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:s...@seas.harvard.edu] > Sent: Wednesday, November 30, 2011 12:30 PM > To: Michael Miller > Cc: Tim Clark; HCLS IG; scidiscou...@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_cl...@harvard.edu] > Sent: Wednesday, November 30, 2011 8:30 AM > To: Michael Miller > Cc: HCLS IG; scidiscou...@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_cl...@harvard.edu] > Sent: Monday, November 21, 2011 7:32 AM > To: Tim Clark; HCLS IG; scidiscou...@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 > > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > >
