Observational Health Data Sciences and Informatics

Encourage members put their emails on the WG wiki page.

Richard will share his slides on wiki

Each group will put their mappings and use cases on wiki pages as follows.

- Mappings between OHDSI CDM and FHIR

- OHDSI FHIR WG Use Cases

Guoqian will follow up with Mitra for her CDM harmonization project

Guoqian will reach out offline for agenda items next month

[4/19/17, 12:13:10 PM] Eric Prud'hommeaux: notes:

richard: presenting on Tue at the OHDSI call

[4/19/17, 12:13:20 PM] Eric Prud'hommeaux: … will get into F2F and projects

[4/19/17, 12:13:33 PM] Eric Prud'hommeaux: … right now we have two versions of OMOP-on-FHIR

[4/19/17, 12:13:50 PM] Eric Prud'hommeaux: … 1st was built ih-house – we can go back and forth to FHIR

[4/19/17, 12:14:08 PM] Eric Prud'hommeaux: … 2nd version is more widely applicable

[4/19/17, 12:14:40 PM] Eric Prud'hommeaux: … use cases: if you have an OMOP repo, want to drop in a FHIR server in front

[4/19/17, 12:14:47 PM] Eric Prud'hommeaux: … allows you to use FHIR apps

[4/19/17, 12:15:26 PM] Eric Prud'hommeaux: … 2nd: lots of interest in using FHIR to map from FHIR-enabled EHR to OMOP

[4/19/17, 12:15:45 PM] Eric Prud'hommeaux: … we built some static staging tables and procedures wrapped around them.

[4/19/17, 12:15:51 PM] Eric Prud'hommeaux: … we want it to work with CSV

[4/19/17, 12:16:14 PM] Eric Prud'hommeaux: … since we don't ahve a med school, we work with external data and have to be very flexible

[4/19/17, 12:16:33 PM] Eric Prud'hommeaux: … we don't have MBI functions so we're relying on source value for uniquenless

[4/19/17, 12:17:08 PM] Eric Prud'hommeaux: … of course for each incoming feed, you need a custom uniqueness system (if yo udon't have an MPI)

[4/19/17, 12:17:27 PM] Eric Prud'hommeaux: … the main prob we have is mapping the FHIR Observation to multiple tables

[4/19/17, 12:17:42 PM] Eric Prud'hommeaux: … also had to extend omop to include demographics data

[4/19/17, 12:18:12 PM] Eric Prud'hommeaux: … we have standardized rights and logic for pushing data into the tables

[4/19/17, 12:18:36 PM] Eric Prud'hommeaux: … we need to handle real-time load from individual fhir sources that happne in real life

[4/19/17, 12:18:59 PM] Eric Prud'hommeaux: … from my perspective, we see lots of interest in leveraging for FHIR mapping to OMOP

[4/19/17, 12:19:22 PM] Eric Prud'hommeaux: … i didn't persue any new FHIR apps (sitting on top of an existing CDM)

[4/19/17, 12:19:46 PM] Eric Prud'hommeaux: … @@1 probably has a different POV 'cause he's involved in FHIR, not OMOP

[4/19/17, 12:20:09 PM] Eric Prud'hommeaux: @@1: we developed a system with three componentns:

[4/19/17, 12:20:19 PM] Eric Prud'hommeaux: … .. web app for visualizing data

[4/19/17, 12:20:25 PM] Eric Prud'hommeaux: … .. emr for pulling data

[4/19/17, 12:20:39 PM] Eric Prud'hommeaux: … .. web api (developed by another group)

[4/19/17, 12:20:49 PM] Eric Prud'hommeaux: … we used those for the F2F meeting

[4/19/17, 12:21:31 PM] Eric Prud'hommeaux: … assuming your EHR is FHIR-enabled, the GT-FHIR server has OMOP V5 has a backend DB

[4/19/17, 12:21:48 PM] Eric Prud'hommeaux: … we have patients, medications, … to simulate the EHR

[4/19/17, 12:22:20 PM] Eric Prud'hommeaux: … i used a FHIR client to POST new data (medications) to the OMOP DB

[4/19/17, 12:22:36 PM] Eric Prud'hommeaux: … so it works as a FHIR-to-OMOP

[4/19/17, 12:23:04 PM] Eric Prud'hommeaux: … i can create lots of tables in OMOP (practitioner)

[4/19/17, 12:23:23 PM] Eric Prud'hommeaux: … i used all that to populate OMOP V5 and used the loaded server

[4/19/17, 12:23:56 PM] Eric Prud'hommeaux: richard: we were really only involved in the dissemination group

[4/19/17, 12:24:34 PM] Eric Prud'hommeaux: cali: Q re FHIR impl on OMOP: i understand that your FHIR server can read one patient data at a time?

[4/19/17, 12:24:44 PM] Eric Prud'hommeaux: … can it write to the OMOP db

[4/19/17, 12:25:14 PM] Eric Prud'hommeaux: @@1: you can read by patient or search [across patients]

[4/19/17, 12:25:22 PM] Eric Prud'hommeaux: … we write one resource at a time

[4/19/17, 12:25:29 PM] Eric Prud'hommeaux: … thinking about writing a bundle

[4/19/17, 12:26:10 PM] Eric Prud'hommeaux: richard: assuming existing patient

[4/19/17, 12:26:19 PM] Eric Prud'hommeaux: … otherwise we get NULLs in the CDM

[4/19/17, 12:27:04 PM] Eric Prud'hommeaux: ericP: limited to one by the FHIR API?

[4/19/17, 12:27:17 PM] Eric Prud'hommeaux: @@1: think we can write bundles

[4/19/17, 12:27:35 PM] Eric Prud'hommeaux: richard: we've talked about developing a cohort, which would be a huge packet

[4/19/17, 12:28:17 PM] Eric Prud'hommeaux: guoqian: when you load FHIR into OMOP, you created additional tables (beyond CDM)

[4/19/17, 12:28:40 PM] Eric Prud'hommeaux: richard: we created F-Person (demographcics, address, contact info)

[4/19/17, 12:28:52 PM] Eric Prud'hommeaux: @@1: OMOP has a location table as well

[4/19/17, 12:29:30 PM] Eric Prud'hommeaux: … so write Person/location info to the [CDM] IMOP location table

[4/19/17, 12:29:50 PM] Eric Prud'hommeaux: … if someone writes “street” and another writes “st”, that's a differetn addr

[4/19/17, 12:29:58 PM] Eric Prud'hommeaux: richard: that will come from the source value table

[4/19/17, 12:30:42 PM] Eric Prud'hommeaux: @@1: if the FHIR resource has a reference, we can use that ID in the source column

[4/19/17, 12:30:59 PM] Eric Prud'hommeaux: … but if the address is in the FHIR, we can't merge it against existing location records

[4/19/17, 12:31:13 PM] Eric Prud'hommeaux: richard: we can use USPS services for that

[4/19/17, 12:31:30 PM] Eric Prud'hommeaux: guoqian: so the purpose is to capture all FHIR information?

[4/19/17, 12:31:38 PM] Eric Prud'hommeaux: richard: i think it's useful info.

[4/19/17, 12:31:49 PM] Eric Prud'hommeaux: … the search might include names.

[4/19/17, 12:32:03 PM] Eric Prud'hommeaux: … (OMOP is considered de-identified)

[4/19/17, 12:32:17 PM] Eric Prud'hommeaux: … but we're trying to support other tools beyond OHDSI

[4/19/17, 12:32:37 PM] Eric Prud'hommeaux: @@1: we can use the Person ID has a name field

[4/19/17, 12:33:01 PM] Eric Prud'hommeaux: … those fields are not required in FHIR so nothing will break if they're not there.

[4/19/17, 12:33:12 PM] Eric Prud'hommeaux: … but there are tools that use them for [disambiugation?]

[4/19/17, 12:33:50 PM] Eric Prud'hommeaux: … if we can come up with a coding mapping, that would help people outside get interop

[4/19/17, 12:34:23 PM] Eric Prud'hommeaux: guoqian: from hwat i understand, OHDSI has its one concept ID. do you transformation or allignment?

[4/19/17, 12:34:37 PM] Eric Prud'hommeaux: richard: we use generic ETL procedures to do the translation

[4/19/17, 12:35:06 PM] Eric Prud'hommeaux: … we've talked about serveral optionns for what to do when we want to e.g. back-translate from CDM to ICD-9/10

[4/19/17, 12:35:29 PM] Eric Prud'hommeaux: @@1: our test env uses @@2

[4/19/17, 12:35:43 PM] Eric Prud'hommeaux: … the Vista EMR sends huge lists of different codings

[4/19/17, 12:35:58 PM] Eric Prud'hommeaux: … e.g. drugs: RxNorm/NDC

[4/19/17, 12:36:12 PM] Eric Prud'hommeaux: … so in our FHIR, we picked what we wanted

[4/19/17, 12:36:33 PM] Eric Prud'hommeaux: richard: we can still do those translations firom …

[4/19/17, 12:36:51 PM] Eric Prud'hommeaux: … the VA way is good. if you put them all in, the user can pick their fave

[4/19/17, 12:37:43 PM] Eric Prud'hommeaux: … the prob we've had (last week): what if you don't map to the source concept, e.g. an item ID from MIMIC? do yo give them free text?

[4/19/17, 12:38:01 PM] Eric Prud'hommeaux: guoqian:: need further discussion on two points:

[4/19/17, 12:38:20 PM] Eric Prud'hommeaux: … .. 1 collab on standard mappings between HFIR resources and OHDSI CDM

[4/19/17, 12:38:40 PM] Eric Prud'hommeaux: … .. 2 if we want to load FHIR into OHDSI CDM, what extesnions do we need?

[4/19/17, 12:39:14 PM] Eric Prud'hommeaux: richard: we tried our best to do it in a new table so it wouldn't affect existing processes

[4/19/17, 12:39:36 PM] Eric Prud'hommeaux: guoqian: at Mayo, we used NoSQL tech to store extension data

[4/19/17, 12:39:47 PM] Eric Prud'hommeaux: richard: we're working with a Hadoop group

[4/19/17, 12:39:57 PM] Eric Prud'hommeaux: … but that's OMOP into Hadooop

[4/19/17, 12:40:55 PM] Eric Prud'hommeaux: ericP: should we start with yours?

[4/19/17, 12:41:17 PM] Eric Prud'hommeaux: richard: my work needs OMOP review to consider my assumptions

[4/19/17, 12:41:32 PM] Eric Prud'hommeaux: … we're using staging tables.

[4/19/17, 12:41:45 PM] Eric Prud'hommeaux: … i worked with different file structures from different providers

[4/19/17, 12:42:11 PM] Eric Prud'hommeaux: … so i tried to create standard staging tables for what i'd seen from differnent EHRs/claims systems

[4/19/17, 12:42:40 PM] Eric Prud'hommeaux: … so i think i've got the propor CDM process for them, but with the vocab changing and the mapping changing, i don't know if it's correct

[4/19/17, 12:43:17 PM] Eric Prud'hommeaux: ericP: tests cases?

[4/19/17, 12:43:28 PM] Eric Prud'hommeaux: richard: we use the MIMIC dataset for a lot of stuff

[4/19/17, 12:43:45 PM] Eric Prud'hommeaux: … that would allow us to see affects

[4/19/17, 12:43:59 PM] Eric Prud'hommeaux: … i'm not sure there's a consensus in the community about the proper mapping

[4/19/17, 12:44:17 PM] Eric Prud'hommeaux: … at the DC meeting, people were learning lots with each question

[4/19/17, 12:44:59 PM] Eric Prud'hommeaux: @@1: from my (FHIR) side, there's too much flexibility and extensibility. breaks interop

[4/19/17, 12:45:09 PM] Eric Prud'hommeaux: … we we still have to map FHIR to the staging table

[4/19/17, 12:45:41 PM] Eric Prud'hommeaux: … the OMOP side needs the right staging table and we need the right strategy table to map from FHIR to the staging table

[4/19/17, 12:45:55 PM] Eric Prud'hommeaux: … we're more confortable working with the staging table

[4/19/17, 12:46:48 PM] Eric Prud'hommeaux: … so folks in the field, testing, clinical data, etc, it would help to eval our strategy

[4/19/17, 12:54:25 PM] Eric Prud'hommeaux: @@3: Laurrie Phillips (dev) linked I2B2 to OMOP

[4/19/17, 12:54:36 PM] Eric Prud'hommeaux: … I2B2 is a star schema which can adapt to any data model

[4/19/17, 12:54:59 PM] Eric Prud'hommeaux: … deviated a bit from that to use the I2B2 cell to talk to an existing OMOP database

[4/19/17, 12:55:09 PM] Eric Prud'hommeaux: ,,, we just put out a releas to test it out

[4/19/17, 12:55:20 PM] Eric Prud'hommeaux: … i've been working on the FHIR API over I2B2

[4/19/17, 12:55:35 PM] Eric Prud'hommeaux: … we were tied to the default I2B2 model

[4/19/17, 12:55:49 PM] Eric Prud'hommeaux: … the focus was on running SmART apps on I2B2

[4/19/17, 12:56:05 PM] Eric Prud'hommeaux: … we're adapting that to the PicorNet data model

[4/19/17, 12:56:29 PM] Eric Prud'hommeaux: … limitation: reading, not writing

[4/19/17, 12:56:36 PM] Eric Prud'hommeaux: … … no population queries

[4/19/17, 12:57:04 PM] Eric Prud'hommeaux: guoqian: we can consider yours an indeirect map (I2B2-FHIR and I2B2-OMOP)

[4/19/17, 12:58:41 PM] Eric Prud'hommeaux: ericP: minimize imagination

[4/19/17, 12:58:55 PM] Eric Prud'hommeaux: guoqian: aggregate approaches and then review details

[4/19/17, 12:59:05 PM] Eric Prud'hommeaux: @@3: what does mapping mean?

[4/19/17, 12:59:18 PM] Eric Prud'hommeaux: … .. you can map to a Picornet, FHIR element

[4/19/17, 12:59:32 PM] Eric Prud'hommeaux: … .. but you can also translate the codes in the element

[4/19/17, 1:00:53 PM] Eric Prud'hommeaux: richard: we had translations to CDM

[4/19/17, 1:01:18 PM] Eric Prud'hommeaux: … i had problems finding terminology mappings

[4/19/17, 1:02:33 PM] Eric Prud'hommeaux: ericP: structural vs. open term mappings

[4/19/17, 1:02:53 PM] Eric Prud'hommeaux: @@1: right, FHIR focuses on clinical workflow

[4/19/17, 1:03:13 PM] Eric Prud'hommeaux: … my decision to ask if you'd use it in a workflow