COVID-19 Knowledge Accelerator (COKA) WEEKLY Progress December 6, 2020

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Brian Alper

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Dec 6, 2020, 5:33:07 PM12/6/20

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.

20 people (AS, BA, BK, BS, EA, GA, HL, IK, IO, JD, JJ, JO, KR, KS, MA, MT, RC, SB, TN-R, VS) participated in up to 11 active working group meetings this week.

FHIR Resource Updates:

No changes made this week to the following FHIR Resource StructureDefinitions

· 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 61 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.
Step 3 (Draft terms): 444 non-redundant concepts identified to support the 24 commonly used tools and systems.

Code System	Updates
Risk of Bias	13 commonly used tools or systems mapped. There are now 225 draft terms in the Simplified/Refactored Risk of Bias Code System Concept List. Recent changes included revision of the Detection Bias category for simpler implementation.
Statistic Type	3 commonly used tools or systems mapped. There are now 94 draft terms in the Statistic Type Code System Step 3 spreadsheet.
Statistic Model	2 commonly used tools or systems mapped. There are now 69 draft terms in the Statistic Model Code System Step 3 spreadsheet.
Study Design	6 commonly used tools or systems mapped. There are now 56 draft terms in the Study Design Code System Step 3 spreadsheet.

Step 4 (Identify relevant ontologies): We have 27 eligible Ontologies Identified for Code System Development. Feel free to suggest any missing ontologies that you may be aware of.
Step 5 (Ontology mapping) is completed for 9 ontologies (Step 5 EDDA Ontology Mapping, Step 5 OBCS Ontology Mapping, Step 5 STATO Ontology Mapping, Step 5 NCIt Ontology Mapping, Step 5 OCRe Ontology Mapping, Step 5 OBI Ontology Mapping, Step 5 CTO Ontology Mapping, Step 5 SCO Ontology Mapping, Step 5 Catalogue of Bias Ontology Mapping).
We will take a break from Step 5 Ontology mapping for a few weeks.

The Project Management Group will be exploring using the FHIR CodeSystem Resource as a basis for data management for this project. Then we can resume with a more efficient infrastructure for the project and be better prepared for integration into interoperable systems.
In the interim the Code System Development Steering Groups may use the meeting times to review the current draft code systems and consider categorical restructuring that will improve application efforts.

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 initial combined collection has 656 unique articles to be considered.
Article selection efforts (to efficiently select articles from the set of 656) is underway. The group will support tools development (if needed) that facilitates this effort.
The next tool development discussed for this group is a MEDLINE XML to FHIR Citation Converter Tool.

The Evidence Evaluation and Reporting Tools Development Work Group

The group was highly interested in integrating the Clinical Trial Results Reporter into other systems, such as the SRDR+ platform.
Sharing login user experience across systems was identified as a critical early step in interoperability support, regardless of schema and terminology used.
The group is now exploring optimal solutions for foundational development.

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

We continued to develop the Steroids for COVID-19 Systematic Meta-Review Protocol. The search strategies are completed and modified the article selection process based on pilot efforts that are underway. Once we confirm feasible efficiency for article selection we will be ready to formally start this project.

Communications Work Group

Presentations (December 2-5) to Guidelines International Network/North America webinar, Hopkins Center for Clinical Trials webinar, and International Conference for Knowledge Management audiences were all well received.
The next publication of interest is an “organized list of risk of bias concepts to inform Risk of Bias Code System Development”. This “expanded catalog of bias” that incorporates 12 risk of bias assessment tools seems like a major scholarly contribution that is ready to share now. We will assemble a writing group in the next 24 hours to take this further, so let us know ASAP if you would like to join this group.

Knowledge Ecosystem Liaison Updates:

Discussions with the ACTS COVID-19 Collaborative Learning Community continued discussions with the AHRQ evidence-based Care Transformation Support (ACTS), including developments related to creating Knowledge Ecosystem Recommendations, discussing systematic methods to develop functional requirements and technical requirements for multiple tools to support this knowledge ecosystem, and discussing coordination of EBMonFHIR/COVID-19 Knowledge Accelerator efforts with PCORI-supported projects to use FHIR standards to support patient-centered outcomes research related to the long-term sequelae of COVID-19.
The Project Management Group followed up on a request to consider how to map JSON Cohort Definitions from OMOP (used by OHDSI with ATLAS) to FHIR Group Resource specifications fitting the EBMonFHIR/COKA developments. For those who don’t read alphabet soup, what this means is structured definitions of groups of people are very useful for applying computers to research development. There are standards and systems mapping out numerous structured definitions for this purpose in ways not using FHIR. If that effort can be mapped to FHIR it can be interoperable with electronic health record data without having to reproduce all the work many others have done. We reviewed the structural schema being used to prepare for discussions about this mapping, and scheduled further discussions for Friday, December 11.

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
Thursday	4-5 pm	Project Management
Friday	9-10 am	Risk Of Bias Code System Development
Friday	10-11 am	Communications (Awareness, Scholarly Publications)

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.

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

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

Lead, COVID-19 KNOWLEDGE ACCELERATOR

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