eDNA is here!

[mkoo]

I thought we would tackle this eventually-- looks like now is good.

We have a few samples of eDNA uploaded (https://geome-db.org/workbench/project-overview?projectId=365). I will be contacting the project owner, but meanwhile here's a few tweaks we need on our side.

• add new sampleType = water and soil
• in required genus field, I think we need to allow non-generic value to indicate eDNA, otherwise the api cannot chart since it fails taxonomy-checks. I suggest allowing genus = eDNA or similar, allow specificEpithet = NULL

@jdeck88 thoughts on last point?

[jdeck88]

i would suggest "Unknown" for genus and "unknown" for specificEpithet. This is our work-around for cases that do not know, for example, country or year. BasisOfRecord would be "MaterialSample" John

On Sun, Dec 13, 2020 at 8:10 PM Michelle Koo notifications@github.com wrote:

I thought we would tackle this eventually-- looks like now is good.

We have a few samples of eDNA uploaded ( https://geome-db.org/workbench/project-overview?projectId=365). I will be contacting the project owner, but meanwhile here's a few tweaks we need on our side.

• add new sampleType = water and soil
• in required genus field, I think we need to allow non-generic value to indicate eDNA, otherwise the api cannot chart since it fails taxonomy-checks. I suggest allowing genus = eDNA or similar, allow specificEpithet = NULL

@jdeck88 https://github.com/jdeck88 thoughts on last point?

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[mkoo]

However, "Unknowns" get tossed out of charts and still assumes there is an organism associated with the sample. Unless we can conditionally have basisofRecord= MaterialSample, then genus=unknown could be included in a chart. Seems like a lot of rules still. (btw, the user did use MaterialSample for basisofRecord)

How about genus =  Sample ? then we can still include these data in a histogram and other charts. 

What would be easier to graph @birbjam ? if genus = unknown and basisofRecord= MaterialSample, then display those separately as eDNA records? Or if genus = Sample

here's the use case: https://amphibiandisease.org/projects/?id=365

[mkoo]

Following up on this issue as I would like to write up guidelines and contact our friends at the above project...

• sampleType is straightforward as its controlled vocab, not defined by Geome -- I will update.

• Can we tweak Genus to allow Sample or Other as I think Unknown is inaccurate or misleading. @jdeck88

• and lastly can charts be changed to allow these conditions listed above? @birbjam

Let me know if we need to reserve this for a chat!