[New template] Create GEO minimal templates

nfdi4plants / Swate-templates

A collection of templates for Swate (https://github.com/nfdi4plants/Swate).

4 stars 18 forks source link

[New template] Create GEO minimal templates #27

Closed Martin-Kuhl closed 1 year ago

Martin-Kuhl commented 1 year ago

Is your feature request related to a problem? Please describe. As discussed yesterday, templates with the minimal required information by public repositories are desired.

Describe the solution you'd like Templates for growth, extraction, the assay, and computation only with the minimal required information by GEO.

Martin-Kuhl commented 1 year ago

@Brilator Could you please check the GEO minimal templates?

Martin-Kuhl commented 1 year ago

Was a bit quick in pushing to the main branch. Will open a pull request next time..

Brilator commented 1 year ago

Growth_GEO_minimal.xlsx

the only GEO-mandatory attribute: organism
the rest is rather generic and probably has limited use
Maybe the "organism" part could be covered with another very small template (currently called "plant_srouce.xlsx")

Extraction_GEO_minimal.xlsx

Not sure, if bio entity is still "wanted"

Computation_GEO_minimal.xlsx

Could be cut down into 1. Data filtering and 2. Read Alignment. But makes sense to keep them, since required like that for GEO.

Assay_GEO_minimal.xlsx

Could be cut down into 1. Library prep and 2. sequencing.
Rationale: these are somewhat independent protocols. Some labs prepare their own libraries and submit them to a facility. So at that point they also get an ID (Sample Name), which the facility might pick up (Source Name).

Martin-Kuhl commented 1 year ago

GEO has a new template for submission.

Growth

Tissue, cell line, or cell type is required. Genotype and treatment are the remaining suggestions by them.

Extraction

bio entity corresponds to molecule, which is still in the template. We could think about replacing it with molecule, but I think this can also be handled by a converter.

Assay

Do you think the size of the template in its current state is acceptable? If yes, I would keep the template as one, as I have the impression that users are somehow "overwhelmed" by more templates and thereby, worksheets in Excel

Brilator commented 1 year ago

Tissue, cell line, or cell type is required. Genotype and treatment are the remaining suggestions by them.

Ah, good to know. I didn't check the "mapping" sheet.

bio entity corresponds to molecule, which is still in the template. We could think about replacing it with molecule, but I think this can also be handled by a converter.

I'm just wondering if it's really used. If yes, it would be good to link it to a specific ontology and make selections easier. But this is somehow also linked to protocol type and technology type.

Do you think the size of the template in its current state is acceptable?

Yes

users are somehow "overwhelmed" by more templates and thereby, worksheets in Excel

Multiple templates could still be combined into one sheet. (e.g. plant source + plant growth + plant treatment, all with 3-4 building blocks)

Martin-Kuhl commented 1 year ago

I'm just wondering if it's really used. If yes, it would be good to link it to a specific ontology and make selections easier. But this is somehow also linked to protocol type and technology type.

I think the field is mandatory, too. But you are right, as they have a controlled vocabulary for the child terms of molecule. Accordingly, this can be handled via our ontology

Multiple templates could still be combined into one sheet. (e.g. plant source + plant growth + plant treatment, all with 3-4 building blocks)

Yes and no. Only one protocol type per Swate table is allowed. Splitting them would result in the need of two columns and just using one would result in the template as it currently is.

Brilator commented 1 year ago

ah, sorry, I forgot "molecule" comes from GEO.

And true: multiple templates per sheet are not ideal..