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From: Tim Clark <tim_clark@harvard.edu>
Date: Wed, 30 Nov 2011 11:29:34 -0500
Cc: HCLS IG <public-semweb-lifesci@w3.org>, scidiscourse@googlegroups.com, Alberto Accomazzi <aaccomazzi@cfa.harvard.edu>, "Bradley P (ELS-SDG) Allen" <B.Allen@elsevier.com>, Sophia Ananiadou <Sophia.Ananiadou@manchester.ac.uk>, Philip Bourne <bourne@sdsc.edu>, Gully Burns <gully@usc.edu>, "Ronald (ELS-SDG) Daniel" <R.Daniel@elsevier.com>, Rahul Dave <rahuldave@gmail.com>, Alf Eaton <A.Eaton@nature.com>, Alexander Garcia Castro <alexgarciac@gmail.com>, Matthew Gamble <matthew.gamble@gmail.com>, Yolanda Gil <gil@isi.edu>, Alyssa Goodman <agoodman@cfa.harvard.edu>, Paul Groth <pgroth@gmail.com>, Tudor Groza <tudor.groza@deri.org>, ellen hays <E.Hays@elsevier.com>, Maryann Martone <maryann@ncmir.ucsd.edu>, David R Newman <drn05r@ecs.soton.ac.uk>, "Antony (ELS-CAM) Scerri" <A.scerri@elsevier.com>, Jack Park <jackpark@gmail.com>, Silvio Peroni <speroni@cs.unibo.it>, Steve Pettifer <steve.pettifer@manchester.ac.uk>, Philippe Rocca-Serra <proccaserra@googlemail.com>, Cartic Ramakrishnan <cartic@isi.edu>, Jodi Schneider <jodi.schneider@deri.org>, David Shotton <david.shotton@zoo.ox.ac.uk>, Kaitlin Thaney <k.thaney@digital-science.com>, Karin Verspoor <Karin.Verspoor@ucdenver.edu>, Lynette Hirschman <lynette@mitre.org>, Susanna-Assunta Sansone <sa.sansone@gmail.com>, Kees van Bochove <business@keesvanbochove.nl>, Katy Wolstencroft <katy@cs.man.ac.uk>, Jun Zhao <jun.zhao@zoo.ox.ac.uk>, "Taylor, Michael (ELS-OXF)" <Mi.Taylor@elsevier.com>
Message-Id: <1C0034C9-2B04-4C11-9FAE-BC97C2ED81CF@harvard.edu>
To: Michael Miller <Michael.Miller@systemsbiology.org>
Hi Michael,

Thanks for your comments.  I appreciate them.  I've incorporated the one about factors into a subsequent version of the model, and decided to pass on the protocol relationships to data output, for pragmatic reasons, although I am certain you are formally correct.
Factors were associated with the assays via a series of subclasses in previous versions of the model.  In this model I omitted the subclasses for improved readability but I should not have omitted the relationship with assays. I am adding them back at your suggestion.
Protocols we decided to leave formally unconnected to the data output in this model for simplicity. As my colleague Sudeshna Das points out, Protocols "... could be assay protocols, sample processing protocols or data processing protocols."  It is always a tradeoff and judgement call between increased formalization and additional burdens on the scientist to input the data.


On Nov 28, 2011, at 2:05 PM, Michael Miller wrote:

> hi tim,
> looks like you all are making good progress.
> this is just from looking at the diagram, so this may already be covered,
> but both protocol and factor are also related to other concepts.
> protocols would be associated with 'has_output' and 'computed_from', and
> there would be factor values associated with each factor of the study and
> each assay would be associated with a set of factor values, one pre factor,
> e.g. for dosage and time factors an assay might be associated with 1mg and
> 10 seconds.
> also, is there any desire to track sample processing?
> cheers,
> michael
> Michael Miller
> Software Engineer
> Institute for Systems Biology
>> -----Original Message-----
>> From: Tim Clark [mailto:tim_clark@harvard.edu]
>> Sent: Monday, November 21, 2011 7:32 AM
>> To: Tim Clark; HCLS IG; scidiscourse@googlegroups.com; Alberto
>> Accomazzi; Bradley P (ELS-SDG) Allen; Sophia Ananiadou; Philip Bourne;
>> Gully Burns; Ronald (ELS-SDG) Daniel; Rahul Dave; Alf Eaton; Alexander
>> Garcia Castro; Matthew Gamble; Yolanda Gil; Alyssa Goodman; Paul Groth;
>> Tudor Groza; ellen hays; Maryann Martone; David R Newman; Antony (ELS-
>> CAM) Scerri; Jack Park; Silvio Peroni; Steve Pettifer; Philippe Rocca-
>> Serra; Cartic Ramakrishnan; Jodi Schneider; David Shotton; Kaitlin
>> Thaney; Karin Verspoor; Lynette Hirschman; Susanna-Assunta Sansone;
>> Kees van Bochove; Katy Wolstencroft; Jun Zhao; Taylor, Michael (ELS-
>> OXF)
>> Subject: SWAN-myExp-OBI-ISA
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Received on Wednesday, 30 November 2011 16:30:18 UTC

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