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mcwdsi / dron

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Update Labels #26

Closed jamesaoverton closed 3 weeks ago

jamesaoverton commented 1 month ago

This PR loads ChEBI and RxNorm, then uses them to update the DrOn templates with the latest labels from those sources.

Please test a full build with:

cd src/ontology
sh run.sh make all_components -B
sh run.sh make prepare_release -B COMP=false MIR=false IMP=false

There's too much to review completely, so I suggest checking the new scripts, then spot-checking the updated templates.

hoganwr commented 1 month ago

Here's an interesting, non-synonymous, yet apparently correct label change in RxNorm: DRON:00841115 Gibberella fujikuroi allergenic extract 2101340 DRON:00841115 Fusarium moniliforme antigen 2101340

Turns out the Gibberela one now has RxCui 2043450.

I am still reviewing but so far the ingredients are checking out.

hoganwr commented 1 month ago

Some of the diffs show a large addition to the label. I am wondering if the old MySQL database was limited to 255 character fields, and therefore the diff shows a huge addition of everything that got cut off previously. I also wonder if this was the genesis of many duplicate labels.

hoganwr commented 1 month ago

I was reviewing duplicate labels and I see we have duplicate classes. I wonder if the pattern I noticed for ingredients, where the old Scala code created a new ingredient when the label changed (except for purely a change in case), is also reproduced for clinical drugs, clinical drug forms, etc.

For example, look at http://purl.obolibrary.org/obo/DRON_00733166 and http://purl.obolibrary.org/obo/DRON_00058661. Both classes have the same rdfs:label and same RxCui annotations.

hoganwr commented 1 month ago

They had different labels before we fixed them based on RxCUI match. Here's what I see in Ontobee:

DRON_00733166 Zolpidem tartrate 6.25 MG Extended Release Oral Tablet DRON_00058661 Zolpidem tartrate 6.25 MG Extended Release Tablet

Now they both have the label: zolpidem tartrate 6.25 MG Extended Release Oral Tablet