reopened: Questions and requests regarding options in ReDU metadata

[YasinEl]

Transferred from from: mwang87/ReDU-MS2-GNPS#280

[YasinEl]

Hello,

thank you for contributing!

add 1) Interesting. We currently do not have term for "infected" but would sure be interesting to add something like that. I would for now suggest to add a term "infected organism" to SampleTypeSub1. Do you think that would be enough for now? You can also add another column to your redu table giving the infecting organism in the same format as the NCBITaxonomy if the organism is known. We wont use it for now but maybe we can add another controlled ontology column in the future if this is something that comes up more often.

add 2) I have now added a term "pool_QC" for SampleType and SampleTypeSub1 that can be used for pooled samples.

add 3) For SampleExtractionMethod we have a term "methanol-water (4:1)" which should correspond to 85% methanol.

add 4) For InternalStandardsUsed I have now added "caffeine;sambunigrin"

add 5) Is https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1002280 the instrument you mean? If yes the respective ReDU term is "compact|MS:1002280"

Let me know if this solves everything?

[MetteMariedk]

Hi,

Thank you for your elaborate and quick reply!

1. Perhaps "infected tissue" as SampleTypeSub1 could be an idea? In this case, I could choose this for infected samples and just "tissue" for control samples. What do you think?
   I think it is a good idea to add another column with information on the NCBITaxonomy of the infecting organism, I'll do that.

Regarding 2), 3) + 4) sounds good! However, they do not appear in my local copy of the ReDU template - would I have to download a newer version?

5. I think that's correct. Thanks!

Best,
Mette Marie

[YasinEl]

Actually, regarding the infection. I just realized that within the DOID column we have the term "fungal infectious disease" (https://www.ebi.ac.uk/ols4/ontologies/doid/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_1564?lang=en). Within in the UBERONBODYPART column you could the specify the relevant tissue or bio fluid. Would that accurately represent your samples?

Regarding the infecting organism, I suggest adding an "Infecting_NCBITaxonomy" column with the same requirements as the NCBITaxonomy column. It won't get used/displayed in the selection page (https://redu.gnps2.org/selection/) for now but I will add the column if this comes up more often. Until then people can see this added column by looking at your uploaded sheet directly. Does that work for you?

Regarding, the terms not showing up in your local copy: At least "methanol-water (4:1)" should show up in the Allowed Terms sheet (https://docs.google.com/spreadsheets/d/10U0xnJUKa_mD0H_9suH1KJAlJD9io9e4chBX8EAHneE/edit?usp=sharing). The others terms ("caffeine;sambunigrin" and "pool_QC") won't show up before I push the changes, but you can already submit your ReDU sheet and they will be accepted into ReDU as soon as we deploy the changes.