Dear Dr. Schneider,
enough. Thanks in advance.
> Hi Ricardo,
>
> (Let's continue to discuss this on the list because other people
> might be interested in this topic too.)
>
> Yes, FMA is really big, and I know of several colleagues who have
> had problems loading it into tools such as Protégé.
>
> If it's just heap problems that you have, you could try to change
> one of Protégé's config files to increase the heap size assigned to
> the Java machine. I only know how this is done for Protégé 4, and
> it's certainly different for Protégé 3. So if it's for 4, I'm happy
> to describe the few steps necessary. If you're using 3, just ask the
> list.
>
> But even if you get FMA to fit into memory, Protégé will be slow
> performing any kind of operation on it. So extracting a module seems
> to make things much easier. Since there are different approaches to
> extracting modules, it would be helpful if you could specify what
> you intend to do with the desired part of FMA.
>
> Cheers
>
> Thomas
>
> On 25 Jun 2009, at 13:58, Ricardo de Abajo Llamero wrote:
>
>> Dear Dr. Schneider,
>>
>> Thank you for your very prompt reply and your help. I have tried
>> the web
>> module extraction service without no great success. Now I am going
>> to try
>> your adapted version of the Protégé. I promises you that I will not
>> despair :D
>> The main problem that I have found is that the OWL FMA ontology is
>> a really
>> huge file. I have tried several ways to work with the OWL file
>> without
>> success. I can't open the OWL file with the Protége because I have
>> heap
>> space problems. I have tried open the owl file with a visual xml
>> editor and
>> nothing. Thank you again.
>>
>> All the best,
>>
>> Ricardo
>>
>> On Wed, 24 Jun 2009 16:28:15 +0100, Thomas Schneider
>> <
[hidden email]> wrote:
>>> Hi Ricardo,
>>>
>>> if you want to "cut out" a piece of FMA that represents "a brain
>>> ontology", it will be necessary that you specify what you mean by
>>> this, and by "brain classes" / "non-brain classes". For instance, if
>>> you knew which classes (and properties, perhaps) you are interested
>>> in, then certain module extraction services could give you a
>>> module of
>>> FMA -- even one that captures *all* knowledge in FMA about the
>>> specified terms.
>>>
>>> If you're interested in these strong guarantees, you might want to
>>> try
>>> the module extraction service at
>>>
http://owl.cs.manchester.ac.uk/modularity/>>> , but please don't despair if it chokes on FMA, which is likely to
>>> happen for the full version. Alternatively, you can use an adapted
>>> version of Protégé 4 (!) from last year's Modularity Tutorial at
>>> ISWC,
>>
>>> see
http://owl.cs.manchester.ac.uk/2008/iswc-modtut/ . If this
>>> chokes
>>> as well, let me know, and I'll be happy to help you find a
>>> workaround.
>>>
>>> Cheers
>>>
>>> Thomas
>>>
>>> On 24 Jun 2009, at 16:15, Ricardo de Abajo Llamero wrote:
>>>
>>>> Hello everybody,
>>>>
>>>> I am trying to get a brain ontology from the FMA but... I can't! I
>>>> must
>>>> recognise that I am not a protege nor owl expert, but it seems
>>>> impossible
>>>> to get a brain ontology just deleting classes of the FMA ontology.
>>>> Do you
>>>> know if there is a easy way to delete all the non-brain classes in
>>>> the FMA
>>>> ontology? Or even better, do you know if exists a whole brain
>>>> ontology?
>>>> Thank you for your help.
>>>>
>>>> Ricardo
>>>>
>>>> _______________________________________________
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>>>>
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>>>>
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>>>
http://protege.stanford.edu/doc/faq.html#01a.03>>>
>>> +
>>> ----------------------------------------------------------------------+
>>> | Dr Thomas Schneider schneider (at)
>>> cs.man.ac.uk |
>>> | School of Computer Science
http://www.cs.man.ac.uk/~schneidt
>>> |
>>> | Kilburn Building, Room 2.114 phone +44 161
>>> 2756136 |
>>> | University of
>>> Manchester |
>>> | Oxford Road _///
>>> _ |
>>> | Manchester M13 9PL
>>> (o~o) |
>>> +-----------------------------------------------------oOOO--(_)--
>>> OOOo--+
>>>
>>> Cheb (n.)
>>> An embarrasing nickname by which a fourteen-year-old boy insists
>>> that
>>> he now wishes to be known.
>>>
>>> Douglas Adams, John Lloyd: The Deeper Meaning of
>>> Liff
>>
>
> +
> ----------------------------------------------------------------------+
> | Dr Thomas Schneider schneider (at)
> cs.man.ac.uk |
> | School of Computer Science
http://www.cs.man.ac.uk/
> ~schneidt |
> | Kilburn Building, Room 2.114 phone +44 161
> 2756136 |
> | University of
> Manchester |
> | Oxford Road _///
> _ |
> | Manchester M13 9PL
> (o~o) |
> +-----------------------------------------------------oOOO--(_)--
> OOOo--+
>
> Cheb (n.)
> An embarrasing nickname by which a fourteen-year-old boy insists that
> he now wishes to be known.
>
> Douglas Adams, John Lloyd: The Deeper Meaning of Liff
>
>
>
>
>
>
>
>
>
>
>
>
