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Re: SWAN-myExp-OBI-ISA

From: Jim McCusker <james.mccusker@yale.edu>
Date: Fri, 2 Dec 2011 14:39:38 -0500
Message-ID: <CAAtgn=Tsuzo5dJNoQJPmLaSi5WtsAZR5WA9ttS+Jv-yVvBiQcA@mail.gmail.com>
To: Sudeshna Das <sdas@seas.harvard.edu>
Cc: Michael Miller <Michael.Miller@systemsbiology.org>, 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>
Is there a mapping for describing experiment factors and factor values
using OBI/EFO/etc?

Jim

On Thu, Dec 1, 2011 at 10:57 AM, Sudeshna Das <sdas@seas.harvard.edu> wrote:

> I meant that factors are associated with Biomaterial & Population
> characteristics, you'll see that In Tim's revised values.
>
> Sudeshna
>
> On Dec 1, 2011, at 10:30 AM, Michael Miller wrote:
>
> 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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-- 
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccusker@yale.edu | (203) 785-6330
http://krauthammerlab.med.yale.edu

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mccusj@cs.rpi.edu
http://tw.rpi.edu
Received on Friday, 2 December 2011 19:40:32 UTC

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