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Space where we collaborate on assembling the ontology and shape files
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replicates in our ontology #7

Open kmexter opened 1 month ago

kmexter commented 1 month ago

Putting on me for now because I still need input from others, but I will forget if I don't do this

The "replicate" column in the logsheets should be added to https://github.com/emo-bon/observatory-profile/blob/main/logsheet_schema_extended.csv. with http://vocab.nerc.ac.uk/collection/P01/current/IDTCRE01/ and how will it then be treated in https://github.com/emo-bon/emobon-ontology/blob/master/ontology/EmoBonOntology_sampleExtension.ttl?

--> CHECK with EMO BON HQ if that is the correct definition, and it should not be https://vocab.nerc.ac.uk/collection/P01/current/IDBIRE01/ instead.

Naturally, field replicate for ARMS will be http://vocab.nerc.ac.uk/collection/P01/current/IDSPRE01/

We will need IDs for blank (control) and negative also. I will have to consult - perhaps there is something in MiXS to be used here?

kmexter commented 5 days ago

I have to ask @cpavloud : are the replicates - by that I mean the 4 replicates collected per sample for wa, so, and arms - are they better described as http://vocab.nerc.ac.uk/collection/P01/current/IDBIRE01/ or as http://vocab.nerc.ac.uk/collection/P01/current/IDTCRE01/?

cpavloud commented 5 days ago

The correct definition is the technical replicate.

I don't think there is something in the MIxS for negative controls and blanks. In general, I have been using terms from EMPO (which unfortunarely doesn't have URL identifiers).

kmexter commented 4 days ago

thanks, have updated the logsheet schema accordingly, no further action required. however, passing this on to Laurian now because I added a term for ARMS_unit_id as well as the two types of replicate, but the former has no specific vocab term - there will be an ENVO term for "arms unit" and there is a BODC term for "replicate" and the combination of the two would suit us, but we need to discuss whether this is the way to go to include this column in our ttl/ontology. Note also @laurianvm that in that logsheet schema I had made some mistakes before in referring to the ARMS type (should be arms, not hard) and I missed out some values. We can check and discuss