem addressed in PANTHER.db version 1.02. However the 
version available on bioconductor is not v1.02.
The method type2col in PANTHER.db 1.02 should look like this:

> type2col <- function(x){
>
>   column_names <- 
> c("family_id","goslim_id","ontology","uniprot_id","species","family_term","subfamily_term","class_id","class_term","go_id","go_term","component_go_id","component_term","evidence","evidence_type","confidence_code","entrez_id")
>   names(column_names) <- .cols(x)
>   column_names
> }

What's puzzling to me is that there are unit tests included in the 
loading routine, so checking the version currently available on 
bioconductor should have choked executing PANTHER.db:::.test()
I remember when I first uploaded the new version to Jim, I have send an 
old version by accident and then later on the correct version. This 
might have caused some confusion.
Can somebody send me another aspera invite, then we can make sure that 
you have got the right version?

Many thanks and apologies if this caused any troubles,
Julius


On 20/11/2015 09:46, Morgan, Martin wrote:
>  From the head of
>
>> PANTHER.db:::.keys
> function (x, keytype)
> {
>      t2t <- .type2table(x)
>      t2c <- .type2col(x)
>   
> I wonder if many of the columns / keytypes are mislabeled, e.g.,
>
>> PANTHER.db:::.type2col(PANTHER.db)
>           CLASS_ID        CLASS_TERM      COMPONENT_ID    COMPONENT_TERM
>        "family_id"       "goslim_id"        "ontology"      "uniprot_id"
>    CONFIDENCE_CODE            ENTREZ          EVIDENCE     EVIDENCE_TYPE
>          "species"     "family_term"  "subfamily_term"        "class_id"
>          FAMILY_ID       FAMILY_TERM         GOSLIM_ID       GOSLIM_TERM
>       "class_term"           "go_id"         "go_term" "component_go_id"
>         PATHWAY_ID      PATHWAY_TERM           SPECIES    SUBFAMILY_TERM
>   "component_term"        "evidence"   "evidence_type" "confidence_code"
>            UNIPROT
>        "entrez_id"
>
> probably because columns() is used in .type2* but was changed at some point to return sorted values
>
>> showMethods(PANTHER.db:::.type2col, includeDefs=TRUE)
> Function: .type2col (package PANTHER.db)
> x="PANTHER.db"
> function (x)
> {
>      cls <- c("family_id", "goslim_id", "ontology", "uniprot_id",
>          "species", "family_term", "subfamily_term", "class_id",
>          "class_term", "go_id", "go_term", "component_go_id",
>          "component_term", "evidence", "evidence_type", "confidence_code",
>          "entrez_id")
>      names(cls) <- columns(x)
>      cls
> }
>
>> columns
> nonstandardGenericFunction for "columns" defined from package "AnnotationDbi"
>
> function (x)
> {
>      value <- standardGeneric("columns")
>      sort(value)
> }
>
>> selectMethod("columns", "PANTHER.db")
> Method Definition:
>
> function (x)
> {
>      c("FAMILY_ID", "GOSLIM_ID", "GOSLIM_TERM", "UNIPROT", "SPECIES",
>          "FAMILY_TERM", "SUBFAMILY_TERM", "CLASS_ID", "CLASS_TERM",
>          "PATHWAY_ID", "PATHWAY_TERM", "COMPONENT_ID", "COMPONENT_TERM",
>          "EVIDENCE", "EVIDENCE_TYPE", "CONFIDENCE_CODE", "ENTREZ")
> }
>
> Probably a better design is to define a package-global constant
>
> .TYPE2COLUMN = c(FAMILY_ID="family_id", GOSLIM_ID="goslim_id", ...)
>
> and implement columns,PANTHER.db-method as names(.TYPE2COLUMN)
>
> Martin Morgan
> ________________________________________
> From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Steve Lianoglou [lianoglou.steve at gene.com]
> Sent: Friday, November 20, 2015 4:24 AM
> To: bioc-devel at r-project.org
> Subject: [Bioc-devel] PANTHER.db GOSLIM_ID hosed?
>
> Hi all,
>
> I'm running the latest Bioc + PANTHER.db
>
> I think we've got the GOSLIM_TERM where the GOSLIM_ID should be:
>
> In the vignette, we have this:
>
> R> go_ids <- head(keys(PANTHER.db,keytype="GOSLIM_ID"))
> R> go_ids
>
> ## [1] "GO:0000003" "GO:0000165" "GO:0000166" "GO:0000228"
> "GO:0000375" "GO:0000398"
>
> But what we really get is:
>
> R> head(keys(PANTHER.db,keytype="GOSLIM_ID"))
>
> [1] "2-arachidonoylglycerol biosynthesis"
> [2] "5-Hydroxytryptamine biosynthesis"
> [3] "5-Hydroxytryptamine degredation"
> [4] "5HT1 type receptor mediated signaling pathway"
>
> R> packageVersion('PANTHER.db')
> [1] '1.0.2'
>
> Thanks,
> -steve
>
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-- 
Julius Müller
1A All Saints Road
OX3 7AU, Oxford
United Kingdom
Phone: +44 750 828 0522
mail at jmuller.eu <mailto:mail at jmuller.eu>


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