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ebi-ait / hca-ebi-wrangler-central

This repo is for tracking work related to wrangling datasets for the HCA, associated tasks and for maintaining related documentation.
https://ebi-ait.github.io/hca-ebi-wrangler-central/
Apache License 2.0
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Modelling Tier 2 in HCA metadata schema #1279

Closed arschat closed 3 weeks ago

arschat commented 4 months ago

In this ticket we will keep track of the discussions on how to model the Tier 2 fields across all bionetworks.

We have decided to model the Tier 2 fields in content specific modules rather than bionetwork modules.

For the lung bionetwork, we received a list of fields that are going to be part of their Tier 2 (mentioned in #1235). We've grouped them in 3 modules.

There is a PR for the addition of the medical_tests module in the donor level here. There is a $comment keyword added to specify that this is for lung bionetwork and that these fields describe the pulmonary_function_parameter.

arschat commented 3 months ago

Latest HLCA Tier 2 list of fields (apr-24)

arschat commented 3 months ago

After discussions with Amnon, the keyword $comment was replaced by the attribute bionetwork which allows an array of strings and conveys meaning compared to $comment. We dropped the pulmonary_function_parameter description in that attribute. bionetwork attribute is going to be filled only in non-generic fields. lung medical tests PR is now merged.

Next PR is smoking related fields.

arschat commented 4 weeks ago

In ticket #1313 we describe the modelling for dissociation protocol fields across different bionetworks.