mixs MISIP-MIMS & MISIP-MIMARKS checklist addition

Collection of issues for addition to MIxS to create SIP checklist (SIP-MIMS & SIP-MIMARKS) Some term descriptions, examples, and syntax are still being updated (2023-06-05)

[x] New term proposal : isotope
[x] New term proposal : isotopologue
[x] New term proposal :isotopolog_label
[x] New term proposal :isotopolog_approach
[x] New term proposal :gradient_position
[x] New term proposal :gradient_pos_density
[x] New term proposal :gradient_pos_rel_am
[x] New term proposal :sip_method
[ ] Include source_mat_id in SIP checklist
[x] https://github.com/GenomicsStandardsConsortium/mixs/issues/584
[x] New term proposal :isotopolog_atom_pos
[x] New term proposal :isotopolog_dose
[x] https://github.com/GenomicsStandardsConsortium/mixs/issues/587
[x] New term proposal :isotopolog_incu_time
[x] New term proposal :internal_standard

Additional Term, not MISIP specific

[x] https://github.com/GenomicsStandardsConsortium/mixs/issues/290
[x] #640

Checklists MISIP was designed to be paired with an extension and a checklist. So a 3 combination. This is not likely to happen for v7. As such, I'm proposing the addition of MISIP-MIMARKS and MISIP-MIMS.

[ ] #1000
[ ] #1001

Any other checklists that should definitely be matchable with MISIP?

Jun 02 '23 19:06 mslarae13

source_mat_ID was supposed to link to the sample that was collected in the field / experimental sample.

should be these samples came from the same soil

Jun 06 '23 15:06 mslarae13

Okay! source_mat_ID may not be appropriate for this then. Is there an existing MIxS field that fits this better? Otherwise, we can use a new term (we briefly talked about prefractionation_ID ?)

Jun 06 '23 21:06 simpso91

from my perspective, source_mat_id is correct .. @only1chunts curious on your thoughts.

We need to be able to say SIP sample or fractionated DNA 1,2,and 3 all came from soil A.

Jun 16 '23 21:06 mslarae13

elution volume and DNA concentration request for calculating concentration DNA concentration needs added. To discuss To do: check if elution volume exists.

Aug 03 '23 18:08 mslarae13

@only1chunts I've looked through GSC's checklists and extensions and didn't see a DNA concentration slot or elution volume. I can make 2 more issues to add these, but i wanted to check with you on how best to do this.

These 2 terms seem valuable to the other checklists. Not just MISIP. Should I still put them in this one?

Also, FYI, I will likely miss the compliance and interoperability call unfortunately. I have a week long training to attend. Do you know if it's still scheduled for the 26th or might it be moved?

Sep 12 '23 21:09 mslarae13

@mslarae13 - we also requested a term for dna concentration for the urobiome package. Details are in https://github.com/GenomicsStandardsConsortium/mixs/issues/290

Sep 12 '23 22:09 lakarstens

@only1chunts should we make an issue for source_mat_id?

Oct 17 '23 22:10 mslarae13

Until we reach a point in the Link-ML work where multiple checklists and extensions can be combined we probably need to consider these are multiple (3) new checklists, e.g SIP-MIMS (or maybe it should be MIMS-SIP? ) and SIP-MIMARKS-Survey and SIP-MIMARKS-Cultured, (or does the SIP part only relevant for one of those?)

Oct 25 '23 09:10 only1chunts