[Bioc-devel] PANTHER.db GOSLIM_ID hosed?

[Morgan, Martin]

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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