#Interleave
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An application for managing longitudinal clinical research databases and registries that is based on the OHDSI/OMOP Common Data Model (CDM). See http://www.ohdsi.org/
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The application layers the following features on top of the OHDSI CDM.
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Multitenant housing of registries.
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Enrichment of the CDM to include protected health information fields.
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Registry-scoped configuration of datapoints and the relationship between datapoints. Dynamic display of datapoints per registry.
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Datapoint restriction of the list of possible values of CDM concept ID values.
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Provenance tracking per imported standardized CDM clinical entity back to source system rows.
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Support for the incremental load of data from multiple outside source systems.
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A user interface to allow for the creation 'ex nihlo' of standardized CDM clinical entities.
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A user interface to allow for the override of externally imported standardized CDM clinical entities.
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Why the name 'Interleve'?
- Because clinical reserach databases and registries requrie the 'inteleaving' of manually created data and automatically pulled data from external systems (EHRs, billing/claims systems...)? Data must be stacked on top of each other and the provenance of each entity must be tracked. The data must be interleaved.
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Live Demo
- Here is a live demo of the application: https://interleave.herokuapp.com/
- The demo is setup with a subset of the datapoints necessary for the Northwestern Prostate SPORE: http://cancer.northwestern.edu/prostatespore/
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Setup
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Open a psql command prompt
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CREATE DATABASE interleave_development;
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CREATE USER interleave_development WITH CREATEDB PASSWORD 'interleave_development';
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ALTER DATABASE interleave_development OWNER TO interleave_development;
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ALTER USER interleave_development SUPERUSER;
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CREATE DATABASE interleave_test;
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CREATE USER interleave_test WITH CREATEDB PASSWORD 'interleave_test';
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ALTER DATABASE interleave_test OWNER TO interleave_test;
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ALTER USER interleave_test SUPERUSER;
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bundle exec rake db:migrate
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Downlod ODHSI vocabularies from http://www.ohdsi.org/web/athena/. Make sure to include CPT4, LOINC, RXNORM, ICD9, ICD10, SNOMET. Follow the instructions on how to generate the CPT codes.
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Place the OHDSI vocabulary files in '/db/omop_common_data_model/PostgreSQL/VocabImport/CDMV5VOCAB/'.
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bundle exec rake setup:omop_vocabularies
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bundle exec rake setup:interleave_registries
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Heroku setup
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heroku create interleave
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git push heroku master
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PGUSER=postgres PGPASSWORD=password heroku pg:push interleave_development DATABASE_URL --app interleave