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Can't convert OBO file requiring imports #15

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GoogleCodeExporter opened this issue Mar 12, 2015 · 4 comments
Open

Can't convert OBO file requiring imports #15

GoogleCodeExporter opened this issue Mar 12, 2015 · 4 comments
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auto-migrated Priority-Medium Type-Defect

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@GoogleCodeExporter
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The obo2owl conversion currently does not utilise or convert import statements. 
 It also doesn't convert files containing relationships to classes that are not 
predeclared (in obo parlance, it doesn't convert files with dangling 
references). The combination of these means that files requiring imports to 
declare all entities cannot be converted.

There are a number of ways that this could be fixed, but perhaps the best would 
be if the conversion script followed import statements in obo files, converting 
all the files it finds and adding the relevant import statements and 
predeclarations (if necessary) to the OWL files.

What steps will reproduce the problem?
1. Try converting one of the imports files here:
http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/anatomy/anatomy_xp/


What version of the product are you using? On what operating system?
rev 71 on OSX 10.6.6 
$ java -version 
java version "1.6.0_22"
Java(TM) SE Runtime Environment (build 1.6.0_22-b04-307-10M3261)
Java HotSpot(TM) 64-Bit Server VM (build 17.1-b03-307, mixed mode)

Original issue reported on code.google.com by dosu...@gmail.com on 3 Mar 2011 at 10:07
@GoogleCodeExporter
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You can use the --allow-dangling flag to suppress errors for undeclared 
references. I believe it should create the required class declarations in the 
OWL (todo - check).

Will get back on imports, tricky.

Original comment by cmung...@gmail.com on 3 Mar 2011 at 6:03

@GoogleCodeExporter
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tried --allow-dangling as an argument in multiple positions.  Still get a 
dangling reference exception 
(org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException).

Is there any usable doc on this conversion tool yet?  Couldn't spot one on the 
respository.

Original comment by dosu...@gmail.com on 4 Mar 2011 at 1:43

@GoogleCodeExporter
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Original comment by shahid.m...@gmail.com on 16 Jun 2011 at 6:17

@GoogleCodeExporter
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Can you point out one file from the link 
http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/anatomy/anatomy_xp/ that 
produces this error.

Original comment by shahid.m...@gmail.com on 7 Jul 2011 at 2:55

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