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

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

Brochhausen, Mathias
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:

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: "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", Laura Slaughter, "[hidden email]", Mathias Brochhausen, "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]"
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


Meeting:

  • Update from the Content subteam


  • Progress on definitions

    • Discussion of stakeholders

    • We agreed as a team to use the following process for moving the current suggested definitions 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

      • 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

    • We reviewed Knowledge Representation Core Considerations  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

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

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

  • Next steps

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

    • 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

    • 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

[hidden email]

Office: 412-648-9219

Twitter: @bhaapgh


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

Michael Miller-13

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:[hidden email]]
Sent: Wednesday, May 25, 2016 9:08 AM
To: 'Brochhausen, Mathias'; 'Richard Boyce'; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]
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

 

 

 

 

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:

 

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: "
[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", Laura Slaughter, "[hidden email]", Mathias Brochhausen, "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]", "[hidden email]"
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

 

Meeting:

·        Update from the Content subteam

o   The content workgroup has agreed upon 10 PDDIs to include: https://goo.gl/rYpmjt

§  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

·        Example draft : http://goo.gl/7ZaE94

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  and also listed here:

·        Introduction and motivation for the  W3C DDI Minimum Information Model IG Note

·        Stakeholder Descriptions

·        DDI Minimum Information Model User Scenarios

·        Knowledge Representation Core Considerations  

 

·        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 and DDI Minimum Information Model User Scenarios

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 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

§  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  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
 
[hidden email]
 
Office: 412-648-9219
 
Twitter: @bhaapgh
 

Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.