Consolidate storage condition terms

[pvangay]

From MIxS

• short name: store_cond
• attribute name: storage conditions (fresh/frozen/other)
• example: -80°C, up to 6 weeks
• definition: Explain how and for how long the soil sample was stored before DNA extraction
• value syntax: {text};{duration}

I thought that there was a decision to break up this term into two terms? I presume, storage temperature and storage duration?

• I see "sample storage temperature" and "EMSL Sample Storage Temperature, deg. C" in the DH interface -- these should be consolidated into one.
• I see that "storage conditions" is still in the DH interface and appears to be an enumeration. I don't think this is correct usage of this term and likely resulted from the attribute name (see above). My suggestion is to remove this term.
• Do we need a new term to represent the sample storage duration? Did I miss this in the DH interface?

Please review @mslarae13 and reassign to @turbomam once next steps are determined.

[turbomam]

This makes sense and I will wait for @mslarae13's feedback.

I check several different resources when researching a DH issue like this. Apologies if you already know all of this!

• The hosted DH interface, at a location like https://data.dev.microbiomedata.org/submission/samples
• Soil-NMDC-Template_Compiled (using "find in all sheets", but generally ignoring a few sheets like 'example use', 'soil_biosample_regex_insight_snapshot')
• The compiled DH interfaces, namely the data.tsv or the data.js, which can be access form a location like https://github.com/microbiomedata/DataHarmonizer/tree/master/docs/template/soil_emsl_jgi_mg
  • I really like looking at data.tsv because all of the DH columns are represented as rows on a single sheet.

In this case, I have prepared a summary of all what I believe to be all data.tsv rows relating to sample storage. It also confirms the provenance of each term. The necessary and sufficient step was filtering the label column on 'stora'. I also looked for 'store' but didn't get any hits. Searching for 'stor' also brings up all of the 'history' columns.

Ontology ID	label
emsl:EMSL_store_temp	EMSL Sample Storage Temperature, deg. C
mixs_modified:storage_condt	storage conditions
MIXS:0000110	sample storage temperature

[mslarae13]

I see "sample storage temperature" and "EMSL Sample Storage Temperature, deg. C" in the DH interface -- these should be consolidated into one.

• samp_store_temp isn't in the MIxS soil package. It's in plant & sediment though, so it's borrowed. Storage conditions and EMSL sample storage are meant to capture the sample sent to EMSL. General sample storage temperature is like "what did you store your sample at before taking these subsample" ... For example.. from the field I put my soil at 4C but the subsample I'm sending to EMSL is stored at -80C. This could be because you are preserving the microbes of the parent soil but want to stall biology in the sample you're sending to EMSL. This isn't totally clear in the MIxS definition, or what we've provided here... We replaced storage conditions because it specifically called out the DNA sample. I don't think consolidating them into one is the answer.. but maybe deciding if "sample storage temperature" is actually important for this stage of metadata & if it is, adding clarification.

I see that "storage conditions" is still in the DH interface and appears to be an enumeration. I don't think this is correct usage of this term and likely resulted from the attribute name (see above). My suggestion is to remove this term. Do we need a new term to represent the sample storage duration? Did I miss this in the DH interface?

• storage conditions is actually an EMSL term. It should be moved. It's for us to know if a sample is fresh, it can be at 4C or room temperature. If a sample is air dried, it could be frozen or at room temp or at 4C , etc.

[pvangay]

Ok what I'm reading here is that one action is to: remove "EMSL Sample Storage Temperature, deg. C" and keep "sample storage temperature".

That leaves "storage conditions". Right now, "storage conditions" and "sample storage temperature" are both in MixS modified. Do we need to remove "storage conditions" and replace it with a "sample storage duration"? @mslarae13