Make sure that `parse` can work without needing to pass a metadata `.yml`

[joeflack4]

See: https://github.com/mapping-commons/sssom-py/issues/227#issuecomment-1101205374

The following should work w/out needing a metadata .yml: sssom parse omim.json -I obographs-json -o omim.sssom.tsv

It should warn and populate with defaults if any of the following are missing:

• license
• (the other ones in the yaml)

And should have the prefixes for HGNC, Orphanet, etc loaded.

[matentzn]

@joeflack4 We are working on related code so its probably best if @hrshdhgd takes care of this.

[cmungall]

Note that it's now possible to use OAK to export SSSOM on either a per-term or per-ontology basis

https://incatools.github.io/ontology-access-kit/cli.html#runoak-mappings

longer term we may want sssom-py to focus on processing operations and leave conversion operations to other libs?

[matentzn]

I think there are so many non-ontology parsing processes we are working on (alignment API, complex map), that probably some redundancy is unavoidable. Basically the only piece of overlap is the obographs json parser - I think this is ok.

[cmungall]

Agreed, just wanted to make sure we weren’t spending too much time on it

On Mon, May 2, 2022 at 10:44 AM Nico Matentzoglu @.***> wrote:

I think there are so many non-ontology parsing processes we are working on (alignment API, complex map), that probably some redundancy is unavoidable. Basically the only piece of overlap is the obographs json parser - I think this is ok.

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[matentzn]

Hopefully fixed by #238