RE: Knowledge Representation Goal: PDDI Info Task Force (Standard sub-group)

hi all,



as a board member of FGED (1) i've been involved with MIAME and am one of
the lead developers of MAGE and FuGE.  both MAGE-ML, based on MAGE-OM, and
FuGE-ML, based on FuGE-OM, are implementations (rather than minimum
information models) that are intended to be able to allow users to specify
and interchange their experiments in compliance with the minimum
information standards.  MAGE was specifically for microarrays and MIAME,
FuGE was an attempt to broaden the scope to any minimum information
standard in the -omics arena.  although at Rosetta Biosoftware we had a
robust implementation of MAGE-ML for our Resolver microarray product, it
proved difficult for many organization with limited developer resources.
so, spearheaded by the EBI, MAGE-TAB (2) was developed, also based on
MAGE-OM, a spreadsheet approach that has worked quite well.  although not
as robust as MAGE-ML it is much simpler to implement and captures about 90%
of what MAGE-ML can.  similarly, ISA-TAB (3,4) was come up with to be a
spreadsheet counterpart to FuGE.



cheers,

michael



1) http://fged.org/

2) http://fged.org/projects/mage-tab/

3) http://www.isacommons.org/

4) https://isatools.wordpress.com/



Michael Miller

Software Engineer

Institute for Systems Biology



*From:* Oya Deniz Beyan [mailto:beyan@dbis.rwth-aachen.de]
*Sent:* Wednesday, May 25, 2016 9:08 AM
*To:* 'Brochhausen, Mathias'; 'Richard Boyce'; public-semweb-lifesci@w3.org;
linikujp@gmail.com; brian.lebaron@va.gov; BHocum@genelex.com;
CJVITALE@PARTNERS.ORG; Cui.Tao@uth.tmc.edu;
daniela.oliveira@insight-centre.org; eric@squishymedia.com; gmcevoy@ashp.org;
jschneider@pobox.com; jschneider@pobox.com; kim.nolen@pfizer.com;
laura.slaughter@gmail.com; maria.herrero@kcl.ac.uk;
matthias.samwald@meduniwien.ac.at; michel.dumontier@stanford.edu;
Michael.Miller@systemsbiology.org; nancy@worldvista.org;
yongqunh@med.umich.edu; nytroe@idi.ntnu.no; ratnesh.sahay@insight-centre.org;
Freimuth.Robert@mayo.edu; valerie@genelex.com; xjing2007@gmail.com
*Subject:* RE: Knowledge Representation Goal: PDDI Info Task Force
(Standard sub-group)



Dear Mathias, Dear Richard,

I did a quick literature check and identified other minimum information
models used in different domains. My aim was to see how they represent the
minimum information. Results range from using specified ontologies to free
text entries as check list. I picked four different approaches from well
established standards. MIAME has layers (for min information data model,
then ontologies to annotate the data, then data exchange language. Some
others such as MiMIx just provides checklist. HUPO uses control
vocabularies to capture protein interactions (when it is available).  And
FuGE has a work flow based approach and again uses ontologies to annotate.

I am not sure how do you plan to proceed. I thought looking to different
implementations might facilitate the discussion. Here is the links and some
notes for each of them.



*1) MIAME Minumum Information about microarray experiment*

MIAME specifies the minimum information needed to describe a microarray
experiment

http://www.nature.com/ng/journal/v29/n4/pdf/ng1201-365.pdf



MAGE-OM provides terms for annotating all aspects of a microarray
experiment from the design of the experiment and array layout, through to
the preparation of the biological sample and the protocols used to
hybridize the RNA and analyze the data.

The MGED Ontology (MO) is a semantic resource that includes terminology for
all aspects of microarray experiments.

http://bioinformatics.oxfordjournals.org/content/22/7/866.short



MAGE-MLprovide a mechanism to standardize data representation for data
exchange

http://link.springer.com/article/10.1186/gb-2002-3-9-research0046



*2) The minimum information required for reporting a molecular interaction
experiment (MIMIx)*

http://www.nature.com/nbt/journal/v25/n8/pdf/nbt1324.pdf

provides minimum information check list



*3) The HUPO PSI's Molecular Interaction format*—a community standard for
the representation of protein interaction data

http://www.nature.com/nbt/journal/v22/n2/abs/nbt926.html

applies control vocabularies



*4) The Functional Genomics Experiment model (FuGE)*

http://www.nature.com/nbt/journal/v25/n10/full/nbt1347.html

work flow based - ontology driven approach

FuGE relies on ontologies for enumerated lists of values, such as units.
The Ontology of Biomedical Investigation (OBI), formerly called the
Functional Genomics Investigation Ontology17 (FuGO)



Best wishes
Oya







*From:* Brochhausen, Mathias [mailto:MBrochhausen@uams.edu
<MBrochhausen@uams.edu>]
*Sent:* Freitag, 20. Mai 2016 17:09
*To:* Richard Boyce <rdb20@pitt.edu>; public-semweb-lifesci@w3.org;
linikujp@gmail.com; brian.lebaron@va.gov; BHocum@genelex.com;
CJVITALE@PARTNERS.ORG; Cui.Tao@uth.tmc.edu;
daniela.oliveira@insight-centre.org; eric@squishymedia.com; gmcevoy@ashp.org;
jschneider@pobox.com; jschneider@pobox.com; kim.nolen@pfizer.com;
laura.slaughter@gmail.com; maria.herrero@kcl.ac.uk;
matthias.samwald@meduniwien.ac.at; michel.dumontier@stanford.edu;
Michael.Miller@systemsbiology.org; nancy@worldvista.org;
yongqunh@med.umich.edu; beyan@dbis.rwth-aachen.de; nytroe@idi.ntnu.no;
ratnesh.sahay@insight-centre.org; Freimuth.Robert@mayo.edu;
valerie@genelex.com; xjing2007@gmail.com
*Subject:* Knowledge Representation Goal: PDDI Info Task Force (Standard
sub-group)



Dear members of the PDDI Info Task Force,



This is a follow up on our conversation on April 29. In this meeting we
started a sub-group on knowledge representation planning.

Currently the following peoples have signed up for that sub-group:

Mathias Brochhausen

Oliver He

Oya Beyan

Daniela Oliveira

Ratnesh Sahay

Øystein Nytrø



PDDI Info Task members who want to join this sub group, please let me know.



We are tasked to clarify the statements discuss and clarifying the scope of
formalization of the minimum information model to be found here:

Knowledge Representation Core Considerations
<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_14saXL4qhusPHxxN1Aymc5z-5Fu7vH3j3V-2DYF9TKNjRxLQ_edit&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=5AEOAn-leKHL4tqzIYL5BZeZcxy7iZl60kZKsyzT_1s&e=>



Those of you interested in participating in the work of the subgroup,
please look at the document and add comments or questions. If you have the
chance to do that before the meeting next week (May 26) that would be
awesome.



If you have any questions or concerns, please don’t hesitate to contact me.



Best,

Mathias









*From: *Richard Boyce
*Date: *Saturday, April 30, 2016 at 6:44 AM
*To: *"public-semweb-lifesci@w3.org", "linikujp@gmail.com", "
brian.lebaron@va.gov", "BHocum@genelex.com", "CJVITALE@PARTNERS.ORG", "
Cui.Tao@uth.tmc.edu", "daniela.oliveira@insight-centre.org", "
eric@squishymedia.com", "gmcevoy@ashp.org", "jschneider@pobox.com", "
jschneider@pobox.com", "kim.nolen@pfizer.com", Laura Slaughter, "
maria.herrero@kcl.ac.uk", Mathias Brochhausen, "
matthias.samwald@meduniwien.ac.at", "michel.dumontier@stanford.edu", "
Michael.Miller@systemsbiology.org", "nancy@worldvista.org", "
yongqunh@med.umich.edu", "beyan@dbis.rwth-aachen.de", "nytroe@idi.ntnu.no",
"ratnesh.sahay@insight-centre.org", "Freimuth.Robert@mayo.edu", "
valerie@genelex.com", "xjing2007@gmail.com"
*Subject: *PDDI Info Task Force (Standard sub-group) - Minutes/recording
for 4/29



Dear Colleagues,

Below are pasted the minutes of the Standard sub-group for the PDDI DDI
Minimum Information Model Task Force [1].

Minutes for 4/29/2016 (Standard subgroup)



*In Attendance : Matthias Samwald, Xia Jing, Brian LeBaron, Schneider,
Jodi, Chris Vitale (PHS), Michael Miller, Oliver He, Kim Nolen, Øystein
Nytrø, Oya Beyan, Richard Boyce, Mathias Brochhausen, Daniela & Ratnesh*



Meeting recording: http://goo.gl/UTX6pY
<https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_UTX6pY&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=CPnBhvotbk9dmtTGKfk19-mXUKaB3Iyxp0ZBqd-7ZdQ&e=>



Meeting:

·        Update from the Content subteam

o   The content workgroup has agreed upon 10 PDDIs to include:
https://goo.gl/rYpmjt
<https://urldefense.proofpoint.com/v2/url?u=https-3A__goo.gl_rYpmjt&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=aXfyizf3TL_LSWwc05XG4dDDEYW4QsY0DlSCXm_08bE&e=>

§  These cover the following information aspects:

·        can (and should) be contextualized for specific patients or
clinical circumstances,

·        applies at the class level, does not apply at the class level,

·        the mechanism is known and is pharmacokinetic, the mechanism is
known and is pharmacodynamic

§  More forthcoming...

o   Decision trees useful for contextualizing the PDDIs, provide management
options, and linking to relevant evidence will be created for all of them

§  Done already for 2 of the 10 now included

·        Toward writing an Interest Group Note

o   Rich re-organized the initial draft note to focus on introduction and
background with stakeholder descriptions, use cases, and user scenarios

§  An github project and initial draft:

·        GitHub project: https://github.com/W3C-HCLS/w3c-ddi
<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_W3C-2DHCLS_w3c-2Dddi&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=IVSIVs4fSj5DSExmVk4SnZgpDtxrsNhcbB5PySxg9B0&e=>

·        Example draft : http://goo.gl/7ZaE94
<https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_7ZaE94&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=AMgghCoVAxHkhQ_U3RnuZliuVhFW9JcD7UgATj0DMbI&e=>

o   Rich created google docs that we will write in and then the editors
will migrate the content into the W3C note format

§  These are linked to from the http://goo.gl/7ZaE94
<https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_7ZaE94&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=AMgghCoVAxHkhQ_U3RnuZliuVhFW9JcD7UgATj0DMbI&e=>
 and also listed here:

·        Introduction and motivation for the  W3C DDI Minimum Information
Model IG Note
<https://urldefense.proofpoint.com/v2/url?u=https-3A__goo.gl_YWRMV3&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=Fekzbx23J_vAgwIxh5Kfmytyc7GVc553-LDg-o_uCqw&e=>

·        Stakeholder Descriptions
<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1AbWuONYTrFOV95OhjlRwrm3ZJy5jjvzJ-2DdywO5OZyFY_edit-23&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=g2XCJtrfEOwRofZS4NHehiLZAENWr3dEcOa7kPqhjOw&e=>

·        DDI Minimum Information Model User Scenarios
<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1HE8r8nmJBHRrtbE6YrNfK00Ztkev44-2DdNk-2DRm6MP92U_edit&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=sStRq6tixz4JO4_25fxkOZvmz96-MLWiX9vYnwDPY7M&e=>

·        Knowledge Representation Core Considerations
<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_14saXL4qhusPHxxN1Aymc5z-5Fu7vH3j3V-2DYF9TKNjRxLQ_edit&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=5AEOAn-leKHL4tqzIYL5BZeZcxy7iZl60kZKsyzT_1s&e=>




·        Progress on definitions

o   Discussion of stakeholders

§  Rich has pulled this into two google docs in the format of user profile
and scenarios for discussion by the sub-team with the goal of finalizing by
the next call

·        Stakeholder Descriptions
<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1AbWuONYTrFOV95OhjlRwrm3ZJy5jjvzJ-2DdywO5OZyFY_edit-23&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=g2XCJtrfEOwRofZS4NHehiLZAENWr3dEcOa7kPqhjOw&e=>
and DDI Minimum Information Model User Scenarios
<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1HE8r8nmJBHRrtbE6YrNfK00Ztkev44-2DdNk-2DRm6MP92U_edit&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=sStRq6tixz4JO4_25fxkOZvmz96-MLWiX9vYnwDPY7M&e=>

o   He will send a request to complete a qualtrics survey eliciting
feedback on each user scenario

o   We agreed as a team to use the following process for moving the current
suggested definitions
<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_spreadsheets_d_1dhUp496riwZ0AHqRP7I85oEvuP2jjEI0rcw1Fcm2zI8_edit-23gid-3D0&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=nJrs0blKoyQd0OI-8Imalkrbu_w-djr93t7lUjZ6tnM&e=>
to final definitions as follows:

§  For a given information category (e.g., clinical consequences) Rich will
summarize the currently suggested candidate definitions

·        Including any references to the terminologies or publications
where they came from

·        He will also show examples of the definitions from the
contextualizing decision trees created for the included interactions
<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_spreadsheets_d_1DIeIuo7tZ6nVvd6MdO2xzzLtOSPXjAHI-2DDdBe9M3kiw_edit&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=xCCYMwrcQzYWYTQHQSXpMDW6cDeHRne0VysVUb6xXj8&e=>

§  Rich will create a qualtrics survey for each summary to elicit agreement
on a final proposed definition

·        This process likely be iterative



·        Knowledge representation goal for the model

o   We reviewed Knowledge Representation Core Considerations
<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_14saXL4qhusPHxxN1Aymc5z-5Fu7vH3j3V-2DYF9TKNjRxLQ_edit&d=AwMGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=P4QhaQdRjrZgEvQvjDtYyl8_yEsCtQl3og2eO8l3sik&m=Dbg-pziD002H73zsGNUlWMDkwtVloJ1dunLEiFlENKs&s=5AEOAn-leKHL4tqzIYL5BZeZcxy7iZl60kZKsyzT_1s&e=>
 which is meant to suggest the scope of formalization for the minimum
information model

§  It was agreed that we need to define what we mean by information model
and convert those notes to a couple of concise paragraphs that declare the
scope of formalization for the model and how definitions will be created,
accepted, and revised (if needed).

·        Mathias Brochhausen will lead a sub-team this month to finalize
these decisions and develop this write up

o   Oya, Oliver, Daniela & Ratnesh, and Øystein volunteered to participate

§  Invitations will go out to others who could not attend the call

·        Next steps

o   All will complete doodles to schedule new meetings for the next few
months

o   A sub-team led by Mathias B. will develop a statement that clarifies
 the scope of formalization for the minimum information model and process
for creating/accepting/revising definitions

o   We will implement the process process for creating/accepting/revising
definitions



-- 



Richard D Boyce, PhD



Assistant Professor of Biomedical Informatics



Faculty, Center for Pharmaceutical Policy and Prescribing



Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics
Research and Training Program



University of Pittsburgh



rdb20@pitt.edu



Office: 412-648-9219



Twitter: @bhaapgh



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