[Fwd: numbers in concept names]

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[Fwd: numbers in concept names]

Nick Drummond


Hello Nick,

I am working on an ontology that should contain chemicals. Since concept
names
can also contain numbers I have a problem, because numbers are not allowed.
Do you know why there is such a constraint on concept names? Could this
be changed
in a future release of protege?


Best greetings,

Corinna

--

Corinna Kolarik

Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
Schloss Birlinghoven
D-53754 Sankt Augustin

Tel.: +49 - 2241 - 14 - 2549
E-mail: [hidden email]




--

Nick Drummond

http://www.cs.man.ac.uk/~drummond/ <http://www.cs.man.ac.uk/%7Edrummond/>
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Re: [Fwd: numbers in concept names]

Almut Herzog
Nick Drummond wrote:
> I am working on an ontology that should contain chemicals. Since concept
> names
> can also contain numbers I have a problem, because numbers are not allowed.
> Do you know why there is such a constraint on concept names? Could this
> be changed
> in a future release of protege?

I don't know why this is so but maybe you can change your concept names
to something like <underscore><number> or <conceptname><number>. If the
name does not start with a number Protege will gladly accept it.

Cheers,
/Almut
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Re: [Fwd: numbers in concept names]

Nick Drummond
Yep, sorry this is a legacy issue and is unlikely to change in the near
future.

Nick

Almut Herzog wrote:

> Nick Drummond wrote:
>  
>> I am working on an ontology that should contain chemicals. Since concept
>> names
>> can also contain numbers I have a problem, because numbers are not allowed.
>> Do you know why there is such a constraint on concept names? Could this
>> be changed
>> in a future release of protege?
>>    
>
> I don't know why this is so but maybe you can change your concept names
> to something like <underscore><number> or <conceptname><number>. If the
> name does not start with a number Protege will gladly accept it.
>
> Cheers,
> /Almut
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>
>  

--

Nick Drummond

http://www.cs.man.ac.uk/~drummond/ <http://www.cs.man.ac.uk/%7Edrummond/>
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Re: [Fwd: numbers in concept names]

Mark Feblowitz
Is this a legacy issue or an Owl Rec issue? Aren't XML names used,
and don't they prohibit names beginning with digits?

Mark



  At 11:57 AM 5/5/2006, you wrote:

>Yep, sorry this is a legacy issue and is unlikely to change in the
>near future.
>
>Nick
>
>Almut Herzog wrote:
>>Nick Drummond wrote:
>>
>>>I am working on an ontology that should contain chemicals. Since concept
>>>names
>>>can also contain numbers I have a problem, because numbers are not allowed.
>>>Do you know why there is such a constraint on concept names? Could this
>>>be changed
>>>in a future release of protege?
>>>
>>
>>I don't know why this is so but maybe you can change your concept names
>>to something like <underscore><number> or <conceptname><number>. If the
>>name does not start with a number Protege will gladly accept it.
>>
>>Cheers,
>>/Almut
>>-------------------------------------------------------------------------
>>To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>>
>>
>>
>
>--
>
>Nick Drummond
>
>http://www.cs.man.ac.uk/~drummond/ <http://www.cs.man.ac.uk/%7Edrummond/>
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Re: [Fwd: numbers in concept names]

whetzel-2
In reply to this post by Nick Drummond
Would your ontology allow the use of numeric identifiers as the concept
name (value of rdf:ID field)? I have seen ChEBI in OWL using this form:

<owl:Class rdf:ID="CHEBI_22502">
     <rdfs:label xml:lang="en">2-aminoethyl group</rdfs:label>
     <rdfs:subClassOf rdf:resource="#CHEBI_23993"/>
   </owl:Class>

Trish



> Yep, sorry this is a legacy issue and is unlikely to change in the near
> future.
>
> Nick
>
> Almut Herzog wrote:
>> Nick Drummond wrote:
>>
>>> I am working on an ontology that should contain chemicals. Since
>>> concept
>>> names
>>> can also contain numbers I have a problem, because numbers are not
>>> allowed.
>>> Do you know why there is such a constraint on concept names? Could this
>>> be changed
>>> in a future release of protege?
>>>
>>
>> I don't know why this is so but maybe you can change your concept names
>> to something like <underscore><number> or <conceptname><number>. If the
>> name does not start with a number Protege will gladly accept it.
>>
>> Cheers,
>> /Almut
>>
>> -------------------------------------------------------------------------
>> To unsubscribe go to
>> http://protege.stanford.edu/community/subscribe.html
>>
>>
>>
>
> --
>
> Nick Drummond
>
> http://www.cs.man.ac.uk/~drummond/ <http://www.cs.man.ac.uk/%7Edrummond/>
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Re: [Fwd: numbers in concept names]

Nick Drummond
Yes, this is another good reason to use them

Nick

On 5 May 2006, at 19:22, Trish Whetzel wrote:

> Would your ontology allow the use of numeric identifiers as the  
> concept name (value of rdf:ID field)? I have seen ChEBI in OWL  
> using this form:
>
> <owl:Class rdf:ID="CHEBI_22502">
>     <rdfs:label xml:lang="en">2-aminoethyl group</rdfs:label>
>     <rdfs:subClassOf rdf:resource="#CHEBI_23993"/>
>   </owl:Class>
>
> Trish
>
>
>
>> Yep, sorry this is a legacy issue and is unlikely to change in the  
>> near future.
>>
>> Nick
>>
>> Almut Herzog wrote:
>>> Nick Drummond wrote:
>>>> I am working on an ontology that should contain chemicals. Since  
>>>> concept
>>>> names
>>>> can also contain numbers I have a problem, because numbers are  
>>>> not allowed.
>>>> Do you know why there is such a constraint on concept names?  
>>>> Could this
>>>> be changed
>>>> in a future release of protege?
>>> I don't know why this is so but maybe you can change your concept  
>>> names
>>> to something like <underscore><number> or <conceptname><number>.  
>>> If the
>>> name does not start with a number Protege will gladly accept it.
>>> Cheers,
>>> /Almut
>>> --------------------------------------------------------------------
>>> -----
>>> To unsubscribe go to http://protege.stanford.edu/community/ 
>>> subscribe.html
>>
>> --
>>
>> Nick Drummond
>>
>> http://www.cs.man.ac.uk/~drummond/ <<a href="http://www.cs.man.ac.uk/%">http://www.cs.man.ac.uk/% 
>> 7Edrummond/>
>> ---------------------------------------------------------------------
>> ----
>> To unsubscribe go to http://protege.stanford.edu/community/ 
>> subscribe.html
>>
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Re: [Fwd: numbers in concept names]

Nick Drummond
In reply to this post by Mark Feblowitz
Actually, it wasn't that - I know they should be OK in OWL but I was  
under the impression that Protege didn't allow this - I've just  
proved myself wrong.

It looks suspiciously like the cause might have something to do with  
simplifying the code generation (ie valid java names cannot start  
with numbers). I'll investigate and get back to you.

Nick

On 5 May 2006, at 17:03, Mark Feblowitz wrote:

> Is this a legacy issue or an Owl Rec issue? Aren't XML names used,  
> and don't they prohibit names beginning with digits?
>
> Mark
>
>
>
>  At 11:57 AM 5/5/2006, you wrote:
>> Yep, sorry this is a legacy issue and is unlikely to change in the  
>> near future.
>>
>> Nick
>>
>> Almut Herzog wrote:
>>> Nick Drummond wrote:
>>>
>>>> I am working on an ontology that should contain chemicals. Since  
>>>> concept
>>>> names
>>>> can also contain numbers I have a problem, because numbers are  
>>>> not allowed.
>>>> Do you know why there is such a constraint on concept names?  
>>>> Could this
>>>> be changed
>>>> in a future release of protege?
>>>>
>>>
>>> I don't know why this is so but maybe you can change your concept  
>>> names
>>> to something like <underscore><number> or <conceptname><number>.  
>>> If the
>>> name does not start with a number Protege will gladly accept it.
>>>
>>> Cheers,
>>> /Almut
>>> --------------------------------------------------------------------
>>> -----
>>> To unsubscribe go to http://protege.stanford.edu/community/ 
>>> subscribe.html
>>>
>>>
>>>
>>
>> --
>>
>> Nick Drummond
>>
>> http://www.cs.man.ac.uk/~drummond/ <<a href="http://www.cs.man.ac.uk/%">http://www.cs.man.ac.uk/% 
>> 7Edrummond/>
>> ---------------------------------------------------------------------
>> ----
>> To unsubscribe go to http://protege.stanford.edu/community/ 
>> subscribe.html
>
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Re: [Fwd: numbers in concept names]

Nick Drummond
OK, so I now have information from every source available (thanks to  
Matthew and Holger).

There have been discussions about this in the past.

Basically, there are multiple reasons for this - the first mentioned  
in the post [1].

It's to do with valid tag names in xml.  The have to be representable  
as QNames, which are PREFIX:LOCALPART
The prefix and local part must be NCNames [2]
To support this in Protege we'd have to give everything a prefix  
(even the default namespace) when serialising which in itself isn't  
such a big issue, but reloading comes with its own problems (the  
current ns handling would likely need rewriting).

According to Holger, the Jena namespace handler also doesn't like this.

And internally this would also have significant knock-on effects for  
the autocomplete/class parser and of course the code generation

I don't think this is likely to change in this version of Protege.

So, using a different browser slot (annotation property) to hold the  
"readable name" might be a good way round this problem.

Nick

[1] http://article.gmane.org/gmane.comp.misc.ontology.protege.owl/ 
14500/match=qnames
[2] http://www.w3.org/TR/REC-xml-names/


On 9 May 2006, at 16:25, Nick Drummond wrote:

> Actually, it wasn't that - I know they should be OK in OWL but I  
> was under the impression that Protege didn't allow this - I've just  
> proved myself wrong.
>
> It looks suspiciously like the cause might have something to do  
> with simplifying the code generation (ie valid java names cannot  
> start with numbers). I'll investigate and get back to you.
>
> Nick
>
> On 5 May 2006, at 17:03, Mark Feblowitz wrote:
>
>> Is this a legacy issue or an Owl Rec issue? Aren't XML names used,  
>> and don't they prohibit names beginning with digits?
>>
>> Mark
>>
>>
>>
>>  At 11:57 AM 5/5/2006, you wrote:
>>> Yep, sorry this is a legacy issue and is unlikely to change in  
>>> the near future.
>>>
>>> Nick
>>>
>>> Almut Herzog wrote:
>>>> Nick Drummond wrote:
>>>>
>>>>> I am working on an ontology that should contain chemicals.  
>>>>> Since concept
>>>>> names
>>>>> can also contain numbers I have a problem, because numbers are  
>>>>> not allowed.
>>>>> Do you know why there is such a constraint on concept names?  
>>>>> Could this
>>>>> be changed
>>>>> in a future release of protege?
>>>>>
>>>>
>>>> I don't know why this is so but maybe you can change your  
>>>> concept names
>>>> to something like <underscore><number> or <conceptname><number>.  
>>>> If the
>>>> name does not start with a number Protege will gladly accept it.
>>>>
>>>> Cheers,
>>>> /Almut
>>>> -------------------------------------------------------------------
>>>> ------
>>>> To unsubscribe go to http://protege.stanford.edu/community/ 
>>>> subscribe.html
>>>>
>>>>
>>>>
>>>
>>> --
>>>
>>> Nick Drummond
>>>
>>> http://www.cs.man.ac.uk/~drummond/ <<a href="http://www.cs.man.ac.uk/%">http://www.cs.man.ac.uk/% 
>>> 7Edrummond/>
>>> --------------------------------------------------------------------
>>> -----
>>> To unsubscribe go to http://protege.stanford.edu/community/ 
>>> subscribe.html
>>
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