Cheek Samples #597
Cheek Samples #597
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| 'env_material': 'sebum', | ||
| 'env_package': 'human-skin', | ||
| 'description': 'Microsetta Initiative Cheek sample', | ||
| 'host_body_site': 'UBERON:skin of head'} | ||
| } |
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In October, I had to check the constant metadata values for human cheek with Gail Ackermann, who is the final arbiter of these values in the Knight lab; she indicated that current best practice (it is constantly changing!) is that host_body_site should be UBERON: cheek, sample_type should be skin of cheek, and env_material should be sebum material. Where does CMI get its guidance from? I'm not surprised there are differences, but I'd be happier if we could align them ...
Also, for some point in the future, it would be nice to get these constants updated to v2 of EMPO, which specifies 4 levels instead of 3 (and it isn't just a bolt-on of one more level ... the whole level structure changes :-/ )
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The values here are based on what was used for skin samples when AGP was actively collecting/processing them. We'll update these (cheek and other types) to reflect current recommendations.
This PR is intended to address the needs surrounding collecting skin samples from cheeks:
It adds Cheek as a valid sample site and adds applicable constants to the metadata pulldown process.
It adds the notion of "barcode metadata," which are fields that are strictly linked to samples, rather than implicitly linked to samples via sources (as all of the existing survey questions are).
From a UX perspective, the reason for this deviation is the temporal importance of the questions. While all metadata are temporally linked to samples, and we strive to close that gap as much as possible, these particular questions are directly related to preparation for the sample collection.
From a technical perspective, I opted to establish a new avenue of storage because neither existing method felt appropriate:
The middle ground I established is sufficient for the purpose - including data validation - and could be extended into a more robust framework if future use calls for it.
Corresponding microsetta-interface PR is biocore/microsetta-interface#334