Add Monarch-KG mappings

[glass-ships]

Attempts to resolve #23 (see issue for relevant errors)

• [x] Update mondo mapping file
• [x] Add monarch gene mapping (will require LFS)
  • [ ] Add an actual mapping_set_id (not sure what this should be)
• [ ] Resolve issues with missing mapping_justification column in apparently every file
• [x] Update SSSOM-Py to >=0.3.40

[glass-ships]

In the meantime I've manually grabbed the files we use and added them to the mappings/ directory, if preferred we can figure out the makefile/boomer/etc. stuff out later

[hrshdhgd]

Looks good to me so far. The GH action fail may be fixed by adding version: 1.3.2 under with: in the workflow test.yaml

- name: Install Poetry
        uses: snok/install-poetry@v1
        with:
          virtualenvs-create: true
          virtualenvs-in-project: true
          version: 1.3.2

[glass-ships]

The main thing holding it back as far as i can tell is the missing mapping_justification column in what appears to be every file, but it's not clear to me where/how to fix this with how the repository works. any suggestions?

[hrshdhgd]

Is it the same issue that you had in the koza PR?

[matentzn]

@glass-ships can you spend some time to go through: https://mapping-commons.github.io/sssom/tutorial/

This should give you all the answers for how to construct a valid SSSOM file.

mapping_justification needs to be added to every SSSOM table!

[glass-ships]

@hrshdhgd yes it seems so @matentzn i'm familiar with the fact that the mapping_justification column needs to exist in every sssom file. as i've mentioned, my confusion comes from the way this repository works, the boomer stuff, the templates, the various files. i don't understand where this column needs to be added within the context of this repository. if getting clear instructions or feedback isn't feasible, i'd recommend @kevinschaper and myself work on a new version of this repository which is more streamlined, clear, and well documented

[matentzn]

Got it. Ok! We can meet together so I can explain to you. Wednesday 27th September?

[glass-ships]

sure, that day works for me. we can coordinate on slack to pick a time if need be

[glass-ships]

Closing in favor of #25