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CDM conversion vendors


(George Hripcsak) #1

We sometimes get asked what vendors can help groups to convert their observational databases to the CDM. If you are such a vendor, it might be helpful to post here with contact information. Thanks. George


Any recommendations on groups which can help implementing the CDM?
(William Stephens) #2

@hripcsa,

My company, Signet Accel LLC, provides a data integration solution that leverages a virtual appliance deployment model to support the creation of distributed data networks leveraging OMOP models. Our appliances can be deployed on premises or in the cloud and contains:

  • Postgres databases containing a OMOP v4 or v5 schema and vocabularies
  • Custom and OHDSI ETL utilities: WhiteRabbit, Achilles
  • Secure web service to enable data sharing
  • Web application to enable ad-hoc queries and saved queries against the web service (can be deployed at a central location to enable federated query capability). Secured Achilles Web integration in progress for February release.

My team performs ETL and conceptual mapping on data sets as well as being available for post-installation support.

Suggestion
I would recommend the creation of an “OHDSI Vendors” page on the web site that would link to organizations that can operate in a variety of areas that would benefit the expansion of the OHDSI. For example, Outcomes Insights is performing contracted epidemiology upon the OMOP models.

In previous organizations, we setup this type of vendor list and vetted the candidates but left the review and selection up to the end user.

Thanks,
Bill Stephens
CTO
Signet Accel, LLC
Contact: sales@signetaccel.com


(Mark Danese) #3

Outcomes Insights, Inc. works with many pharmaceutical and biotech companies to conduct research in epidemiology, economics, and outcomes research. We also adopted the OMOP common data model about a year ago, and we have developed our software to make it easier to build studies (not just cohorts) on top of the common data model (we call it “Jigsaw”).

We do some ETL work and have experience with CPRD and Truven (thanks to the Janssen specifications for CDM v4), and we are leading the OHDSI work group for creating the ETL specification for Medicare data. We are also working with the National Cancer Institute to develop the ETL for the SEER data in conjunction with Bill Stephens at Signet Accel (above).

Mark Danese, MHS, PhD
President, Outcomes Insights, Inc.


(Lee Evans) #4

LTS Computing LLC provides a hosting and support service for OHDSI informatics applications and large CDM databases. We can host and provide support in the cloud or on-premise.

Services:

  • OHDSI application and CDM database hosting
  • Architectural solution development - solution blue-prints and CDM implementation project deliverables
  • OHDSI tool integration with multiple DBMSs - Oracle, PostgreSQL, SQL Server & Netezza
  • Integration with analytic, visualization and reporting tools such as SAS, R, Spotfire & Microstrategy
  • Application development and continuous integration service for customizing OHDSI applications to your specific requirements

We are located in West Chester PA.

Lee Evans
Owner, LTS Computing LLC

OHDSI/CDM Experience

I manage and support the public facing OHDSI informatics applications for OHDSI in the cloud.

Prior to forming LTS Computing LLC, I was the AstraZeneca architect for the Payer & Real World Evidence strategic program where I led the small IT team that deployed a Netezza data warehouse appliance hosting CDM databases. The Netezza appliance contained a number of CDM databases including Truven and CPRD.


(Sajan Khosla) #5

Saama technologies are working with a number of pharmaceutical and biotechnology companies driving their Real World Evidence strategies.

Some of the tools we are developing in the Observational Health Data Science space utilise both OMOP CDM and native forms of data. The latter is generally due to necessity rather than preference.

We’ve spent a lot of time on CPRD/THIN/Truven and some specialist EMR datasets and will certainly be keen to share as much as we can into the OHDSI objectives.

Sajan Khosla, MSc
Director, Health Data Science - Saama


(Chris Andrews) #6

With over 5 years of operating as a database consulting business, Chris and Definitive Data Solutions has recently completed two OMOP conversions in “Big Data” hosted environments acting as the database developer, engineer, and administrator. One conversion has involved a large pharmaceutical company with Truven data along with much help from the documentation found on this site and the other being custom EMR conversion for a well known professional medical association. Both conversions had tables with records that broke into the billions, so properly tuned tables and code was a must to meet deadlines.

Please view my company’s website for more information on my business, experience, and how to contact me. Chris is available for projects starting in October and it is highly preferable to work in a Microsoft SQL and/or Redshift environment. Definitive Data Solutions has the ability to host database environments. I am conveniently located in Watertown, MA, with close access to the Massachusetts tech centers of Burlington, Cambridge, Waltham, and Boston.

Chris Andrews
Owner
Definitive Data Solutions LLC
Watertown, MA

http://www.definitive-data-solutions.com/


ETL file for CDM V4 -> V5.x for Truven CCAE dataset
Welcome to OHDSI! - Please introduce yourself
DRUG_EXPOSURE conventions
Achilles v1.5: Multithreading of analyses
(Gregory Klebanov) #7

Odysseus Data Services, Inc. is an active OHDSI community contributor and offers unique services in Real World data management:

  • OMOP CDM conversions (ETL)
  • OMOP Vocabulary management, including creation and management of custom vocabularies
  • OMOP CDM testing and validation

Odysseus has extensive experience in establishing mature Agile OMOP Data Factory process, including DevOps and OMOP CDM Process Automation. We have built advanced expertise with major commercial data sets as well as internal patient medical data. Odysseus vocabulary team is managing OHDSI vocabularies, including release and distribution of these vocabularies via Athena platform.

Odysseus is proudly serving customers in Pharmaceutical, Healthcare and Insurance industries, Academic Institutions as well as Real-World Data Management and Analytics Platform providers.

Gregory Klebanov
Chief Technical Officer
gregory.klebanov@odysseusinc.com

Office: +1 (888) 550-9968
http://odysseusinc.com


(Marzi) #8

The www.Evalytica.com team has significant experience performing full ETL and periodic data refreshes on Truven, CPRD, PREMIER, OPTUM and CancerLinQ datasets using the latest vocabularies. We published our methods last year at the OHDSI conference (see publication here).

Typical turnaround time for an ETL is approximately 1 week from when the data is ingested by our system if we’ve encountered the dataset previously. Our ETL process includes producing the Achilles data characterization and quality reports. Once the data is ETL’d, we put the data in our cloud-based SaaS platform, Evalytica. We also give our clients a copy of the ETL’d data in CDM format for their own use.

Evalytica enables users to quickly and efficiently perform complex, transparent analysis on patient populations from disparate RWD sources. Users define cohorts in a user-friendly manner and then run multiple apps (Treatment Pathways, Incidence, etc.) on those cohorts. Our Global Library allows users to define, store, share and reuse Health Outcomes of Interest. We provide Customer Support and our dedicated team of software engineers continually update the software and release new apps.

If you need more information, please contact Karen.thomson@evidera.com at 612-910-1787.


(Keesvanbochove) #9

The Hyve is a professional IT services company specialized in open source software packages for biomedical research, including OMOP/OHDSI, tranSMART, cBioPortal, RADAR and FAIR Data solutions. The Hyve has more than 40 employees spread over offices in Utrecht, Netherlands, in Cambridge, MA, United States and Singapore.

At The Hyve, we have a dedicated OMOP/OHDSI team with comprehensive knowledge of medical standards and ontologies (e.g., ICD-10, SNOMED-CT), expertise in OMOP CDM conversions (mapping dictionaries and transformation pipelines) and in deployment, configuration and utilization of the OHDSI tool suite.

Besides using OMOP CDM conversion tools like White Rabbit, Rabbit-in-a-hat and Usagi, we designed, built and implemented custom mapping and transformation pipelines. We also installed and configured applications from the OHDSI tool suite and integrated those tools with existing IT infrastructure at servers from partners and customers. Besides technical and functional support and assistance, The Hyve also provides consultancy services and trainings around OMOP/OHDSI solutions. In particular we have worked with several global pharmaceutical companies on mapping private datasets, and in international consortia such as IMI EMIF and IMI BigData@Heart to map datasets from several European national and regional registries to OMOP CDM.

Lastly, we are working with a number of organisations to build out their Real World Data IT infrastructure and analytics capabilities, integrating other open source tools such as Jupyter and FAIR Data Point tooling to improve data management and reproducibility of both data conversion as well as data analytics.


(Mahtab) #10

Dear @wstephens,
I tried to ask for a use case download from the website you provided, but then in the region menu there’s no option for other countries. I’d appreciate if you guide me on this.

Mahtab


(Ravi Sunkara) #11

Geroge,
Hope you are doing great.
We have a pool of expert resources on the healthcare domain with OMOP (common data model) conversion.
Our resources are experts in AWS, Redshift, Lamda, Postgress, SQL, EMR, Patient and clinical data. We did a POC in AWS (Redshift DB) environment.
We can support the project remotely or on-site with our available pool of over 10 resources.

If you can give us some time this week, We should be able explain you in detail how we can coordinate and make this a successful practice to benefit both the companies.


(Shridhar Bhat) #12

Hi there,

We have done ETL on large data for a university in NSW, Australia and can provide references. Our work involved conversion of MS SQL based EHR data into CDM 5.3. The encompassing work was done on AWS and required writing complex SQL queries. We have specialization in building web and mobile apps on AWS on Python & Java stack, doing data mining using ElasticSearch, R & leveraging NLP on clinical data.

Please feel free to reach out to shridhar DOT bhat AT sarvaha.com for more information, queries or a quote.


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