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GenomicsStandardsConsortium / mixs

Minimum Information about any (X) Sequence” (MIxS) specification
https://w3id.org/mixs
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definition update : sample material processing #21

Closed only1chunts closed 3 years ago

only1chunts commented 5 years ago

Hi, Currently the definition for the attribute "sample material processing" is

Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2013-10-25) terms please see http://purl.bioontology.org/ontology/OBI

Having just been looking through the OBI terms it seems like the ONLY appropriate term in OBI for this field would be lavage ! Perhaps the definition of the term can be changed to:

A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.

ymgan commented 3 years ago

Unfortunately I am not familiar with the OBI terms. I thought there are many relevant vocabularies that can be used for this term under material processing.

I am wondering if it is possible for samples to undergo multiple processes? Should we define how those records should be documented in this field?

@lschriml @ramonawalls do you mind to please lend me a hand here? thank you so much!

lschriml commented 3 years ago

Looking at BioSample, how this term (sample material processing) has been used: 

    Stools Processing Device (bioMerieux) in combination with ZymoBIOMICS DNA Mini kit 
      (ZymoResearch)

     Fecal samples less than 6 hr old were collected from individual mice and stored at -80C 
         (doi:10.1186/s12866-018-1359-5). 

     flash frozen using LN2 and stored at -20C until processing.

--> this term is being populated with textual descriptions. Agree: remove the OBI reference.

Updated in MIxS 6 core and in each of the checklist

Cheers, Lynn