Closed Martin-Kuhl closed 1 year ago
@Brilator Could you please check the GEO minimal templates?
Was a bit quick in pushing to the main branch. Will open a pull request next time..
bio entity
is still "wanted"Sample Name
), which the facility might pick up (Source Name
). GEO has a new template for submission.
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)
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.
ah, sorry, I forgot "molecule" comes from GEO.
And true: multiple templates per sheet are not ideal..
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.