ejp-rd-vp/cde-semantic-model-implementations

This repository contains implementation artifacts related to CDE-semantic-model

cde-semantic-model-implementations's Issues

Multiple variants

@markwilkinson Based on my recent interactions with registry providers. I noticed that often multiple variants are reported per patient. Is it possible to change this csv template to take multiple values for hgvs_string column?

non resolvable edam uris

http://edamontology.org/data_1153 for OMIM ID
http://edamontology.org/data_2295 for HGNC ID are non resolvable, please update according to info on stable version here http://edamontology.org/page

CSV template for consent not clear

In the explanatory text it says:
consent_template: the URI/URL to the raw (not patient-filled) consent document

But it is not clear what exactly needs to be filled in. the answer from fairification steward was that this was not yet correct. Can you please correct this or explain what needs to be done?

Pim

Clinvar URL as type

ClinVar variant url used as rdf:type of variant attribute in undiagnosed module. Is it possible to use sio:sequence variation notation as rdf:type of variant attribute and add ClinVar URI to variant attribute node with sio: refers to predicate?

HGVS pattern

Two different patterns are used to describe HGVS names in undiagnosed and genetic diagnosis modules. Is it possible to use same pattern in these two modules to describe HGVS name?

Please explain "context_id: Time-oriented identifier to relate models with same date of observation"

Hi all,

I'm sorry but I don't understand the column context_id in CDE.csv

The documentation says that this is a "Time-oriented identifier to relate models with same date of observation". If it's really only about the date then why would you need an extra column for that, there already are columns startdate and enddate for each process...?

Or is this introducing some concept of "encounter" or "visit", e.g. to link retrospective data and prospective data?

Maybe let's discuss an example:
A patient had first contact with specialised center on 2020-12-01.
For this patient, a clinical diagnosis was established on 2020-12-05.
This patient signed informed consent for a patient registry on 2020-12-06.
All these infos were entered into a registry during some "enrolment"-event on 2020-12-06.
=> Given that, what are the expected values for column context_id for Care_pathway, Diagnosis, Date_of_diagnosis, Consent?

Thanks!

Dagmar