Post Public Schemas of i2b2tranSMART (HMS-variant)


While there are no current loading mechanisms for outside data, it would be extremely useful to those of us trying to stand it up and test it to get access, or a guide to the SQL Schema and naming scheme.

I understand that it’s current state is along the lines of:

  1. it is i2b2 1.7.09 schema
  2. transmart 16.2 schema
  3. HMS modifications.

The i2b2demodata and i2b2metadata are pure i2b2 schema + some added tables by
transmart 16.2

It would be useful to know the keys and schema to the OracleDB without having to jump into the docker and dump every table header. This also applies to the new PIC-SURE/Wildfly/IRCT schema, whose documentation seems spread around (both web and repo-wise).

One thing that worried me was the tmLoader docs indicate the following:

tissue_type    =>    sample_type
attribute_1    =>    tissue_type
atrribute_2    =>    timepoint

So any possible map/guide/rosetta stone would be useful to the community and the foundation long term.