Confirm metadata call date with Conny

[ESapenaVentura]

No description provided.

[ESapenaVentura]

I'm trying to download the metadata - so far, not very successful! Asked conny to re-send the spreadsheet

[ESapenaVentura]

Renaming fields

Conny has asked for some fields to be renamed. However, I am not fully convinced on these:

• name to sample ID: name is the title used by biosamples to define the sample ID. We could add an extra field of metadata, according to GSC, called samp_name https://genomicsstandardsconsortium.github.io/mixs/0001107/, but seems awfully redundant. Need to ask why this is needed
• biome to sample type. This one may be fine; biome is a MICROBE-unique field, so we could rename it. No strong feelings about this one
• local environmental context to type of ecosystem: not really a thing I can see in GSC, is it an ISO standard??
• environmental medium to ``: Don't really understand this one, although there is a point to make here that we may need to get rid of biome for this term, I think it fits better.
• pH to soil pH: pH is a GSC approved term, and in the context of the metadata it makes sense that it's just pH
• total organic carbon to soil total organic carbon: again, this is a GSC approved field and adding the soil part is redundant based on the other parameters

Clarifications

Some of the fields needed clarifications from Conny. I'll write my thoughts here:

• 'unclear to me: What is "temperate biome"? (is there a definition?) : I think here there is a misunderstanding about the ontologies. The description of the checklist encourages, for this field (broad-scale environmental context) the use of terms under ENVO. These terms come with descriptions of their own.
• which checklist?: Need to explain to her that this is the unique identifier of the checklist in an ENA context. I also may need some clarification as to how these identifiers are formed, since the GSC MIxS page seems to have its own identifiers??
• Comment on composite design/sieving: I really don't know what to tell her here; this is the field as per the checklist
• Move fields up/down: There is no specified order for any of the fields, nor I think we should enforce importance based on that. We can tailor our services to show what's important first.
• Collection method: there is a sample collection method field, specifically from the checklist, that we could add. On the topic of the methods; we should enforce a public page like protocols.io and link from there. I don't think providing links to sharepoint, being private, is a good idea.

Add to soil harmonisation task

Some of the points are valid and straight-forward things to implement:

• Add unit to depth
• Add unit to elevation
• add unit to latitude
• add unit to longitude

## From MICROBE guidance doc comments

Some fields we have:

• preservation date
• preservation method
• Stirage duration of preserved sample until DNA isolation (aka, timepoint, or assay finish date - `assay start date)
• DNA isolation date (aka, analysis date)

Some fields we don't have:

• Storage duration of native sample until preservation
• DNA isolation method/kit: also, we need some specificity here
• DNA storage buffer

Need some clarification on the rest of the storage conditions, as I don't understand them

[ESapenaVentura]

Conny answered - Probably setting up meeting mid-december

[Jeena-Rajan]

Confirm metadata call date with Conny in January