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Re: Microarray Experiment Context

From: Melanie Courtot <mcourtot@gmail.com>
Date: Mon, 7 Dec 2009 14:10:46 -0800
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>
Message-Id: <5293C8C5-C6A2-4214-8313-E0D891B223D3@gmail.com>
To: Kei Cheung <kei.cheung@yale.edu>
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 


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
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada
Received on Monday, 7 December 2009 22:11:30 UTC

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