equivalent pairs error #16
Comments
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From HDie...@lbl.gov on December 02, 2011 17:02:25 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" ) |
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From HDie...@lbl.gov on September 18, 2012 15:29:43 Status: Done |
From midori.h...@gmail.com on November 10, 2011 03:53:05
What steps will reproduce the problem?
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: http://code.google.com/p/owltools/issues/detail?id=16
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