Stream: python
Topic: PyFHIR side chat with Pascal!!
Eric Haas (May 05 2019 at 18:39):
We are planning a Python FHIRClient breakfast chat in Montreal (HL7 WGM) Tuesday 8AM on the the second floor at the table next to the exit (SouthWest Corner). Pascal will be there to help answer questions and coordinate the next steps.
Topics include:
- Sharing what we are doing with the FHIRClient
- Learn about all the methods available first hand (e.g smart on fhir - in Python)
- Issues/Feature requests
- pip for version R4 - FHIRPrimitive classes - Others
- Identify who can review and accept PRs.
- How to expand the PyFHIR community
- Community Jupyter Binder?
Please respond if you plan to be there so we notify of any last minute changes
Grahame Grieve (May 05 2019 at 19:23):
I'm hearing that that the python code is getting a lot of use in the research / AI / big data community
Andrew Patterson (May 06 2019 at 01:17):
The genomics world is very python-centric (bioinformatics wise) - so I think there is a community there who would naturally fall into using the Python FHIR client (we certainly do for our stuff).. now I just need to wean all my bioinformatics colleagues off 'structuring' all their data as CSV files (and introduce them to FHIR)
Eric Haas (May 06 2019 at 05:19):
That is funny because I use excel + Pandas + Python and I expect they do too.
Andrew Patterson (May 06 2019 at 06:01):
It's when they start nesting hierarchical data inside CSV columns ("this patient had 3 different specimens so we've concatenated them together using underscores") that I start sending them links to FHIR resource web pages!
Harold Solbrig (May 06 2019 at 14:14):
Happy to help with pip for FHIR (pipenv is the new tool). Also want to talk about using dataclasses library and the like. See you at 8 AM tomorrow
Viet Nguyen (May 07 2019 at 03:17):
Unfortunately, I have to give a Da Vinci update during breakfast. I’ll join if I can. I also invited Duncan who works with James at SmileCDR.
Harold Solbrig (May 07 2019 at 11:57):
Ok - second floor, table next to exit makes no sense. Any chance you are sitting somewhere in the eating room on the 4th floor?
Bob Milius (May 07 2019 at 12:00):
I'm at the second floor, in front of salon 1. Am I in the wrong place?
Harold Solbrig (May 07 2019 at 12:00):
I looked around there and it didn't look promising.
Harold Solbrig (May 07 2019 at 12:01):
I went up to where there was food, but can come back down if where you are is what was intended
Bob Milius (May 07 2019 at 12:01):
just saw pascal, on 2, but moved to behind the escalators
Harold Solbrig (May 07 2019 at 12:02):
2 it is. Behind the escalators ... be right down
Harold Solbrig (May 07 2019 at 12:36):
https://github.com/hsolbrig/pyshex -- see notebooks
Harold Solbrig (May 07 2019 at 12:38):
https://docs.python.org/3/library/dataclasses.html
Harold Solbrig (May 07 2019 at 12:42):
https://github.com/biolink/biolinkml/blob/master/biolinkml/utils/metamodelcore.py -- has some sample type wrappers, bool in particular
Harold Solbrig (May 07 2019 at 12:48):
https://github.com/NCATS-Tangerine/cq-notebooks
Last updated: Apr 12 2022 at 19:14 UTC
