MISIP-MIMS & MISIP-MIMARKS checklist addition

[mslarae13]

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)

• [ ] New term proposal : isotope
• [ ] New term proposal : isotopologue
• [ ] New term proposal :isotopolog_label
• [ ] New term proposal :isotopolog_approach
• [ ] New term proposal :gradient_position
• [ ] New term proposal :gradient_pos_density
• [ ] New term proposal :gradient_pos_rel_am
• [ ] New term proposal :sip_method
• [ ] Include source_mat_id in SIP checklist
• [ ] New term proposal :isotopolog_atom_per
• [ ] New term proposal :isotopolog_atom_pos
• [ ] New term proposal :isotopolog_dose
• [ ] New term proposal :nucleobase_atom_perc
• [ ] New term proposal :isotopolog_incu_time
• [ ] New term proposal :internal_standard

Additional Term, not MISIP specific

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

[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

[simpso91]

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 ?)

[mslarae13]

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.

[mslarae13]

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

[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?

[lakarstens]

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

[mslarae13]

@only1chunts should we make an issue for source_mat_id?

[only1chunts]

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?)