OHDSI Home | Forums | Wiki | Github

CDM and ETL maintenance cycle

General
#1

Hi everyone,

Hope you are well.

Thinking of the CDM & ETL maintenance cycle (discussed in Chapter 6 Extract Transform Load | The Book of OHDSI), are there any tried and tested maintenance frameworks used within the EHDEN community that could be shared?

Kind Regards,
Solmaz Eradat

#2

Hi @solmaz.eradat ,
Would you please give more explanation of what do you looking for?
Best
Reza

#3

Hi @Reza_Baharmand.

Section Chapter 6 Extract Transform Load | The Book of OHDSI provides a theoretical approach on points to consider when considering the ETL maintenance. I wanted to see if anyone in the community who has already mapped a OMOP database has tested the approach outline in the book and can share any learnings.

During last week’s community call there was a great presentation on vocabulary mapping exercise and the use of git for tracking changes by one of the Finnish data partners. I saw their presentation as a tried and tested exercise on vocabulary mapping. We are hoping to do a similar thing during our development work on the vocabulary mapping which should aid the future maintenance cycle.

Many thanks,
Solmaz

#4

Hi @solmaz.eradat ,
Sorry for delay. I am not sure that I understand correctly what are you looking for. Maybe my knowledge is not enough to help you.
My experience is different from The Book of OHDSI.
But If you like to know it, it is my pleasure and we can arrange the meeting.
Best
Reza

#5

Hi @Reza_Baharmand . A meeting might be easier to discuss questions on this topic!
Many thank,
Solmaz

#6

FYI @Reza_Baharmand - this post rises a similar topic - OMOP CDM refreshes and versioning

#7

Hi @solmaz.eradat ,
Thank you.
Best
Reza

#8

Hi @solmaz.eradat ,
Good to hear that.
I´ll learn from you.
Best
Reza

#9

@solmaz.eradat Is there a link to the presentation on Finnish data that you are referring to?
I would be interested in seeing that.
many thanks
Amelia

#10

Hi @Amelia_Taylor - The presentation happen on the 17th January during one of the EHDEN community calls. The recoding of the call is still to be shared again as the Teams recording didn’t work for me. If I hear anything will post here. Many thanks, Solmaz

#11

Hi All. the Community call covering the Finnish OMOP CDM work was shared recently. Found the call very useful and picked up some useful tips that should be considered during a mapping exercises and using version control OMOP mapping collaboration in Finland and national node development, Auria Clinical (CC#4) – ehden.eu

#12

Hi Everyone,

As part of our ETL cycle and maintenance we have incorporated version control using an open source tool called Gitea to track changes within the ELT development cycle which we are finding very useful. After seeing the use of GitLab used by the Finnish mapping exercise.

After the ETL has been implemented and with future changes such as:

  • changes in the source data,

  • a bug in the ETL,

  • a new OMOP Vocabulary is released,

  • the CDM itself has changed or updated

Does anyone in the community use a best practice guide to handle these continues future changes?

Many thanks,
Solmaz

t