ga4gh / ga4gh/experiments-metadata

Usefulness of having "experiment_type” and “assay_type” in two separate fields

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Description

Feedback received from Sveinung Gundersen during the Open for Comments period:

7. Another point of feedback that just came up when trying to adopt the Experiments metadata attributes into our harmonised data model: https://docs.google.com/spreadsheets/d/1wqlcnYHwT9yQVCj525n41LQJENbgHeQfn7V572e8ev8/edit?gid=1471635995
What is the reasoning behind including both “experiment_type” and “assay_type”. It seems experiment_type (e.g. “DNA sequencing assay”) is only a generalization of assay_type (e.g. “whole genome sequencing assay”), but such generalizations should (at least in principle) be possible to derive from the ontology (in the example here, “DNA sequencing assay” is the parent term of “whole genome sequencing assay”. Also, if the point is to specify the molecule that are sequenced, there is a “molecule_type” field exactly for that!

I am filling out example data for our data model, and in the chosen example, which is a “ChIP-seq assay”, I have a hard time determining what should go into “experiment_type”. Should that be the more general “ChIP assay”, the even more general “DNA sequencing assay”, or something else?

I am now leaning towards thinking that the “experiment_type” field is unnecessary.

Contributor guide

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Research direction

Start by reviewing the Open for Comments feedback and the linked Google Sheets example for the current meanings of experiment_type, assay_type, and molecule_type. Determine whether the schema needs a decision or change, and consider the work complete when the field semantics or removal are explicitly agreed and reflected in the metadata model.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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