COVID-19 Knowledge Accelerator (COKA) WEEKLY Progress November 22, 2020

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Brian Alper

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Nov 22, 2020, 4:38:00 PM11/22/20
to COVID-19 Knowledge Accelerator, Risk of Bias Code System Expert Working Group, Study Design Code System Expert Working Group, Statistic Type Code System Expert Working Group, Statistic Model Code System Expert Working Group

This is a weekly update on the COVID-19 Knowledge Accelerator (COKA) Initiative.

19 people (BA, BK, EA, GA, HL, IK, JD, JO, JR, KR, KS, LT, MA, MG, MT, RA, RC, TN-R, VS) participated in up to 10 active working group meetings this week.

 

FHIR Resource Updates:

  • No changes made this week to the FHIR Resource StructureDefinitions. We are currently working with the following FHIR Resources:
  • One change discovered this week (for the EvidenceVariable Resource) is to add a new element (EvidenceReport.section.entryQuantity) with cardinality 0..* and datatype Quantity.  This will allow quantities to be a type of content included in Evidence Reports.

·         2021-01 Evidence-Based Medicine/COVID-19 Knowledge Accelerator (EBM/COKA) Connectathon Track Proposed for the Virtual HL7 FHIR Connectathon 26 on January 13-15, 2021.

o   The key goal: Demonstrate data exchange using Citation, Evidence, EvidenceVariable, Group and EvidenceReport resources to communicate clinical trial and systematic review findings.

o   We tentatively scheduled a Track Orientation webinar for Monday, December 14, 2020 at 10 am Eastern to introduce this Track to interested participants.

 

Code System Development Updates:

 

  • We are following a 13-step Code System Development Protocol to develop and maintain 4 code systems.
  • Step 1 (Assemble Expert Working Group)
    • You are welcome to join this effort -- see Invitation to join Expert Working Group. At this time we currently have 62 people signed up from 27 countries in 6 continents (Australia, Austria, Bangladesh, Brasil, Canada, Costa Rica, Czech Republic, Egypt, Finland, France, Ghana, Greece, India, Ireland, Italy, Japan, Lebanon, Malaysia, Nigeria, Peru, Romania, South Africa, South Korea, Sri Lanka, Switzerland, United Kingdom, United States).
    • You can sign up now with the Code System Development Intake Form to join the expert working group for any of the first 4 code systems.
  • Step 2 (Identify common tools): 24 commonly used tools and systems identified for the code systems to support. (Catalog of Bias added to consider terms for the Risk of Bias code system.)
  • Step 3 (Draft terms): 398 non-redundant concepts identified to support the 23 commonly used tools and systems.

Code System

Updates

Risk of Bias
  • 13 commonly used tools or systems mapped.
  • There are now 181 draft terms in the Risk Of Bias Code System Step 3 spreadsheet.
  • Recent changes included addition of 7 terms: Admission rate bias, Apprehension bias, Detection Bias – Availability Bias, Analysis Selection Bias – Availability Bias, Selective theory reporting, Selection reporting – Availability Bias, and Biases of rhetoric.

Statistic Type
  • 3 commonly used tools or systems mapped.
  • There are now 93 draft terms in the Statistic Type Code System Step 3 spreadsheet.
  • Recent changes included addition of 4 terms: Difference, Ratio, Odds, and Rate

Statistic Model

Study Design

 

 

Tools Development Updates:

The Content Citation and Classification Tools Development Work Group

  • The group’s goal is to Create infrastructure standards and tools to support interoperable, reusable efforts for Citation Repositories.
  • We are working with PICO Portal to support management of a citation collection for our Steroids for COVID-19 Systematic Meta-Review based on searching 7 databases (MEDLINE via 3 different strategies [PubMed, Ovid, LitCovid], CORD-19, L-OVE/Episteminokos, NIH iSearch COVID-19, EuropePMC, WHO COVID-19 Database, EMBASE). These 9 search result collections will be compiled and de-duplicated.

 

The Evidence Evaluation and Reporting Tools Development Work Group

  • The demonstration of SRDR+ content being viewable in FHIR format, starting with what we have demonstrated in Outcome Definition Viewer – you can see screenshots now at SRDR-to-ODV example – may resume. It was shown briefly in the AMIA conference ACTS Panel presentation.
  • The Clinical Trial Results Reporter is now functional for use. You can enter any number of dichotomous and continuous baseline measures and outcome measures for a clinical trial.  It will capture the data in structured format and automate conversion to FHIR resources.

The Apollo Accelerator

  • We established a functional mechanism for organizations to pool financial resources (Apollo Accelerator Membership Program) to support software development for computable publishing of evidence and guidance.
  • The tools developed in the Apollo Accelerator will be made freely available for the COVID-19 Knowledge Accelerator (COKA) participants for use specific to COVID-19 knowledge.

 

Scholarly Communications Updates:

 

Systematic Meta-Review Project Group

 

 

  1. MEDLINE (via PubMed)
  2. MEDLINE (via Ovid)
  3. MEDLINE (via LitCOVID)
  4. CORD-19 (via COVID-19 Advanced Literature Classifier)
  5. L-OVE (Epistemonikos)
  6. NIH OPA's iSearch Tool - iSearch COVID-19 Portfolio https://icite.od.nih.gov/covid19/search/
  7. EuropePMC
  8. World Health Organization (WHO) COVID-19 Database
  9. EMBASE (via Ovid)

 

and follow up with PROSPERO to identify potential systematic reviews with results not found in these 8 searches.

 

  • We achieve manageable search strategies (< 300 results) for 8 of 9 databases, then discovered additional terms for inhaled steroids so will be revising the search strategies to include those terms.
  • We expect to be ready to complete the protocol and prepare to formally start the project over the next two weeks.

 

 

Communications Work Group

 

  • Upcoming presentations (December 2-5) include Guidelines International Network/North America webinar, Hopkins Center for Clinical Trials webinar, and International Conference for Knowledge Management. 
  • Determined the next priority for the group is attention to dissemination of COKA activities, especially related to Tools Development as we now have tools that provide tangible benefits to encourage and support participation. Specific interest in disseminating case examples of the Clinical Trial Results Reporter and furthering research proposals for it (Protocol Draft for Feasibility Testing of Making Clinical Trial Results Computable). 

 

Knowledge Ecosystem Liaison Updates:

 

 

Project Management Updates:

 

  • Meetings for Thursday, November 25 and Friday, November 26 will be canceled for the Thanksgiving holiday in the US.
  • The Thursday 7 am Eastern meeting series for Project Management is canceled.  There are 2 other weekly meetings still intact.

 

To get involved or stay informed:

 

You can learn more about the COVID-19 Knowledge Accelerator (COKA) project at https://www.gps.health/covid19_knowledge_accelerator.html

 

You can find all the progress notes at a Google Drive folder for the project and each Work Group has a Progress Report document where you can find the details. 

 

You can join any of the groups that are now meeting in the following schedule:

 

Weekly Meeting Schedule

Day

Time (Eastern)

Team

 

Monday 

7-8 am 

Project Management

 

Monday 

9-10 am

Systematic Meta-Review

 

Monday

4-5 pm

Statistic Model Code System Development

 

Tuesday

10-11 am

Evidence Evaluation and Reporting Tools Development (CANCELLED November 17 for AMIA session)

 

Tuesday 

2-3 pm 

Study Design Code System Development

 

Wednesday

8-9 am 

Knowledge Ecosystem Liaison

 

Wednesday

9-10 am

Statistic Type Code System Development

 

Thursday

9-10 am

Content Citation and Classification Tools Development (CANCELED Nov 26 for Thanksgiving holiday)

 

Thursday 

4-5 pm 

Project Management (CANCELED Nov 26 for Thanksgiving holiday)

 

Friday

9-10 am 

Risk Of Bias Code System Development (CANCELED Nov 27 for Thanksgiving holiday)

 

Friday

10-11 am 

Communications (Awareness, Scholarly Publications) (CANCELED Nov 27 for Thanksgiving holiday)

 

 

To join any of these meetings:

________________________________________________________________________________

Join Microsoft Teams Meeting

+1 929-346-7156   United States, New York City (Toll)

Conference ID: 324 918 025#

Local numbers

Meeting support by ComputablePublishing.com

________________________________________________________________________________

Email bal...@computablepublishing.com if you would like to be added (or removed) to any of the specific meeting invites or to this COKA Distribution List email.  You are welcome to join any meeting at any time whether you have signed up or not.   The COKA Distribution List receives daily progress update emails.  This weekly progress update email is also being shared with the Code System Development Expert Working Group email distribution lists.

 

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Brian S. Alper, MD, MSPH, FAAFP, FAMIA

CEO, Computable Publishing LLC
http://computablepublishing.com Making Science Machine-Interpretable

Lead, COVID-19 KNOWLEDGE ACCELERATOR

 

Read about The Mission Change of a Lifetime

"It only takes a pebble to start an avalanche."

Schedule a meeting with me.

 

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