2021-09-20 SEC Call notes

Date

Sep 20, 2021

Discourse SEC calls

Participants

  • @Thomas Beale

  • @Seref Arikan

  • @Sebastian Garde

  • @Diego Bosca

  • @Sebastian Iancu

  • @Pieter Bos

  • @Rong Chen

  • @Erik Sundvall (@gmail profile)

  • @Pablo Pazos

Goals

  • previous meeting:

Discussion topics

AM Release 2.3.0

 

Item

Presenter

Notes

 

Item

Presenter

Notes

5 min

Opening

 

USEFUL Jira RESOURCE: CRs I have not accepted.

 

Berlin Oct 13th SEC meeting - agenda topics

Likely presential:

  • IM, PB, TB, ?SI, SG, DB

Remote:

  • Pablo, Erik, Shinji

Location

All

Potential items:

  • Conformance approach

  • Progress on flat JSON / simplified data formats (draft spec)

  • REST API - directions / plans ; review current CRs - headers question (@Ian McNicoll , @Erik Sundvall )

  • ‘Ians stuff’: AQL link following, terminology tricks, …

  • Moving openEHR to ADL2 technology

    • CKM issues; other tools;

    • OPT handling

    • establish scope on value set handling; nested value value sets; asserting relationships;

  • next steps AQL: @Seref Arikan : one vendors group AQL call prior to SEC meeting;

    • initial AQL roadmap;

    • work out scope - e.g.demographics; joins; terminology resolution

    • what’s in 2.0? Formalised semantics; what breaks?

    • @Seref Arikan blog posts; permutations

    • IDEALLY: get vendor statements of what permutation handling looks like today (e.g sets v bags)

  • ?view Entries & managed lists

  • OMOP - @Diego Bosca ? (otherwise on a dedicated call)

 

 

 

 

15 min

Archie update.

@Pieter Bos

 

 

AQL grammar review

@Thomas Beale

See TB Antlr repo.

Discourse discussion.

20 min

@Ian McNicoll AQL - ELEMENT-level querying

Example:
SELECT
el/name/defining_code as someElement
FROM
EHR e
CONTAINS COMPOSITION c
CONTAINS OBSERVATION o
CONTAINS ELEMENT el
WHERE
el/name/value/mappings/target = 'SNOMED-CT::12345'

 

  • could we do ELEMENT-level querying on e.g. OBS-based Entries

  • ex: get PEWS total score value via code in defining_code or in mappings

  • @Erik Sundvall - definitely exists where need to query on code system A but data are recorded in internal codes, or other code system (hence looking in mappings).

  • Assumption: the codes we want to query on are in the data

  • Requirements:

    • PRIMARY NEED: get back (e.g) OBS on the basis of term codes used to tag them, without knowing archetype or at-code etc

    • possible subsumption inferencing needed (actual codes in data are children of query code)

    • possible lookup of mappings that are not in the data, but may be in archetypes

    • make the AQL query simpler / more intuitive,

    • dirty import data scenario: need to use the codes that came in the data

    • handle terminology-tagged OBSERVATIONs (presumably other ENTRYs also)

  • @Seref Arikan can get a (probably unwanted) permutations effect - question on DISTINCT semantics etc

  • ACTION: find out from vendors if ELEMENT-level querying allowed / works / …

 

Terminology ids & codes problem

@Pablo Pazos

We should agree terminology_id is either

  • normal name, decide allowed chars - Unicode sub-ranges; can’t have ‘:' - must be quoted; allow '.’, typical language characters

  • URI

See FHIR terminology URI registry

Check also

  • Archetype ids - agree that these are [a-zA-Z0-9] based;

  • pre-ADL2 - template ids - also agree [a-zA-Z0-9] based

Concept identifier - @Ian McNicoll - potential case for adding an archetype-wide (usually template-wide) id e.g. ‘Scottish BP’. Need is for a human-friendly description - not in data; avoid having to have in technical id

?Optional field; could default to root-node.

NB: Better tools allow Swedish chars in template ids.

Next SEC call

 

Agenda items for next call:

  • @Seref Arikan Archie-based TS generation based on JSON schema.

 

Outstanding topics:

Action items

ALL IMPLEMENTERS: please check your OPT14s against ITS XSDs on spec site. E.g. at least report diffs please. NB namepace v1/v2 question & importing (all versions have to be the same in XSD).
@Thomas Beale : create conformance discussion online
@Diego Bosca at some future point, propose some initial OMOP-related mapping resource