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

From: Brochhausen, Mathias <MBrochhausen@uams.edu>
Date: Fri, 20 May 2016 15:08:52 +0000
To: Richard Boyce <rdb20@pitt.edu>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>, "linikujp@gmail.com" <linikujp@gmail.com>, "brian.lebaron@va.gov" <brian.lebaron@va.gov>, "BHocum@genelex.com" <BHocum@genelex.com>, "CJVITALE@PARTNERS.ORG" <CJVITALE@PARTNERS.ORG>, "Cui.Tao@uth.tmc.edu" <Cui.Tao@uth.tmc.edu>, "daniela.oliveira@insight-centre.org" <daniela.oliveira@insight-centre.org>, "eric@squishymedia.com" <eric@squishymedia.com>, "gmcevoy@ashp.org" <gmcevoy@ashp.org>, "jschneider@pobox.com" <jschneider@pobox.com>, "jschneider@pobox.com" <jschneider@pobox.com>, "kim.nolen@pfizer.com" <kim.nolen@pfizer.com>, "laura.slaughter@gmail.com" <laura.slaughter@gmail.com>, "maria.herrero@kcl.ac.uk" <maria.herrero@kcl.ac.uk>, "matthias.samwald@meduniwien.ac.at" <matthias.samwald@meduniwien.ac.at>, "michel.dumontier@stanford.edu" <michel.dumontier@stanford.edu>, "Michael.Miller@systemsbiology.org" <Michael.Miller@systemsbiology.org>, "nancy@worldvista.org" <nancy@worldvista.org>, "yongqunh@med.umich.edu" <yongqunh@med.umich.edu>, "beyan@dbis.rwth-aachen.de" <beyan@dbis.rwth-aachen.de>, "nytroe@idi.ntnu.no" <nytroe@idi.ntnu.no>, "ratnesh.sahay@insight-centre.org" <ratnesh.sahay@insight-centre.org>, "Freimuth.Robert@mayo.edu" <Freimuth.Robert@mayo.edu>, "valerie@genelex.com" <valerie@genelex.com>, "xjing2007@gmail.com" <xjing2007@gmail.com>
Message-ID: <944055ED-35D8-4996-A599-FDEE0BD63EA6@uams.edu>
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=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=z5vkuelmaTgOzJPzgfd9C_RBMjbZOIwRPxv9DR2RJ50&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<mailto:public-semweb-lifesci@w3.org>", "linikujp@gmail.com<mailto:linikujp@gmail.com>", "brian.lebaron@va.gov<mailto:brian.lebaron@va.gov>", "BHocum@genelex.com<mailto:BHocum@genelex.com>", "CJVITALE@PARTNERS.ORG<mailto:CJVITALE@PARTNERS.ORG>", "Cui.Tao@uth.tmc.edu<mailto:Cui.Tao@uth.tmc.edu>", "daniela.oliveira@insight-centre.org<mailto:daniela.oliveira@insight-centre.org>", "eric@squishymedia.com<mailto:eric@squishymedia.com>", "gmcevoy@ashp.org<mailto:gmcevoy@ashp.org>", "jschneider@pobox.com<mailto:jschneider@pobox.com>", "jschneider@pobox.com<mailto:jschneider@pobox.com>", "kim.nolen@pfizer.com<mailto:kim.nolen@pfizer.com>", Laura Slaughter, "maria.herrero@kcl.ac.uk<mailto:maria.herrero@kcl.ac.uk>", Mathias Brochhausen, "matthias.samwald@meduniwien.ac.at<mailto:matthias.samwald@meduniwien.ac.at>", "michel.dumontier@stanford.edu<mailto:michel.dumontier@stanford.edu>", "Michael.Miller@systemsbiology.org<mailto:Michael.Miller@systemsbiology.org>", "nancy@worldvista.org<mailto:nancy@worldvista.org>", "yongqunh@med.umich.edu<mailto:yongqunh@med.umich.edu>", "beyan@dbis.rwth-aachen.de<mailto:beyan@dbis.rwth-aachen.de>", "nytroe@idi.ntnu.no<mailto:nytroe@idi.ntnu.no>", "ratnesh.sahay@insight-centre.org<mailto:ratnesh.sahay@insight-centre.org>", "Freimuth.Robert@mayo.edu<mailto:Freimuth.Robert@mayo..edu>", "valerie@genelex.com<mailto:valerie@genelex.com>", "xjing2007@gmail..com<mailto: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: https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_UTX6pY&d=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=GoSSZjb87oo8poBrDPwyLwmkCUfrCt-zP1gedV9f9G8&e= 


Meeting:

  *   Update from the Content subteam

     *   The content workgroup has agreed upon 10 PDDIs to include: <https://urldefense.proofpoint.com/v2/url?u=https-3A__goo.gl_rYpmjt&d=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=nGDG-ugS4RuU35P60QYqGYc3sctq7OtCjxDD-rVUUh0&e= > https://urldefense.proofpoint.com/v2/url?u=https-3A__goo.gl_rYpmjt&d=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=nGDG-ugS4RuU35P60QYqGYc3sctq7OtCjxDD-rVUUh0&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...

     *   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

     *   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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_W3C-2DHCLS_w3c-2Dddi&d=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=bTv_4e8ygmrkeCCMijk3fU6gmATc-rpe7fbRZvWtBz8&e= > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_W3C-2DHCLS_w3c-2Dddi&d=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=bTv_4e8ygmrkeCCMijk3fU6gmATc-rpe7fbRZvWtBz8&e= 

           *   Example draft : https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_7ZaE94&d=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=x_Det3LEYOSxxrNfeq0xeINkEdTeCUQx2xO3HRdM1uI&e= 

     *   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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_7ZaE94&d=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=x_Det3LEYOSxxrNfeq0xeINkEdTeCUQx2xO3HRdM1uI&e= > https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_7ZaE94&d=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=x_Det3LEYOSxxrNfeq0xeINkEdTeCUQx2xO3HRdM1uI&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=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=_ultbCVyAfc9R8mJTAxYH9SJKE47Mm9x_E-H8qwDCkc&e= >

           *   Stakeholder Descriptions<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1AbWuONYTrFOV95OhjlRwrm3ZJy5jjvzJ-2DdywO5OZyFY_edit-23&d=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=zaPug41wvxOxrDIcu1Uc4lowEiI7knAzACLRLfoaFGc&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=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=52xH48LbNB_n5gsi-bhywiqbJH1lmyC4fwZoOQ91zi8&e= >

           *   Knowledge Representation Core Considerations<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_14saXL4qhusPHxxN1Aymc5z-5Fu7vH3j3V-2DYF9TKNjRxLQ_edit&d=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=z5vkuelmaTgOzJPzgfd9C_RBMjbZOIwRPxv9DR2RJ50&e= >


  *   Progress on definitions

     *   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=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=zaPug41wvxOxrDIcu1Uc4lowEiI7knAzACLRLfoaFGc&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=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=52xH48LbNB_n5gsi-bhywiqbJH1lmyC4fwZoOQ91zi8&e= >

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

     *   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=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=6GnjzYPWnCdW2ch30oyxnU4MTI9X0Qt4lY06bNr_T0I&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=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=L3_Tngt5gZVpd10_hkExyqOjY7GsXdQnX8n9RTv0ahQ&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

     *   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=AwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=PT776KVlHOxIjUaokCOHdtQ9Aox4bJzWuoRg0AmtOTs&m=M7E6tr957Qg6QJzVMPAfTqj_TH9Vr7LLnOsHB4WLpHQ&s=z5vkuelmaTgOzJPzgfd9C_RBMjbZOIwRPxv9DR2RJ50&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

              *   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
rdb20@pitt.edu<mailto:rdb20@pitt.edu>
Office: 412-648-9219
Twitter: @bhaapgh


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Received on Tuesday, 24 May 2016 07:19:49 UTC

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