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Re: [ontolog-forum] isacommons.org for life-science data-sharing

To: ontolog-forum@xxxxxxxxxxxxxxxx
From: Susanna Sansone <sa.sansone@xxxxxxxxx>
Date: 2012年2月02日 13:10:48 +0000
Message-id: <4F2A8B58.20503@xxxxxxxxx>
Dear Christopher and all,
yes, you are right, the framework supports use of terms from ontology (better described in the first paper http://www.ncbi.nlm.nih.gov/pubmed/20679334). 
But it is also correct that we present several systems - powered by ISA tools or ISA-Tabformat. Maybe these could also be seen as 'competitive' systems, as you says, but this is the reality: in data management there are manysystems around and all have different features and functionality etc. We are dealing with this a real situation, see howto best harmonize the description of experiments, in different systems, one step at thetime, piloting the approach and leading by examples. This first stepshows how these existing systems work to use a common format (thatenables use of terms for ontology, and meet requirements of somecheckists) 
that can be converted to some other formats (as requiredby public repositories).I hope this helps, but am happy to reply to any questions.
Kind regards,
Susanna
-- 
Susanna-Assunta Sansone, PhD 
Team Leader
Projects: www.isa-tools.org|www.mibbi.org|www.biosharing.org
University of Oxford		Tel: +44(0)1865 610622 
Oxford e-Research Centre	Fax: +44(0)1865 610612 
7 Keble Road, Oxford		skype: susanna-a.sansone 
OX1 3QG, UK			uk.linkedin.com/in/sasansone
---------- message ----------
From: Christopher Spottiswoode <cms@xxxxxxxxxxxxx>
Date: 2 February 2012 11:04
Subject: [ontolog-forum] isacommons.org for life-science data-sharing
To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>


Does anybody here, perhaps with bio-ontology or data federation interests, have any comment on this effort (see http://www.isacommons.org/) ?
The software suite Fact Sheet at http://isatab.sourceforge.net/docs/ISAinfrastructure-Fact-Sheet-Dec2010.pdf does allege their support of bio-ontologes.
But does the whole effort have the support of the bio-ontology community? Or does the latter community not have parallel and perhaps competitive facilities addressing the same needs?
ACM TechNews last Monday had this news item:
Oxford, Harvard Scientists Lead Data-Sharing Effort
Harvard University (01/29/12)

More than 50 collaborators at over 30 scientific organizations worldwide, led by researchers at the University of Oxford and Harvard University, have developed a common standard that will enable scientists to share data from different databases in fields ranging from genetics to environmental studies. The new standard provides a way for researchers in different fields to coordinate each other's findings by combining the different data sets. "We are now working together to provide the means to manage enormous quantities of otherwise incompatible data," says Oxford's Susanna-Assunta Sansone. The data-sharing effort's online presence is known as the ISA Commons. "One of the things that I find most empowering about this effort is that now small research groups can begin to store laboratory data using this framework, complying with community standards, without their own dedicated bioinformatics support," says the University of Cambridge's Jules Griffin. Sansone says a common standard was necessary due to the deluge of data and technologies used by scientists. "There are hundreds of new technologies coming along but also many ways to describe the information produced," she says. "We can take a jigsaw puzzle of different sciences and now fit the many pieces together to form a complete picture."


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