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[bioontology-support] How to submit labels with numbers and alpha characters

Zachariah Schmidt zack at sterlingbio.com
Wed Jan 4 08:04:57 PST 2012


Possible resolution:  

Class Naming:    This appears to be an OWL2 language problem though and not
specifically a Protege problem.  I think it has to do with the inability of
OWL2 to support 'outline numbering'

For example, naming a class using outline numbering as follows causes
problems in OWL2 language:

10  Class 1
11  Class 2

or: 

10.1 Class 1
10.2  Class 2

When OWL2 is converted to RDF/XML multiple 'prefixes' are generated for each
class.  This could be due to the fact that W3C XML doesn't allow an element
to be named with a number.  Also the char '.' is not allowed in W3C XML
element names.

However I've seen one ontology that seems to have solved the outline
numbering problem - iCat or ICD Categories published by Tania Tudorache.  
They have published ICD's classification system as follows:

01 I Certain infectious diseases
02 II Neoplasms

iCat's ICD ontology is published in WebProtege.   Maybe the iCat ontology is
'escaping' the numeric characters or somehow has a work-around for outline
numbering?

--> Perhaps Tania has some answers as to how she was able to use outline
numbering with protege and OWL?  Or maybe the iCat OWL file is published for
others to see how they handled outline numbering with OWL.  I believe
WebProtege uses Protege v3 and OWL1.

I would appreciate it if someone could propose a solution or workaround for
outline numbering - not just for NCBO, but for protege and OWL as well. 
Outline numbering is a fundamental element of classification
systems/schemas.

Thanks

-----
Zachariah Schmidt
SterlingBio
--
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