is_a is omitted

[beny]

Hi,

I have few obo files which use tag is_a to connect betweet each other but after parsing trough this gem they disappear from the parsed object. I actually don't know much about the standard (even if it is standard or not) but I'm not able to find all the items I want without this info.

The original term is

[Term]
id: UO:0000054
name: area density unit
def: "A density unit which is a standard measure of the mass exerting an influence on a given area." [Wikipedia:Wikipedia "http://www.wikipedia.org/"]
subset: unit_group_slim
synonym: "mass per unit area unit" EXACT []
is_a: UO:0000182 ! density unit
relationship: unit_of PATO:0001351
created_by: george gkoutos

and the output object is this, as you can see without the is_a tag

#<Obo::Stanza:0x007faf330b11e0
 @name="Term",
 @tagvalues=
  {"id"=>["UO:0000054"],
   "name"=>["area density unit"],
   "def"=>
    ["\"A density unit which is a standard measure of the mass exerting an influence on a given area.\" [Wikipedia:Wikipedia \"http://www.wikipedia.org/\"]"],
   "subset"=>["unit_group_slim"],
   "synonym"=>["\"mass per unit area unit\" EXACT []"],
   "relationship"=>["unit_of PATO:0001351"],
   "created_by"=>["george gkoutos"]}>

And the question is, is it a bug or this is how it should behave?

[beny]

I look into it little bit and the is_a tag is omitted because of the regexp on line https://github.com/robsyme/obo/blob/master/lib/obo/parser.rb#L7. And the standard allow situation like this (http://www.geneontology.org/GO.format.obo-1_2.shtml#S.1.3) so it's a bug ... and pull request is on the way :)

[beny]

Oh, it's already fixed (#4) but still not on rubygems. Can you please update the gem?

[robsyme]

Done, v0.1.5. Thanks for the prompt.