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There are some missing MONDO mappings because some of the disease IDs are prefixed with "MIM:" rather than "OMIM:".
I would guess it's probably easier to translate those IDs in the 'did' column to "OMIM:" before you do the mapping than to patch it afterwards. Then those IDs can be more consistent in the other places they show up anyway
Here's an old response from Lars and others about OMIM and MIM being the same.
https://www.biostars.org/p/4271/
Here's the selection of missing MONDO IDs.
SELECT
did, mondo_xref.*
FROM
disease,
mondo_xref
WHERE
did LIKE 'MIM:%'
and mondo_xref.db = 'OMIM'
AND SUBSTRING_INDEX(did, ':', - 1) = mondo_xref.value
and mondo_xref.equiv_to
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