Documentation updates

[joeflack4]

Sub-task list

• [ ] 1. New OMIM ingest process
• [ ] 2. Descriptions of source files

Sub-task details

1. New OMIM ingest process

In last Mondo Friday meeting, was written:

need documentation for new OMIM ingest process

@nicolevasilevsky @matentzn I'm not sure what this new process is? The process is the same right now. Just been doing small tweaks over time. Is this talking about how we're starting to handle gene::disease relationships from morbidmap.txt?

2. Descriptions of source files

Sabrina got a start on it here: https://docs.google.com/spreadsheets/d/1kPthfc9ailWhKSy5TVSQMAwkJGjW25MCCgRW-0DaiVc/edit?usp=sharing

More info

Copy/paste from workflowy so I can move this out of personal notes and into issues: Docs: need documentation for new OMIM ingest process #83

• (About)
  • https://github.com/monarch-initiative/omim/issues/83
• docs/sources/omim.md
• 1. let them know skipping the MIM #s, and as much detail as i can add about that
     • research: Any documentation for morbidmap.txt
• 2. itd be helpful for sabrina if i included:
     • list of all the files we are downloading from omim (.txt)
• 3. RO (contributes to)
     • nico asked something of me with relation to this: https://github.com/monarch-initiative/omim/issues/75#issuecomment-1320575124

[nicolevasilevsky]

We used to do this: https://mondo.readthedocs.io/en/latest/editors-guide/omim-slurp/

But I'm unclear if we are still meant to be doing this? cc @matentzn

@joeflack4 the other task is for you to write up documentation of how the OMIM sync/slurp works now. I am not clear how this process works. Thanks!

[joeflack4]

@nicolevasilevsky will do. Also, Nico just adding this here for me. One particular that Nico asked is to our use of RO when there is more than 1 mapping evidence: https://github.com/monarch-initiative/omim/issues/75#issuecomment-1320854609