Re: 'Gene WIki' announced

Sorry for the confusion. My query was based on the following:

http://dbpedia.org/page/Category:Cerebrum

I  pasted the wrong DBpedia page (http://dbpedia.org/page/Cerebrum).

However, Nigam brought up a important point that the design, creation, 
and improvement of wikipedia's infoboxes may be guided by standard 
ontologies.

Cheers,

-Kei

Peter Ansell wrote:

>I think you want to take the Category bit out. The following works
>
>SELECT ?brainregion WHERE {
>  ?brainregion dbpedia2:ispartof
>    <http://dbpedia.org/resource/Cerebrum>
>}
>
>Cheers,
>
>Peter
>
>2008/7/15 Nigam Shah <nigam@stanford.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 Tuesday, 15 July 2008 01:46:37 UTC