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Post-Symposium 2023 sprint

Past due by about 1 year 66% complete

At the OHDSI 2023 Symposium, we highlighted progress in finalizing core Gaia features, developing OMOP-aligned GIS vocabularies, and prototyping CDM extension tables. This progress was well-received and generated conversation about next steps for the workgroup's development directions. Paired with our drive to serve the INSPIRE project, here are our goals…

At the OHDSI 2023 Symposium, we highlighted progress in finalizing core Gaia features, developing OMOP-aligned GIS vocabularies, and prototyping CDM extension tables. This progress was well-received and generated conversation about next steps for the workgroup's development directions. Paired with our drive to serve the INSPIRE project, here are our goals for the next two months' sprint:

Projects

These are research projects that use or plan to use the Infrastructure from this WG. Development goals of this group should all link back to one or more of these projects. These projects should have project leads that will help to manage the work order on which they depend, and outputs that they are expected to produce.

  • INSPIRE (APHRC)

Documentation. (#294)

  • Rethinking public facing representation of work group goals
  • how should things be organized visually
  • architecture diagram (#274)
  • vignette for use of R packages that defines functions (#273)
  • Represent code and software maturity (how bug-free is code, how documented is code, general code maturity metrics)
  • Roadmap of future development (#231)
  • geom_spec/attr_spec documentation (#276)
  • Finalize documentation on registering a data_source (#57)
  • Update geocoding documentation (#251)
  • Create user documentation for using offline data_sources (#284)

Data Source Curation and Creation. (#272)

  • Environmental Justice Index (#287)
  • Child Opportunity Index (#286)
  • Global geometry data (GADM, DIVA-GIS) (#271)
  • SDG Indicators (API) (#198)
  • Area Deprivation Index (#267)

Data Model/ Core functionality improvement (#264).

  • Decouple geom and attr spec logic away from R, towards generic JSON (#285)
  • Write metadata to JSON during gaiaR's initializeDatabase function (#278)
  • Ensure a single source of truth for data model and data_sources/variable_sources (#200)
  • geom_dependency_uuid to move to variable_source (#263)
  • reworking of data types (varchar(x) -> varchar, much more) (#268)
  • support API data_sources/variable_sources (#127)
  • Enabling offline storage of source data to specified directory (#269)
  • Enabling authenticated data_sources (#270)
  • Enabling non-hosted data_sources (#270)
  • Ensure proper indexing of created tables (#258)

Vocabulary. (#295)

  • Define set of "exposure types" necessary for OMOP Vocabularies (#245)
  • Create a omop.geom_omop_location table (geocoded addresses) DDL (#252)
  • Add Toxin Toxin-Target Database (T3DB) to vocabulary (#218)
  • Define political boundary terms and hierarchies (#250)
  • Add missing codes and data sources
  • Test the vocabulary coverage
  • Improve the hierarchy
  • Documentation
  • Submit the GIS vocabulary package to the OHDSI Vocabulary team
  • Incorporate new concepts from local vocabulary into data sources and staging tables (#229)
  • Application for integrating development vocabulary
  • Understanding coverage of the new GIS Vocabularies (Toxins, SDoH)
  • Testing the coverage of the new GIS Vocabularies (Toxins, SDoH)
  • What's next?

Packaging. (#297)

  • Making components truly modular
  • versioning components
  • rethinking names of database, R package
  • Determine relationships between "core" functionality, determine relationships to "gaiaOhdsi" and other external components
  • establishing stable versions (0.1) of gaiaCore (aka DB) and gaiaR (fka gaiaCore)
  • Question: how do you distinguish between changes in the data model a/o core functionality, compared to metadata within the catalog? Both would be good to track, version, and have releases.
  • Package search/catalog app from GDSC in a shareable way (#279)
  • Split the OHDSI specific functions out of GaiaCore R Package into new GaiaOhdsi R Package (#296)

OHDSI Integration. (#298)

  • Presentation to the CDM WG
  • Split the OHDSI specific functions out of GaiaCore R Package into new GaiaOhdsi R Package (#296)
  • what's next?

Other.

  • Explore RO Crate and document potential use (#280)
  • Next steps for "repository"... can we host the data catalog. This might change the way we think about it as we develop.
  • "smoke test": an executable that can be run at the site to return a quick and clear response that this worked or did not (see linkML approach to validating JSON)
  • Variable_source/ data_source validator. Similar to test connection in a DBMS gui. Could be run as a developer putting variable_sources together, could be run as a routine to validate all data_sources and variable_sources as a test. (#84)
  • Next steps for DCAT metadata/ metadata coverage enhancements
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