Reporting and Representing Experimental Protocols in the Biomedical Domain

[Olga Ximena Giraldo]

Dear all, as replicability and reproducibility are central to scientific activities, representing experimental protocols is just as important as representing data. Data is a great asset, BUT how was data generated? how can I get the same data in my lab? what are the experimental conditions under which data was generated? help me to make replicability and reproducibility a reality in life sciences:

https://docs.google.com/forms/d/1BSMBvulx2ZX5k12i4_garoDnM1rMGzyPSCHzMWiA_CY/viewform

[Melissa Haendel]

Dear Olga, 

You are singing my song!

Your work deals with similar issues to those that we are documenting wrt identification of research resources (presented at btpdf2: http://www.slideshare.net/mhaendel/reproducibility-ofscience-final)

Would love to talk to hear more about your project and reference it in our upcoming publication of our results.

Best,

Melissa

On May 2, 2013, at 3:35 AM, Olga Ximena Giraldo wrote:

Dear all, as replicability and reproducibility are central to scientific activities, representing experimental protocols is just as important as representing data. Data is a great asset, BUT how was data generated? how can I get the same data in my lab? what are the experimental conditions under which data was generated? help me to make replicability and reproducibility a reality in life sciences:

https://docs.google.com/forms/d/1BSMBvulx2ZX5k12i4_garoDnM1rMGzyPSCHzMWiA_CY/viewform

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Dr. Melissa Haendel

Assistant Professor
Ontology Development Group, OHSU Library

http://www.ohsu.edu/library/

Department of Medical Informatics and Epidemiology
Oregon Health & Science University
hae...@ohsu.edu
skype: melissa.haendel

503-407-5970

[Kaveh Bazargan]

You might also talk to Susanna-Assunta Sansone, at Oxford e-Research Centre (sa.sa...@gmail.com). 

She gave a talk on that topic at this conference:

http://rigourandopenness.org/schedule/

On 2 May 2013 12:35, Olga Ximena Giraldo <oxgi...@gmail.com> wrote:

Dear all, as replicability and reproducibility are central to scientific activities, representing experimental protocols is just as important as representing data. Data is a great asset, BUT how was data generated? how can I get the same data in my lab? what are the experimental conditions under which data was generated? help me to make replicability and reproducibility a reality in life sciences:

https://docs.google.com/forms/d/1BSMBvulx2ZX5k12i4_garoDnM1rMGzyPSCHzMWiA_CY/viewform

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Kaveh Bazargan 

Twitter: @kaveh1000
www.river-valley.com | www.river-valley.tv | www.bazargan.org

[Susanna-Assunta Sansone]

Thanks Kaveh, I was indeed about to reply.
Olga, I suggest you have a look at (life science/environmental/biomedical) community reporting guidelines, much of what you are trying to identify has been done by domain experts (as each domain is different and will require different info to be reported). See: http://www.biosharing.org/standards/reporting_guideline
Philippe and Alejandra from team were at beyond-the-pd, presenting both on BioSharing and on our http://isacommons.org/ effort to apply these community reporting guidelines (along with the respective terminologies) to collect/curate data to enable reproducibility.
Hope it helps.
Kind regards,
Susanna

Susanna-Assunta Sansone, PhD
skype: susanna-a.sansone
http://uk.linkedin.com/in/sasansone

University of Oxford e-Research Centre
Associate Director, Principal Investigator
www.isacommons.org|www.biosharing.org

Nature Publishing Group
Consultant, Scientific Data
www.nature.com/scientificdata
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[Maryann Martone]

So my question is, how do we coordinate and align all of these efforts so that they synergize with each other?  Would like to propose that we use Melissa's 1K challenge winner as the impetus to gather materials together, list related efforts and perhaps work to define some way of coordinating among the different efforts.  I would like to capture this thread on Melissa's FORCE11 page, if she agrees to it (no pressure).

Maryann Martone, Ph. D.

Professor-in-Residence

Department of Neuroscience

University of California, San Diego

San Diego, CA 92093-0446

858-822-0745

[Melissa Haendel]

That sounds great Maryann, I would be happy to help coordinate. 

Susanna, Philippe, and Alejandra and I all spoke recently too, about making the resource identifiers that we are collecting and generating guidelines for, available to Biosharing/ISA-tab, so we are already working together :-).

Best,

Melissa

[Gully Burns]

Hey Guys,

This is very consistent and related to the way that we've been modeling protocols within the KEfED project. 

An incredibly important aspect of this is that we don't necessarily need to curate the protocol at the finest level of granularity for every task. If you're building a representation of  an experimental design so that someone is going to be able to precisely follow the process then yes, you need to describe exactly in which cupboard every single piece of equipment lives. If you're describing the protocol so that people can understand the overall organization of the experiment just to understand the data better, you'll use a much coarser representation. Thus, the framework needs to be able to describe processes and subprocesses within them and a lot of the questions that were being asked about the necessary and sufficient elements to describe things like buffer and reagents and suchlike may depend on the context in which each description is being used. 

Susanna talks about this when she discusses Minimum Information Checklists (my point is that we need to specify "minimum information for what?").

Best

Gully 

[Olga Ximena Giraldo]

Hi everybody,

Thank you for your comments, I really appreciate it :)

Olga

Olga Ximena Giraldo
http://www.usefilm.com/photographer/116483.html

http://oxgiraldo.wordpress.com

[Fabiana Kubke]

Hi everyone -

A PhD student I co-supervise (Cameron McLean) is working on a related issue (making implicit methodological knowledge implicit)

He just built this website https://sites.google.com/site/labpatterns/home and he shares his stuff mainly on figshare.

Not sure whether this is of any use to y'all.

Cheers

Fabiana

M Fabiana Kubke

Department of Anatomy | University of Auckland | New Zealand
(+64) 9 373-7599 Ext 86002 | (+64)9 923 6002 (direct) | Mobile: (+64) 210 437 121

Skype: superfabs | http://twitter.com/Kubke | http://identi.ca/kubke | http://buildingblogsofscience.wordpress.com | http://sciblogs.co.nz/building-blogs-of-science | http://popscinz.wordpress.com | http://talkingteaching.wordpress.com

[Gully Burns]

Hey Guys,

I just realized that my last email was probably a bit heavy handed for the specfic thread. I'd just like to put my name on the list of groups to be involved in this effort.

Thanks!

Gully