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equivalent pairs error #16

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Input: (a local copy of) 
http://pombase.svn.sourceforge.net/viewvc/pombase/phenotype_ontology/fypo_edit.o
bo revision 239

2. Run Oort with default settings; output to local testing directory

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

Expected: release files as described in documentation (still learning about 
specifics of those files' content ..)

Got: popup error box saying "Internal error: will not release inconsistent 
ontology unless forced!" (0.3.3 beta) or "Internal error: will not release 
ontology with equivalent pairs unless forced!" (0.3.4 beta)

The log file contains many lines like these:
"Class FYPO:0000370 has a self reference in its logical definition."
"2011-11-10 11:03:05 ERROR 
Equiv:EquivalentClasses(<http://purl.obolibrary.org/obo/FYPO_0000071> 
<http://purl.obolibrary.org/obo/FYPO_0000126> )"

But there's no self reference in the FYPO:0000370 stanza, and it's not obvious 
if there's a self reference resulting from transitivity, implied links, etc. 
And FYPO:0000071 is_a FYPO:0000126 -- they're not identical, so I think they're 
not "equivalent".

What version of the product are you using? On what operating system?

I tried 0.3.3-beta and 0.3.4-beta, and got essentially the same results, except 
for minor message wording differences.
Mac OS X version 10.6.8

Please provide any additional information below.

Original issue reported on code.google.com by midori.h...@gmail.com on 10 Nov 2011 at 11:53

GoogleCodeExporter commented 9 years ago 
In OORT-0.3.5-beta, the tool lists all the equivalent classes. Is this more 
helpful? For your ontology (rev 239) the listing is as follows:

EquivalentClasses(FYPO:0000120 "abnormal spindle" FYPO:0000132 "abnormal septum 
disassembly" )
EquivalentClasses(FYPO:0000108 "sensitive to menadione" FYPO:0000110 "sensitive 
to pravastatin" )
EquivalentClasses(FYPO:0000101 "sensitive to chlorpropham" FYPO:0000110 
"sensitive to pravastatin" )
EquivalentClasses(FYPO:0000110 "sensitive to pravastatin" FYPO:0000127 
"increased sensitivity to chemical" )
EquivalentClasses(FYPO:0000120 "abnormal spindle" FYPO:0000132 "abnormal septum 
disassembly" )
EquivalentClasses(FYPO:0000110 "sensitive to pravastatin" FYPO:0000127 
"increased sensitivity to chemical" )
EquivalentClasses(FYPO:0000108 "sensitive to menadione" FYPO:0000127 "increased 
sensitivity to chemical" )
EquivalentClasses(FYPO:0000101 "sensitive to chlorpropham" FYPO:0000127 
"increased sensitivity to chemical" )
EquivalentClasses(FYPO:0000071 "resistance to aureobasidin A" FYPO:0000126 
"increased resistance to chemical" )
EquivalentClasses(FYPO:0000567 "decreased septation" FYPO:0000639 "delayed 
septation" )
EquivalentClasses(FYPO:0000108 "sensitive to menadione" FYPO:0000110 "sensitive 
to pravastatin" )
EquivalentClasses(FYPO:0000101 "sensitive to chlorpropham" FYPO:0000108 
"sensitive to menadione" )
EquivalentClasses(FYPO:0000108 "sensitive to menadione" FYPO:0000127 "increased 
sensitivity to chemical" )
EquivalentClasses(FYPO:0000101 "sensitive to chlorpropham" FYPO:0000110 
"sensitive to pravastatin" )
EquivalentClasses(FYPO:0000101 "sensitive to chlorpropham" FYPO:0000108 
"sensitive to menadione" )
EquivalentClasses(FYPO:0000101 "sensitive to chlorpropham" FYPO:0000127 
"increased sensitivity to chemical" )
EquivalentClasses(FYPO:0000567 "decreased septation" FYPO:0000639 "delayed 
septation" )
EquivalentClasses(FYPO:0000405 "normal cell cycle progression through mitotic 
G2/M phase transition" FYPO:0000411 "normal cell cycle progression" )
EquivalentClasses(FYPO:0000619 "mitotic cell cycle arrest in late anaphase" 
FYPO:0000620 "mitotic cell cycle arrest in metaphase" )
EquivalentClasses(FYPO:0000405 "normal cell cycle progression through mitotic 
G2/M phase transition" FYPO:0000411 "normal cell cycle progression" )
EquivalentClasses(FYPO:0000619 "mitotic cell cycle arrest in late anaphase" 
FYPO:0000620 "mitotic cell cycle arrest in metaphase" )
EquivalentClasses(FYPO:0000071 "resistance to aureobasidin A" FYPO:0000126 
"increased resistance to chemical" )

Original comment by HDie...@lbl.gov on 3 Dec 2011 at 1:02

GoogleCodeExporter commented 9 years ago

Original comment by HDie...@lbl.gov on 18 Sep 2012 at 10:29