Exact matches in ontology sources are only "Good" mapping confidence - should be high?

[jamesamcl]

Example to reproduce:

1. Don't search in any datasources, ontology source EFO
2. Search for "complement C4b measurement"

The confidence of the match is "Good". However, it is an exact string match - why is this not a "High" confidence match?

@henrietteharmse

[henrietteharmse]

HIGH confidence mappings are only associated with manually curated mappings. An exact match with an ontology term will give an at most GOOD mapping.

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On Mon, 15 Nov 2021 at 15:05, James McLaughlin ***@***.***> wrote: Example to reproduce: 1. Don't search in any datasources, ontology source EFO 2. Search for "complement C4b measurement" The confidence of the match is "Good". However, it is an exact string match - why is this not a "High" confidence match? [image: Screenshot 2021-11-15 at 15 03 47] <https://user-images.githubusercontent.com/454895/141804471-e0b18a04-c7e6-4cd7-96a4-5320ef900c86.png> @henrietteharmse <https://github.com/henrietteharmse> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#85>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHWUSK52WRAYLGWAP6ZKU63UMEOUHANCNFSM5IB5GDFA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[jamesamcl]

Here is another exact match from EFO, but this time it only returns MEDIUM.

[henrietteharmse]

This is expected behavior when more than 1 mapping is returned for the same string of text.

[jamesamcl]

But the search was against the EFO ontology, not a datasource with curated mappings. One of the matches was an exact text match, the other wasn't, yet they both get the same confidence. That seems wrong to me.

[henrietteharmse]

Ah, what you mean is that is the second 1 should not have come up as a match... or being rank lower. You may have a point.

[henrietteharmse]

For interest sake this call against OLS returns the desired result: https://www.ebi.ac.uk/ols/api/search?q=Apolipoprotein+E+measurement&groupField=iri&exact=on&start=0&ontology=efo