Stream: FAIR
Topic: FAIR track at 26th connectathon
Giorgio Cangioli (Dec 03 2020 at 16:53):
Are you interested in working with HL7 FHIR FAIR health datasets?
Share views on how to measure FAIRness using FHIR ?
Join the FAIR track at the next HL7 FHIR 26th virtual Connectathon (https://tinyurl.com/FAIRTrack)
Yunwei Wang (Dec 10 2020 at 19:09):
Hi @Giorgio Cangioli There are two sessions next week
Tuesday, December 15, 4:00 PM ET (10:00 PM CET): Connectathon Information Session: Connectathon Prep
Thursday, December 17, 11:00 AM ET (17:00 PM CET): Track Orientation Session
Is the first one more general on connectathon (not track specific)?
Giorgio Cangioli (Dec 11 2020 at 07:47):
Hi @Yunwei Wang this is my understanding :-)
As FAIR track we are going to prepare the Thu 17th meeting.
Giorgio Cangioli (Dec 14 2020 at 15:52):
The details for joining the FAIR track presentation session has been added to the FAIR track confluence page
Giorgio Cangioli (Dec 23 2020 at 14:03):
A google sheet has been prepared by @Alicia Martinez-Garcia to facilitate the collection of what we'd like to do and their scheduling (less urgent at this stage).
Giorgio Cangioli (Dec 23 2020 at 14:07):
Three kinds of sessions have been identified:
- Share experiences: experiences relevant for the scope of the track are presented and discussed
- Exercise scenarios: (some of the) presented experiences are exercised by using the test data to collect feedbacks about the FAIR and FHIR compliance.
- Design and Implement: how to face some agreed challenges by using HL7 FHIR is discussed and proof of concept implementation realized and exercised.
Giorgio Cangioli (Dec 23 2020 at 14:13):
The proposed 'challenge' for the Design and Implement session is "describe, publish, discover and retrieve a data set" . Assumptions, preconditions and the possible storyboard is described in this confluence page for your review
Giorgio Cangioli (Dec 23 2020 at 14:14):
A list of suggested actions is also included in the same page
Ian D Harrow (Dec 23 2020 at 14:32):
Typo on the dates in the sheet, as they are Wed Jan 13, 14 & 15 (rather than 12, 13 & 14 in sheet) 2021!
Giorgio Cangioli (Dec 23 2020 at 14:56):
Thanks fixed :fixing:
Giorgio Cangioli (Jan 08 2021 at 13:23):
A draft high-level agenda has been added in the confluence page . Let me know what needs to be updated...
Giorgio Cangioli (Jan 08 2021 at 13:24):
..if you have experiences to be share let me know and I'll add to the list :-)
Oya Deniz Beyan (Jan 13 2021 at 08:29):
I suppose we join via Whova, first I got error but now seems ok
Giorgio Cangioli (Jan 13 2021 at 08:44):
good :-)
Giorgio Cangioli (Jan 13 2021 at 08:44):
let's meet in a few hours
Giorgio Cangioli (Jan 13 2021 at 13:33):
This is a kind reminder : the kickoff session of the FAIR track is scheduled for today at 8:00 AM PT / 11:00 AM ET / 17:00 CET
Giorgio Cangioli (Jan 13 2021 at 16:53):
..sorry my connection suddenly stopped..
steve shore (Jan 13 2021 at 17:05):
Is FAIR - Education on Principles not available in Whova?
Giorgio Cangioli (Jan 13 2021 at 17:06):
it should be
Giorgio Cangioli (Jan 13 2021 at 17:07):
we have 69 people in
steve shore (Jan 13 2021 at 17:08):
I see this when I click on the event:
The event organizer has configured Whova to redirect the session to native Zoom app.
Giorgio Cangioli (Jan 13 2021 at 17:09):
Let me ask the organizer..
Giorgio Cangioli (Jan 13 2021 at 17:09):
meanwhile could you join via zoom ?
steve shore (Jan 13 2021 at 17:12):
I was on my work pc and do not have admin rights. Switching to person pc
Mary Ann Boyle (Jan 13 2021 at 17:12):
@steve shore Hello Steve, yes, you should just follow the zoom link
steve shore (Jan 13 2021 at 17:14):
In in
steve shore (Jan 13 2021 at 17:14):
I'm in
Oya Deniz Beyan (Jan 13 2021 at 17:21):
@Giorgio Cangioli today @Catherine Chronaki covered most of the information I want to cover tomorrow. I do not want to repeat all this information. Shall we think of something more interactive? For example, if I want to measure each principle how can we do that.
Ian D Harrow (Jan 13 2021 at 18:06):
@Oya Deniz Beyan perhaps you could focus interactively on the RDA FAIR MIs for F & A?
Giorgio Cangioli (Jan 13 2021 at 18:08):
@Oya Deniz Beyan I'm not worried about reinforcing some concepts ("repetita iuvant")
Giorgio Cangioli (Jan 13 2021 at 18:09):
But I like the idea of having an interactive session as well..:-)
Catherine Chronaki (Jan 13 2021 at 19:05):
Yes, I agree; it would be great if we would learn more about how to measure and what it means for HL7 FHIR
Giorgio Cangioli (Jan 13 2021 at 19:21):
For those interested in: we planned to have a talk about FAIR data/metadata representation in FHIR scheduled for 12.30 PT / 15.30 ET / 20.30 GMT / 21.30 CET
Ian D Harrow (Jan 13 2021 at 21:32):
FAIR Digital Object Framework Documentation I mentioned: https://fairdigitalobjectframework.org might help with identifier resolution (see Figure 1)?
Oya Deniz Beyan (Jan 14 2021 at 12:09):
I can go over how to measure the conformance to RDA indicators and I can do some interactive session.
Alicia Martinez-Garcia (Jan 14 2021 at 12:11):
This is a kind reminder: the first break-out session (sharing experiences - The FAIR4Health project) of the FAIR track is scheduled for today at 6 am PT / 9 am ET / 15 CET
Giorgio Cangioli (Jan 14 2021 at 13:14):
Ian D Harrow said:
FAIR Digital Object Framework Documentation I mentioned: https://fairdigitalobjectframework.org might help with identifier resolution (see Figure 1)?
Thanks
Giorgio Cangioli (Jan 14 2021 at 13:15):
Oya Deniz Beyan said:
I can go over how to measure the conformance to RDA indicators and I can do some interactive session.
That's would be great ! Thanks @Oya Deniz Beyan
Oya Deniz Beyan (Jan 14 2021 at 13:33):
@Giorgio Cangioli you can find the metadata requirements under this folder https://drive.google.com/drive/folders/1T5TqlnJuJ73LmMB-R82vC1NnzEmZ6rfK?usp=sharing
Giorgio Cangioli (Jan 14 2021 at 14:01):
Alicia Martinez-Garcia said:
This is a kind reminder: the first break-out session (sharing experiences - The FAIR4Health project) of the FAIR track is scheduled for today at 6 am PT / 9 am ET / 15 CET
The session is going to start
Matthias Löbe (Jan 14 2021 at 14:34):
Can one organizer please again explain how we will be able to access the datasets?
Alicia Martinez-Garcia (Jan 14 2021 at 16:11):
Off course, thank you very much Matthias.
It depends on the kind of dataset:
- Dataset with RAW data. Please, email us (alicia.martinez.garcia@juntadeandalucia.es; giorgio.cangioli@gmail.com) and we will send you the link and the password to download it.
- Dataset with FHIR data. You could find it in this link: https://hl7eu.onfhir.io/r4/
In both cases, taking into account anonymized real data has been included, you must undertake to:
- Do not use these testing datasets for any other purpose than the Connectathon.
- Remove the testing datasets at the end of the Connectathon.
- And do not make any attempt to re-identify patients.
In our track page in Confluence, in the section ‘Track Details’ and subsection ‘Security and Privacy Considerations’, you could find the Data Processor Agreement (or here: https://drive.google.com/file/d/1Ja4p8-9oWAzZl0CkKls1Dy0o8BsQ51y_/view?usp=sharing) detailing these conditions.
Alicia Martinez-Garcia (Jan 14 2021 at 18:15):
Now, we are in this session: Educational session: RDA FAIR metrics - Oya Beyan - Thursday - 10 am PT / 13 ET / 19 CET. Join us!
Floyd Eisenberg (Jan 14 2021 at 19:26):
@Oya Deniz Beyan Xn you post a link to the slide deck you used to present the RDA FAIR metrics session? Thank you
Alicia Martinez-Garcia (Jan 15 2021 at 09:42):
@Oya Deniz Beyan if you prefer, you could send me the presentation and I could update it in the FAIR track page in Confluence. Thank you in advance.
Ian D Harrow (Jan 15 2021 at 09:59):
Cathrine's slides too?
Alicia Martinez-Garcia (Jan 15 2021 at 13:48):
@Ian D Harrow Off course, thank you very much
Alicia Martinez-Garcia (Jan 15 2021 at 13:49):
This is a kind reminder: the first break-out session (sharing experiences - Making Biomedical Research Informatics Computing System -BRICS- data FAIR) of the FAIR track is going to start now at 6 am PT / 9 am ET / 15 CET
Alicia Martinez-Garcia (Jan 15 2021 at 16:08):
Now, we are in this session: Break-out session: FAIR principles in the development of Evidence-related FHIR Resources - Brian S. Alper - Fri - 8 am PT / 11 am ET / 17 CET. Join us!
Matthias Löbe (Jan 15 2021 at 16:08):
Does anyone know what happend to FHIR DataElement [http://hl7.org/fhir/STU3/dataelement.html] in R4?
Matthias Löbe (Jan 15 2021 at 16:46):
@Brian Alper : Can you provide a list of the resources you introduced?
Melissa Haendel (Jan 15 2021 at 18:13):
you may be interested in our work on evidence modeling for genetics/research: https://github.com/monarch-initiative/SEPIO-ontology (listening to the COKA/EBMonFHIR report out)
Brian Alper (Jan 15 2021 at 18:58):
Resources I introduced include Citation, Evidence, EvidenceReport, EvidenceVariable and Group as well as datatypes Statistic and OrderedDistribution.
Ian D Harrow (Jan 15 2021 at 20:21):
On FAIR vocabularies/ontologies the OBO principles are useful metrics: http://www.obofoundry.org/principles/fp-000-summary.html
Alicia Martinez-Garcia (Jan 15 2021 at 20:31):
Dear colleagues. In kick off session, we asked to the audience the following question: "What is your opinion regarding the use of health data for research purposes PARPASIS following FAIR principles?". Now, considering we are at the end of the event, we would like to collect answers of the same questions, to measure the FAIR awareness improvement reached thanks to this event. So, if you voted in kick off session, please, go to www.menti.com and answer the question using the code 35 10 91 9. Thank you very much in advance.
Oya Deniz Beyan (Jan 27 2021 at 14:44):
Floyd Eisenberg said:
Oya Deniz Beyan Xn you post a link to the slide deck you used to present the RDA FAIR metrics session? Thank you
sorry fo the late reply https://docs.google.com/presentation/d/15kBRClF-5qJ3VvvwMU6_vimYyopKO1Pv/edit#slide=id.p30
Oya Deniz Beyan (Jan 27 2021 at 14:54):
@Brian Alper I checked how PICO ontology (https://linkeddata.cochrane.org/pico-ontology) aligns with Evidence resource . I think Evidence.exposureBackground= http://data.cochrane.org/ontologies/pico/Population; Evidence.exposureVariant=Intervention; Evidence.outcome== http://data.cochrane.org/ontologies/pico/Outcome. It might be good to have an explicitly aligment
Brian Alper (Jan 27 2021 at 19:20):
The Evidence Resource in R4 is not the structure where PICO ontology will be best mapped. The Evidence Resource in R5 (and soon R4B) uses Evidence.variableDefinition with elements description, note, variableRole (to code the role eg population or exposure), observed, intended, and directnessMatch. We then use EvidenceVariable Resources for the specific variable definitions, but can use Group Resource when the variable role is population or subpopulation to coordinate with other FHIR population descriptions using Group. The EvidenceVariable and Group Resources could be mapped to PICO ontology instances.
Last updated: Apr 12 2022 at 19:14 UTC
