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RE: 'Gene WIki' announced

From: Nigam Shah <nigam@stanford.edu>
Date: Mon, 14 Jul 2008 13:42:37 -0700
To: "'Kei Cheung'" <kei.cheung@yale.edu>, "'Peter Ansell'" <ansell.peter@gmail.com>
Cc: "'Matthias Samwald'" <samwald@gmx.at>, "'w3c semweb hcls'" <public-semweb-lifesci@w3.org>
Message-ID: <007a01c8e5f2$28703df0$7950b9d0$@edu>

Hi Kei,

What I find odd is that the page http://dbpedia.org/page/Cerebrum, has a property ispartof, but on the query page (http://dbpedia.org/snorql/) if I run:

SELECT ?brainregion WHERE {
  ?brainregion dbpedia2:ispartof
    <http://dbpedia.org/resource/Category:Cerebrum>
}

// NOTE: PREFIX dbpedia2: <http://dbpedia.org/property/> is already defined //

I don’t get any parts (only the query you sent, using the skos:subject gets the parts). Having to query the skos:subject property to get parts is a bit non-intuitive, esp when a ispartof property exists.

-Nigam.

>-----Original Message-----
>From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-
>lifesci-request@w3.org] On Behalf Of Kei Cheung
>Sent: Monday, July 14, 2008 12:06 PM
>To: Peter Ansell
>Cc: Matthias Samwald; w3c semweb hcls
>Subject: Re: 'Gene WIki' announced
>
>
>Just want to use the brain as an example:
>
>Wikipedia page:
>http://en.wikipedia.org/wiki/Cerebrum
>
>DBpedia page:
>http://dbpedia.org/page/Cerebrum
>
>SPARQL query through DPpedia's SNORQL interface:
>http://dbpedia.org/snorql/?query=SELECT+%3Fbrainregion+WHERE+%7B%0D%0A++
>%3Fbrainregion+skos%3Asubject+%0D%0A++++%3Chttp%3A%2F%2Fdbpedia.org%2Fre
>source%2FCategory%3ACerebrum%3E%0D%0A%7D
>
>Cheers,
>
>-Kei
>
>Peter Ansell wrote:
>> The edit link for that template page is on the proteins page, you just
>> have to know which one to click, above and right of the infobox. It
>> isn't obvious though!
>>
>> Cheers,
>>
>> Peter
>>
>> 2008/7/14 Matthias Samwald <samwald@gmx.at>:
>>
>>> Oh, I see. The link to this other page should be mentioned in the
>comments
>>> of the original wiki page, since it is rather unlikely that a
>researcher
>>> that wants to quickly update the protein box has the motivation to
>find out
>>> how he can actually reach that other page.
>>>
>>> ~~ Matthias
>>>
>>>
>>>> The Protein Box Bot [1] inserts templates based on the geneid that
>is
>>>> given to it, in particular for that page it inserts a template from
>>>> another page [2]. Editing that page customises the output that is
>seen
>>>> in the infobox on that page. It should be relatively simple to take
>>>> the pages like [2] and retrieve semantic information from them.
>>>>
>>>> Cheers,
>>>>
>>>> Peter
>>>>
>>>> [1]
>http://en.wikipedia.org/w/index.php?title=Template:PBB&action=edit
>>>> [2]
>>>>
>http://en.wikipedia.org/w/index.php?title=Template:PBB/1605&action=edit
>>>>
>>>> 2008/7/14 Matthias Samwald <samwald@gmx.at>:
>>>>
>>>>> It is not surprising that the protein/gene information is missing
>from
>>>>> DBpedia. Looking at
>>>>> http://en.wikipedia.org/w/index.php?title=Dystroglycan&action=edit
>>>>> it seems like this information is not held in the source of the
>wiki
>>>>> page.
>>>>> Maybe someone with better knowledge about Mediawiki could explain
>how
>>>>> this
>>>>> works and how the information could be harvested by DBpedia? I am
>>>>> planning
>>>>> to write a documentation for the DBpedia developers that could help
>them
>>>>> improve the representation of biomedical wiki entries in DBpedia
>(such as
>>>>> creating direct links to the URIs of Uniprot-RDF). This could also
>be a
>>>>> helpful addition.
>>>>>
>>>>> Cheers,
>>>>> Matthias Samwald
>>>>> DERI Galway, Ireland // Semantic Web Company, Austria
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ----- Original Message ----- From: "Peter Ansell"
>>>>> <ansell.peter@gmail.com>
>>>>> To: "w3c semweb hcls" <public-semweb-lifesci@w3.org>
>>>>> Sent: Monday, July 14, 2008 8:48 AM
>>>>> Subject: Re: 'Gene WIki' announced
>>>>>
>>>>>
>>>>>
>>>>>> When Francois Belleau was investigating integrating the infobox
>>>>>> information into Bio2RDF he found that the infoboxes were missing
>in
>>>>>> the dbpedia database. Not sure if that changed since he last
>checked.
>>>>>>
>>>>>> It would be very valuable to have the information from infoboxes
>and
>>>>>> the gene-wiki templates in dbpedia. Might need to do a custom
>parser
>>>>>> for the gene-wiki templates if they aren't similar to infoboxes.
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Peter
>>>>>>
>>>>>> 2008/7/14 Kei Cheung <kei.cheung@yale.edu>:
>>>>>>
>>>>>>> According to http://wiki.dbpedia.org/Datasets#h18-11, DBpedia
>contains
>>>>>>> data
>>>>>>> extracted from infoboxes (which should include gene/protein
>infoboxes).
>>>>>>>
>>>>>>> -Kei
>>>>>>>
>>>>>>> Matthias Samwald wrote:
>>>>>>>
>>>>>>>
>>>>>>>> It seems like the protein/gene infoboxes are not reflected in
>DBpedia,
>>>>>>>> since the information is not held in conventional infoboxes (as
>far as
>>>>>>>> I
>>>>>>>> have understood).
>>>>>>>>
>>>>>>>> Compare
>>>>>>>>
>>>>>>>> http://dbpedia.org/page/Dystroglycan
>>>>>>>> http://en.wikipedia.org/wiki/Dystroglycan
>>>>>>>>
>>>>>>>> ----- Original Message ----- From: "Kei Cheung"
><kei.cheung@yale.edu>
>>>>>>>>
>>>>>>>> What about DBpedia (http://dbpedia.org)?
>>>>>>>>
>>>>>>>> -Kei
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>
>>>
>>
>>
>
Received on Monday, 14 July 2008 20:43:25 GMT

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