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RE: SWAN-myExp-OBI-ISA

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Thu, 1 Dec 2011 07:30:14 -0800
Message-ID: <e2ae45875932ea422b9b08e2371effc7@mail.gmail.com>
To: Sudeshna Das <sdas@seas.harvard.edu>
Cc: Tim Clark <tim_clark@harvard.edu>, 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>
hi sudeshna,



"You are right, it was a typo - Factors are Biomaterial or Population
characteristics and not related to assays."



not directly but they are through their Factor Values.  Factors are also
called out separately from Biomaterial characteristics or Protocol
parameters as the important conditions that vary.  when the Assay Protocol
is run, the Factor Value for each of the Factors at that point are then
associated with the Assay.  this is actually the most important fact to
know to do an analysis, like differentially expressed genes.



cheers,

michael



*From:* Sudeshna Das [mailto:sdas@seas.harvard.edu]
*Sent:* Wednesday, November 30, 2011 12:30 PM
*To:* Michael Miller
*Cc:* 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:* Re: SWAN-myExp-OBI-ISA



HI Michael,



You are right, it was a typo - Factors are Biomaterial or Population
characteristics and not related to assays.



I really like the way you are associating the protocol to the transition
step, makes  a lot of sense. Sometimes we don't have that level of detail
captured for the experiment; hence we are associating it with the design
step as that is the step that produces the protocol and the rest of the
steps follow it.



Best,

Sudeshna



On Nov 30, 2011, at 11:53 AM, Michael Miller wrote:



hi tim,



thanks for your comments, i'll be interested to see how the Factors are
related to the assays, not sure how subclasses would work since one
actually needs different factor values for the factors, i.e. a time factor
can't tell you where in the time sequence the assay was done.



interesting about the protocols.  in implementing Annotare, the fged
sponsored open source tool for creating and editing MAGE-TAB documents, we
faced this same issue.  for various columns, like characteristics, species
and so on, we offer drop down selections based on ontology views from
NCBO.  when it came to protocols, you're exactly right, one has to consider
the position of the column in the mage-tab SDRF file in order to know what
type of protocol to use to populate the drop down.  i'm not even sure if
our UI guy has quite got it right yet.  but in the BioRDF use case where we
are looking at translating MAGE-TAB to RDF triples, since it is already
known, creating the triple associating the instance of a protocol to the
transition between an instance of material and/or data to the next instance
of material and or/data was trivial.  and if one is doing certain
investigations where it's the protocol that is being varied for a certain
step, this would be a tremendous loss to understanding/replicating of the
results to not have the link.



the other interesting case which i haven't seen anyone solve yet is the
fact that factors are duplications of characteristics of the samples or
protocol parameters but it is difficult to model that relationship.  i've
thought that might be some sort of 'is_a' relationship.



cheers,

michael



*From:* Tim Clark [mailto:tim_clark@harvard.edu]
*Sent:* Wednesday, November 30, 2011 8:30 AM
*To:* Michael Miller
*Cc:* 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:* Re: SWAN-myExp-OBI-ISA



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.

Best



Tim



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 Thursday, 1 December 2011 15:30:58 UTC

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