Grouping issue: concept/vocabulary navigation/hierarchy

[Sigfried]

Task list

Also see:

• Grouping Issue: comparison and newCset editing #458
• Grouping issue: Add concepts to csets #768

List

• We want concept set bundle tags - navigate by bundles and see what bundles any concept set is in
• (Janos) Export cset feature #161
• (Janos) Standard vs non-standard codes - mapping flags or navigate vocabularies Distinguish intensional/extensional concepts in cset display #121
• toggle between full-list view and concept-expresssion view
• Visualization of concept hierarchy, specific neighborhoods, especially in relationship to concepts in a code set #110
• Ordering
  • Items don't always show up under their parents
  • Prefer to have parents sorted in order of number of their descendants with greatest first
  • If ordering is done at backend, FastAPI reorders dictionaries in alphabetical order by key, which messes it up; so started trying to do ordering in javascript, but not there yet.
• Filling in gaps
  • If multiple roots or disconnected subgraphs, find shared ancestors to connect them
  • Fill in missing descendents in concept hierarchy #347
  • Do we fill gaps on the server or at the client?
    • Using technique of transforming entire concept graph to undirected and then finding shortest paths, then converting back to directed:
      • probably not feasible on frontend, will slow people's browser's down too much and take too long to load huge graph.

There are several methods of constructing the hierarchy and we should choose one of them

• Backend
  - OAK
  - NetworkX
  - Neo4J
• Frontend
  - D3-Dag
  - Graphology

Issues:

• Should we download as hierarchy (dictionary with concept_id key, children array value), or as edge list?
  • Download hierarchy as an edge list #348

Other related issues:

• MVP: Vocab explorer #613
• Live update of descendants, mapped, excluded while editing #217
• Hierarchy: All leaves & ancestors (outside of selected concepts) #234
• Hierarchy: Via _ancestor or _relationship & multiple hierarchies #235
• Try other ways of showing concept hierarchy #123
• Subgraphs and relationships of any type #307
• Distinguishing concepts that appear multiple times #386

Other related issues (bugs / problems):

• UI: Concepts appearing in 2+ places #412
• Bug: Sorting: new cset + post hierarchy #506
• Concept hierarchy: missing paths, too many paths #609
• NetworkX graph is missing concepts and edges #366

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User ideas from 2022-10-05 Infrastructure Call

Categories of Features (from slides)

• Authoring/modifying concept sets
• Visualization / navigation
  • Including only concepts in selected concept set(s)
  • Including neighboring concepts from the target vocabularies #249
  • Usable navigation of large vocabulary structures (collapse/expand/summarize) #253
  • Concept name/code/concept_id search #254
  • Of concept set overlap
  • Of intensional/extensional concept inclusion
  • Patient count comparison across concept sets and concepts
• Import of concept sets from external sources
• Display and navigation of related data

Meeting notes (moving or deleting items as appropriate)

Termhub - Siggie gave demo (see recording)

• (Lisa/Steph) CSV uploads Enclave Wrangler: Dataset upload & Moffit transform #153
• (Lisa) Would we have any interest in loading N3C Recommended concept sets into VSAC? And would this be a tool you could use for that?
• (Steph) Reviewing mappings we already have would be useful - mostly post coordinated expressions.
  • Looking at transformation from non-standard to standard codes
• (Lisa) is this a tool that would help users addressing vocab change management? Something to keep in mind as those emails go out. What are the pain points? Is there something this tool could address?
• (Chris R) Use prevalence/counts data. Use with OHDSI/OMOP instances. Anna Ostropolets
  • https://github.com/ohdsi-studies/ConceptPrevalence
• Chris R hinted about some FHIR instances in future, not MVP
• Bryan - building a library of rare disease concept: https://athena.ohdsi.org/search-terms/terms/373182
  • AI - Siggie/Bryan - talk offline.
• Bryan - Has visualization use case. Will set up meeting w/ Siggie to discuss.
• Bryan - Rare disease diagnosis and measurement. Mappings between rare disease terms and associated diagnostic tests / measurements, if available.
• Siggie - How much do you want to look in other vocabularies and relationships (not just subsumes) in navigating the concepts

Additional info

Keywords: "Vocabulary explorer"

[joeflack4]

I see I see, strategic planning column. I thought this would be temporary to parse through and create issues out of. I'll leave it to you! Great notes.