COVID-19 Knowledge Accelerator (COKA) WEEKLY Progress November 28, 2020

[Brian Alper]

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

16 people (AS, BA, BK, EA, ER, HL, IK, JD, JO, JR, KS, MT, RA, RC, SB, TN-R) participated in up to 7 active working group meetings this week.(Thursday and Friday meetings were cancelled due to Thanksgiving.)

 

FHIR Resource Updates:

• No changes made this week to the following FHIR Resource StructureDefinitions
• Citation
• Evidence
• EvidenceVariable
• Group
• Statistic (Dataype)
• OrderedDistribution (Dataype)
• Changes made to the EvidenceReport Resource included:
• The EvidenceReport.relatesTo.code element with 4 code choices (replaces | amends | appends | transforms) was expanded to 8 code choices (replaces | amends | appends | transforms | replacedWith | amendedWith | appendedWith | transformedWith). This allows determining when the Evidence Report is updated or modified and tracing to related content.
• A new element (EvidenceReport.section.entryQuantity) addedwith 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 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. (Catalog of Bias added to consider terms for the Risk of Bias code system.)
• 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 Risk Of Bias Code System Step 3 spreadsheet, or if not there yet in the Step 5 CatalogOfBias Ontology Mapping. Recent changes included addition of 44 terms from the Catalogue of Bias.
Statistic Type	3 commonly used tools or systems mapped. There are now 94 draft terms in the Statistic Type Code System Step 3 spreadsheet. Recent changes included addition of 1 term: Geometric mean
Statistic Model	2 commonly used tools or systems mapped. There are now 69 draft terms in the Statistic Model Code System Step 3 spreadsheet. . Recent changes included addition of 1 term: t-test
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. Recent additions include Clinical Trials Ontology (CTO) and Study Cohort Ontology (SCO). Feel free to suggest any missing ontologies that you may be aware of.
• Step 5 (Ontology mapping) is underway. 6 ontologies mapped so far (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).

 

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.

 

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.
• 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

 

• We continued to develop the Steroids for COVID-19 Systematic Meta-Review Protocol. The search strategies are completed and we are preparing to pilot the article selection process.

 

 

Communications Work Group

 

• Upcoming presentations (December 2-4) 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:

 

• Discussions with the ACTS COVID-19 Collaborative Learning Community included developing efforts to create a series of Knowledge Ecosystem Recommendations.  We converted the data requirements (for 16 data elements to express a Recommendation) to mock-up phrasing for survey format for data entry at  https://docs.google.com/document/d/1lkrCPuAJ1Mhvn4DK1SKQzklQycr-NswTYYwfZrTI1lA --- this may be developed in the short term to surveys and later into a system for maintaining ‘Living Guidance’ for Achieving Care Transformation Support.

 

 

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:

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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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