Mapping: notes on mappings from 230330

[sabrinatoro]

First of all, the lexical matches are great!!! Thank you for all your work.

Here are the small things I have found. I think these are mostly related to the data itself, and therefore it is mostly for curators to be aware of when reviewing.

unmapped_doid_lex_exact.tsv The exact lexical matches are okay (I haven’t seen any issues). Some capitalization needs to be reviewed, but this is very minimal (I found only 1 term that needed capitalization... though I cannot tell how many had the correct capitalization)

unmapped_doid_lex.tsv

• Mondo and DO handle OMIM synonyms differently. Therefore some synonyms coming from OMIM are shown as “related” in Mondo, but are “exact” or are the term name in DO. This means that DO would have exact synonyms that would match the mondo label for example. This is just how the data is, so I don't think we can do something at the level of the matches, but curators should definitely keep this in mind when reviewing as the mapping might still be correct. Example: …

• A lot of issues are due to difference in the splitting and lumping in MONDO versus DO:

  • the same DO:id might be mapped to different MONDO terms reported in the same mapping file. Curators should be aware when reviewing.
  • Some DO terms are mapped to Mondo terms that already have exact mapping to other DO terms. See issue #https://github.com/monarch-initiative/mondo-ingest/issues/260
  • In Mondo, synonyms coming from an original DO term that has since then been split (this needs to be reviewed by a curator as 2 or 3 DO terms end up being matched to the same Mondo term)

In summary: I think that all the issues I have found are due to errors in the data itself. Therefore, curators should review the unmapped_..._lex.tsv files carefully and check for multiple source terms mapping to the same mondo, and vice versa.

Question/request: How should we keep track of the mappings to be ignored based on incorrect data? (ie the mappings are "correct" based on the mapping rules, but "incorrect" because the data is incorrect)

[sabrinatoro]

@matentzn @hrshdhgd @joeflack4 @nicolevasilevsky

[joeflack4]

Maybe something like a new file config/mapping_exclusions.tsv? I suppose it would have the Mondo CURIE in one column, and native CURIE in another column, and then maybe an exclusion reason column, and I don't know if it makes sense to include the code for that like MONDO:badData within the normal exclusions enum, or make a new enum just for mappings.

@matentzn It seems like the focus here is on lexmatch, but if for some reason you think my scripts will need any updates, I'll stay posted.

[matentzn]

It is not necessarily just lexmatch, I answered here: https://github.com/monarch-initiative/mondo-ingest/issues/261

We should most definitely keep a record of false mappings.

[matentzn]

@sabrinatoro we need a paragraph on your "handles syn. differently in DO" observation for the paper. Could you write 3 sentences here that explains exactly what is going on, with an example?