[Bioc-devel] GSEABase::getOBOCollection() missing children

hi,

importing an OBO file with GSEABase::getOBOCollection() I have observed missing
children in the imported ontology. Here is an example with the Sequence Ontology:

library(GSEABase)

oboSOXP <-
getOBOCollection("http://sourceforge.net/p/song/svn/HEAD/tree/trunk/so-xp.obo")
Warning message:
In readLines(src) :
   incomplete final line found on
'http://sourceforge.net/p/song/svn/HEAD/tree/trunk/so-xp.obo'
gSOXP <- as(oboSOXP, "graphNEL")
edges(gSOXP)[["SO:0001622"]]
[1] "SO:0001968"

so the term SO:0001622 in principle has only one child term SO:0001968. However,
a free text search for this entry in the OBO file shows the following:

[Term]
id: SO:0001622
name: UTR_variant
def: "A transcript variant that is located within the UTR." [SO:ke]
synonym: "UTR variant" EXACT []
synonym: "UTR_" EXACT ebi_variants
[http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001791 ! exon_variant
is_a: SO:0001968 ! coding_transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:22:58Z

that is, it has two children, not just one. The child SO:0001791 is missing.
Actually, looking to the distribution of the number of children per term, they
all have at most one child:

nchild <- sapply(edges(gSOXP), length)
table(nchild)
nchild
    0    1
  206 2072

I have not found in the manual page of getOBOCollection() that this function
cannot import more than one child per term, so I guess this is either a bug or
an oversight issue.

cheers,

robert.

On 06/05/2015 08:51 AM, Robert Castelo wrote:

hi,

importing an OBO file with GSEABase::getOBOCollection() I have
observed missing
children in the imported ontology. Here is an example with the
Sequence Ontology:

Thanks Robert, the import went ok, but the coercion to graphNEL was
flawed. This is fixed in 1.31.2 in devel, and will be ported to release
/ available via biocLite tomorrow afternoon (all being well...)


Martin

library(GSEABase)

oboSOXP <-
getOBOCollection("http://sourceforge.net/p/song/svn/HEAD/tree/trunk/so-xp.obo")

Warning message:
In readLines(src) :
incomplete final line found on
'http://sourceforge.net/p/song/svn/HEAD/tree/trunk/so-xp.obo'
gSOXP <- as(oboSOXP, "graphNEL")
edges(gSOXP)[["SO:0001622"]]
[1] "SO:0001968"

so the term SO:0001622 in principle has only one child term
SO:0001968. However,
a free text search for this entry in the OBO file shows the following:

[Term]
id: SO:0001622
name: UTR_variant
def: "A transcript variant that is located within the UTR." [SO:ke]
synonym: "UTR variant" EXACT []
synonym: "UTR_" EXACT ebi_variants
[http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001791 ! exon_variant
is_a: SO:0001968 ! coding_transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:22:58Z

that is, it has two children, not just one. The child SO:0001791 is
missing.
Actually, looking to the distribution of the number of children per
term, they
all have at most one child:

nchild <- sapply(edges(gSOXP), length)
table(nchild)
nchild
0 1
206 2072

I have not found in the manual page of getOBOCollection() that this
function
cannot import more than one child per term, so I guess this is either
a bug or
an oversight issue.

cheers,

robert.