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Re: Microarray Experiment Context

From: Kei Cheung <kei.cheung@yale.edu>
Date: Sun, 13 Dec 2009 21:33:35 -0500
Message-ID: <4B25A3FF.8060509@yale.edu>
To: Melanie Courtot <mcourtot@gmail.com>
CC: Satya Sahoo <sahoo.2@wright.edu>, HCLS <public-semweb-lifesci@w3.org>, jun.zhao@zoo.ox.ac.uk, mdmiller <mdmiller53@comcast.net>, Helena Deus <helenadeus@gmail.com>, Jie Zheng <jiezheng@pcbi.upenn.edu>, Chris Stoeckert <stoeckrt@pcbi.upenn.edu>, Bjoern Peters <bpeters@liai.org>
Hi Melanie,

Thanks for mentioning OBI and its alignment with MGED. It's also good to 
hear that OBI incorporates domain ontologies like NIFSTD. Based on some 
reading, MIREOT seems to address some of issues with OWL import (e.g., 
it allows a partial import of an ontology). As we move our use case 
forward, we will keep abreast of all these and other developments and 
see how they fit our needs.

Best,

-Kei

Melanie Courtot wrote:

> Hi all,
>
> It may be worth mentioning that the MGED ontology is working to  
> integrate within the Ontology for Biomedical Investigations (OBI - 
> http://purl.obolibrary.org/obo/obi)  . Jie Zheng in Chris Stoeckert 
> group is currently working on this.
>
> The OBI Release Candidate 1.0 has just been published - see 
> http://obi-ontology.org/page/Releases/2009-11-06 . A mechanism 
> allowing specific lightweight import of specific terms  from external 
> resources, MIREOT (the Minimum Information to Reference  an External 
> Ontology Term, http://precedings.nature.com/documents/3574/version/1) 
>  has also been developed and implemented, and OBI currently imports  
> terms from NIFSTD amongst others.
>
> Feel free to send any comment/question to the OBI users list, at 
> http://groups.google.com/group/obi-users?hl=en .
>
> Regards,
> Melanie
>
>
> On 7-Dec-09, at 7:48 AM, Kei Cheung wrote:
>
>> Hi Satya et al,
>>
>> Thanks for creating the wiki page. I think it's a good start. I hope  
>> our use case can help facilitate some of the ontology alignment  
>> effort. You already listed a few to start. Other might include:  
>> NIFSTD, SenseLab, SWAN, TMO, etc. You can also add my name to the  
>> contact for the page if you want.
>>
>> Cheers,
>>
>> -Kei
>>
>> Satya Sahoo wrote:
>>
>>> Hi all,
>>> I have created a wiki page to collect provenance related terms  
>>> describing experiment conditions and protocols used to generate  
>>> microarray data [1]. The page also lists a set of queries that rely  
>>> on the provenance information associated with gene expression data.
>>> Please add additional terms required to better describe the  
>>> experiment context, such as the statistical tools or process used  
>>> to obtain gene list (published in literature) from raw experiment  
>>> data.
>>> -- thanks to Jun for the wiki page edit rights :)
>>> cheers,
>>> Satya
>>> Kno.e.sis
>>> http://knoesis.wright.edu/researchers/satya
>>> [1] 
>>> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext 
>>>
>>
>>
>>
>>
>
> ---
> Mélanie Courtot
> TFL- BCCRC
> 675 West 10th Avenue
> Vancouver, BC
> V5Z 1L3, Canada
>
>
>
>
>
Received on Monday, 14 December 2009 02:35:17 UTC

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