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Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for the UMLS presentation

From: kei cheung <kei.cheung@yale.edu>
Date: Tue, 06 Jun 2006 12:40:32 -0400
To: "Miller, Michael D (Rosetta)" <Michael_Miller@Rosettabio.com>
Cc: Alan Ruttenberg <alanruttenberg@gmail.com>, public-semweb-lifesci@w3.org
Message-id: <4485B000.3030501@yale.edu>

Hi Michael,

Thanks for sharing your thoughts. MGED still has rooms for ontological 
improvement. As Larry suggested, we would have a better luck if we can 
work with the MGED consortium.

Cheers,

-Kei

Miller, Michael D (Rosetta) wrote:

>Hi Kei,
>
>  
>
>>Is there a converter available which can take existing datasets in 
>>mage-ml format and convert them into mged-owl format?
>>    
>>
>
>You're asking the wrong person here, but not that I know of.
>
>The reason I am the wrong person is that I don't believe that MAGE-OM
>(from which MAGE-ML, MAGEJava and MAGEPerl is generated) is best
>represented as an ontology.  I believe there is much that ontologies can
>do but the best way to capture the process of performing microarray
>experiment is to call out the actual pipeline process of wet lab
>biologist processing samples, bench technicians performing the
>hybridization and scans, the bioinformaticists interpreting the scan
>data and the overall design of the experiment.  The way these different
>steps relate to each other does not, to my mind, fit best into an
>ontology model, that by calling them out as first class objects in the
>UML model and modeling their specific associations/relationships, all
>different from each other and specific to the object).
>
>To be able to annotate all these objects with ontology terms is
>definitely needed but to me a separate piece.
>
>Granted, if you, or anyone, wish to generate an OWL model from MAGE-OM,
>it should be possible and I would certainly be interested in the result.
>The current code to generate the MAGE-ML, MAGEJava and MAGEPerl provide
>good examples how to do this
>(http://mged.sourceforge.net/software/index.php).
>
>But one could also generate a MAGECobol implementation.
>
>cheers,
>Michael
>
>  
>
>>-----Original Message-----
>>From: kei cheung [mailto:kei.cheung@yale.edu] 
>>Sent: Tuesday, June 06, 2006 7:54 AM
>>To: Miller, Michael D (Rosetta)
>>Cc: Alan Ruttenberg; public-semweb-lifesci@w3.org
>>Subject: Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for 
>>the UMLS presentation
>>
>>
>>Hi Michael et al,
>>
>>Is there a converter available which can take existing datasets in 
>>mage-ml format and convert them into mged-owl format?
>>
>>Thanks,
>>
>>-Kei
>>
>>Miller, Michael D (Rosetta) wrote:
>>
>>    
>>
>>>Hi Alan and All,
>>>
>>>The MGED Ontology is now available as OWL.  There has been a recent
>>>revision to correct some of the formal problems such an early
>>>implementation has had.
>>>
>>>http://mged.sourceforge.net/ontologies/MGEDOntology.owl
>>>
>>>Also, the FuGO project would love any feedback, thanks for 
>>>      
>>>
>>pointing out
>>    
>>
>>>the upcoming workshop.
>>>
>>>cheers,
>>>Michael
>>>
>>> 
>>>
>>>      
>>>
>>>>-----Original Message-----
>>>>From: public-semweb-lifesci-request@w3.org 
>>>>[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
>>>>Alan Ruttenberg
>>>>Sent: Tuesday, June 06, 2006 6:40 AM
>>>>To: kc28
>>>>Cc: donald.doherty@brainstage.com; 
>>>>wilbanks@creativecommons.org; 'Daniel Rubin'; 
>>>>public-semweb-lifesci@w3.org; 'Matthew Cockerill'
>>>>Subject: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for the 
>>>>UMLS presentation
>>>>
>>>>
>>>>
>>>>On Jun 5, 2006, at 9:15 PM, kc28 wrote:
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>>>>It might be time to think about how to convert mged ontology or 
>>>>>mage-ml into RDF/OWL. The following are two related articles:
>>>>>
>>>>>http://www.nature.com/msb/journal/v2/n1/full/msb4100052.html
>>>>>http://www.nature.com/nbt/journal/v23/n9/full/nbt0905-1095.html
>>>>>
>>>>>Cheers,
>>>>>
>>>>>-Kei
>>>>>     
>>>>>
>>>>>          
>>>>>
>>>>As I understand it, this is the nature of the FuGO project: 
>>>>http://fugo.sourceforge.net/
>>>>They have an upcoming workshop
>>>>http://www.ebi.ac.uk/microarray/General/Events/FuGO2006/index.html
>>>>
>>>>-Alan
>>>>
>>>>
>>>>
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>> 
>>>
>>>      
>>>
>>
>>
>>    
>>
>
>
>  
>
Received on Tuesday, 6 June 2006 16:41:37 GMT

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