Documentation issue - MIxS update

[ssarrafan]

Update MIxS to use v6

[mslarae13]

Currently, from what I can tell, an instance of MIxS v5 was pulled and added to the schema. This should be removed. MIxS v6 read the docs should be pulled from MIxS instead of copying an instance.

@cmungall , @wdduncan ... can you chime in if you agree with this / provide some context on what we need to do to accomplish this? Will this affect the portal .. or break anything else?

[wdduncan]

@mslarae13 Has MIXS 6 been released yet? I didn't think it had.

Once it is released, our plan is to update the schema with the new version.

[ssarrafan]

Moving documentation issue to April per @kwdavenport

[mslarae13]

@turbomam I think this should be assigned to you? I have NO idea where the MIxS v6 documentation is, or how we will pull it in.

If you disagree, we should disucss soon to ensure the documentation gets completed for the April release.

[ssarrafan]

@turbomam I will re-assign to you.

[turbomam]

I'm going to start collecting some notes here. I don't mean to say that this is all the documentation I'll be providing!.

The mechanism for integrating MIxS terms, specifically those from 12 different packages, is briefly described in nmdc-schema PR #292

Especially see the quick and dirty code that does the integration, util/reconsititute_mixs.py and the resulting LinkML file, src/schema/mixs_6_for_nmdc.yaml

The process is started by examining all slots included by the previous, essentially static MIxS5 import, ../src/schema/mixs.yaml, all slots assigned to the NMDC biosample class, and all classes assigned to the evolving NMDC DH schema, for example here.

I can include/check all slots for a MIMS sample, like the environmental section, etc. (but not the grouping slots themselves!)

section	core terms
environment	10
investigation	6
nucleic acid sequence source	25
sequencing	57

like

• environment
  • alt
  • collection_date
  • depth
  • elev
  • env_broad_scale
  • env_local_scale
  • env_medium
  • geo_loc_name
  • lat_lon
  • temp
• investigation
  • samp_name
  • samp_taxon_id
  • project_name
  • experimental_factor
  • neg_cont_type
  • pos_cont_type

[turbomam]

Rough stream of consciousness draft: Integration of MIxS into the NMDC schema: tech notes

[ssarrafan]

@kwdavenport can we consider this issue closed?

[kwdavenport]

I don't think so. I'll be talking with Mark and Montana tomorrow. I am thinking it should go into the May sprint, but I can let you know after our meeting (at 8am PT).

---

From: ssarrafan @.***> Sent: Thursday, April 28, 2022 3:54 PM To: microbiomedata/NMDC_documentation Cc: Davenport, Karen Walston; Mention Subject: [EXTERNAL] Re: [microbiomedata/NMDC_documentation] Documentation issue - MIxS update (Issue #5)

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[ssarrafan]

I haven't heard back so I will move this to the May sprint @kwdavenport @turbomam

[turbomam]

How can we get the best, most automated integration between @sujaypatil96's https://microbiomedata.github.io/mixs and https://nmdc-docs-sphinx.readthedocs.io/en/latest/reference/metadata/combined_schema_docs.html#mixs-soil-package (for example), which is managed by @kwdavenport and Yan?

[turbomam]

https://github.com/cidgoh/DataHarmonizer/issues/313

[turbomam]

@ssarrafan : There are Makefile steps for ongoing integration of MIxS terms into the NMDC schema, but it should be automated

I haven't really done anything to contribute to the NMDC documentation pages yet. The MIxS content seems like a mixture of narrative content with some cut-and-past that may not be completely accurate any more.

[ssarrafan]

I'll move this to July then but let me know if you are not planning to work on it and I can move it to the backlog. I'm not sure how high the priority for this is? @cmungall @emileyfadrosh

[ssarrafan]

This issue has been in multiple sprints. I'm going to move it to the backlog. Let me know if it should be moved to the active sprint. @turbomam @mslarae13

[ssarrafan]

@shreddd if we discuss documentation at SW Best Practices this is a good issue to refer to