[Obo-owltools] Issue 25 in owltools: multiple def tag exception

[<owl...@go...>]

Status: New
Owner: ----
Labels: Type-Defect Priority-Medium

New issue 25 by midori.h...@gmail.com: multiple def tag exception
http://code.google.com/p/owltools/issues/detail?id=25

What steps will reproduce the problem?

I ran oort on the command line with these options:
/bin/ontology-release-runner -outdir ~/tmp-ont/releases/latest -reasoner  
Elk  ~/pombase/phenotype_ontology/fypo_edit.obo  
http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/phenotype/quality.obo  
http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/anatomy/cell_type/cell.edit.obo  
http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo

(Using FYPO from the source  
http://pombase.svn.sourceforge.net/viewvc/pombase/phenotype_ontology/fypo_edit.obo  
should also do the same.)


What is the expected output? What do you see instead?

I get an "exception in thread" error that seems to be claiming that  
GO:0007126 has multiple def tags (whole error message included below). But  
I looked at GO:0007126 in the GO .obo file, and it sure looks like there's  
only one def tag there.

I've also seen a similar message about a ChEBI term in another test run  
where I included a few more ontologies, ChEBI among them.

Exception in thread "main"  
org.obolibrary.oboformat.model.FrameStructureException: multiple def tags  
not allowedin frame:Frame(GO:0007126 id( GO:0007126{})def( A cell cycle  
process comprising the steps by which a cell progresses through the nuclear  
division phase of a meiotic cell cycle. A meiotic cell cycle is the  
specialized nuclear and cell division in which a single diploid cell  
undergoes two nuclear divisions following a single round of DNA replication  
in order to produce four daughter cells that contain half the number of  
chromosomes as the diploid cell. Meiotic division occurs during the  
formation of gametes from diploid organisms and at the beginning of  
haplophase in those organisms that alternate between diploid and haploid  
generations.{}[GOC:dph GOC:mah PMID:9334324 ])subset( goslim_pombe{})def( A  
cell cycle process comprising the steps by which a cell progresses through  
the nuclear division phase of a meiotic cell cycle, the specialized nuclear  
and cell division in which a single diploid cell undergoes two nuclear  
divisions following a single round of DNA replication in order to produce  
four daughter cells that contain half the number of chromosomes as the  
diploid cell. Meiotic division occurs during the formation of gametes from  
diploid organisms and at the beginning of haplophase in those organisms  
that alternate between diploid and haploid generations.{}[GOC:dph GOC:mah  
PMID:9334324 ])name( meiosis{})xref( Wikipedia:Meiosis{})namespace(  
biological_process{})relationship( part_of GO:0051327{})is_a( GO:0022403{}))


What version of the product are you using? On what operating system?
0.3.5-beta, Mac OS X 10.6.8

Please provide any additional information below.