i2b2 and tranSMART 2017 - Blogs AP-HPblogs.aphp.fr/wp-content/blogs.dir/221/files/2017/10/T3P... ·...
Transcript of i2b2 and tranSMART 2017 - Blogs AP-HPblogs.aphp.fr/wp-content/blogs.dir/221/files/2017/10/T3P... ·...
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i2b2 and tranSMART 2017: first experiences of interoperability
Mauro BucaloMatteo Gabetta BIOMERIS
Ward WeistraJan KanisJarno Van ErpTHE HYVE
OCT 6, 2017 - PARIS
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BIOMERIS
Basic Idea
allow i2b2 and tranSMARTto work on the same databasewith opportune modifications
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BIOMERIS
The idea
● History○ tranSMART was built on top of i2b2 with the
same database, but diverted over time○ tranSMART 17.1 project restored i2b2 star
schema
● Let’s test how similar they really are!○ In Harvard (June) we showed that i2b2 runs
(with minor changes) on tranSMART 2017 database
○ Next up: Does tranSMART 2017 run on an i2b2 database?
i2b2
i2b2 1.7
database
tranSMART 2017
database
tranSMART
✓ ✓*
✓?
=?
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BIOMERIS
i2b2 1.7 database
The i2b2 clinical data model is pictured below.
● The visits, dates on observations and modifiers allow for modelling time series and samples.
● The visit dimension has patient_num in its primary key. Hence these visits can only be linked to one patient.
i2b2 Design Document; Data Repository (CRC) Cell; Partners Healthcare System, 1.7.1
-image created by Jim Campbell, Dan Connolly, PCORI/GPC Standard Data Model
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BIOMERIS
tranSMART 17.1 database
The effective clinical data model in tranSMART 17.1 data model is pictured on the right.
● Reinstatement of the full i2b2 star schema dimensions allows for modelling time series and samples.
● The link with studies is made explicit. It is made on observation level instead of concept level, to allow for cross-study concepts.
● Trial visits are introduced to model visits shared among patients (Baseline, Week 1, ...).
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BIOMERIS
tranSMART 17.1 project: Removed differencesin tranSMART compared to i2b2
● Dimensions
○ Restored the usage the i2b2 dimension columns and tables:start_date, end_date on observations, visit/encounter, modifier_cd, instance_num.
○ Restored observation_fact primary key and nullability by re-adding encounter_num, start_date and instance_num.
● High dimensional data linking
○ Deprecating observation_fact.sample_cd column. Link to high dimensional data is now made with a modifier instead of a tranSMART-specific column.
● Study linking
○ Deprecating observation_fact.sourcesystem_cd for storing the tranSMART study ID.
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BIOMERIS
Flashback to June: i2b2 on tranSMART 2017 database
Works on a tranSMART 2017 database!(sequence names need to be aligned)
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BIOMERIS
1. Take a clean tranSMART database and drop i2b2 tables2. Add i2b2 demodata and metadata tables from i2b2 database:
a. Change table format ■ Convert type integer to numeric■ Add trial_visit_num to observation_fact
b. Adjust metadata for all studies■ Add birn entries to i2b2_secure■ Add study OASIS to study table in i2b2demodata and a trial visit for this
studyc. Change visual attribute in i2b2metadata
■ tranSMART visually differentiates between categorical, numerical and high dimensional nodes (LA to LAN in numeric and LA to LAC in categorical)
d. Satisfy tranSMART security model■ Add one trial visit to each observation, and one study to the trial visit
e. Adjust i2b2 data for tranSMART limitations■ Convert date observations to text■ Convert less than and greater than to exact number
The steps make tranSMART run on i2b2 database
https://github.com/thehyve/transmart-i2b2-migration
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BIOMERIS
transmartApp UI on i2b2 database
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BIOMERIS
Glowing Bear cohort builder on i2b2 1.7 database
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BIOMERIS
The same query on all
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BIOMERIS
The same query on all
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BIOMERIS
The same query on all
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BIOMERIS
Other remaining differences
● Study tree nodes
○ tranSMART Ontology tree has study dimension tree nodes. Could work in i2b2 if corresponding tables are added.
● Sequence names
○ Sequence names in i2b2 different between Oracle and Postgres. tranSMART currently uses Oracle sequence names (as presented at Harvard meeting)
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BIOMERIS
Projects in i2b2
● In i2b2 a user can access to different projects
● The data behind each project are stored in different schema or in different database (we use materialized views to simplify ETL procedures)
● User permission are granted using the PM cell
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BIOMERIS
Studies and trial visits in tranSMART
● Both are essential for modelling clinical trials and tranSMART security
● The data behind each study are stored in the same database
● User permission are granted on a observation level using the added trial_visit column
○ Corresponding study and trial_visit_dimensions tables were added to i2b2demodata.
○ Studies are linked to observations via trial visits, such as to limit the number of additional columns in observation_fact.
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BIOMERIS
Going forward to a shared database
● The i2b2 PMC is already considering:
○ Inclusion of the trial_visit_num column in the i2b2demodata.observation_fact table.
○ Inclusion of the study and trial_visit_dimensions tables to i2b2demodata.
● The tranSMART PMC is already considering:
○ Migration of the tables related to study dimensions and large scale file storage to non-i2b2 schema.
● The Foundation is planning a database working group to think further about alignment (and optimalization)○ We hope this working group will consider our lessons learned and bring the community to
one shared i2b2 tranSMART database!
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BIOMERIS
Credits
● The Hyve’s Team ○ Ward Weistra○ Jan Kanis○ Jarno Van Erp
● Biomeris Team○ Mauro Bucalo○ Matteo Gabetta