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obophenotype / upheno-dev

Framework for the automated construction of uPheno 2.0
MIT License
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upheno_id_map.txt -> some ids have non existent patterns in it #57

Closed matentzn closed 8 months ago

matentzn commented 9 months ago

We should use the log of the create sssom method to figure out which yaml files are not parseable.

upheno_id_map.txt has ids with patterns that have since been renamed, like lesionedAnatomicalEntity.

We should make sure the old ones are removed.

matentzn commented 9 months ago

Could not get id columns: /home/james/upheno-dev/src/scripts/../curation/patterns-for-matching/abnormalFractureOfAnatomicalEntity.yaml Could not get id columns: /home/james/upheno-dev/src/scripts/../curation/patterns-for-matching/apoptoticAnatomicalEntityInLocation.yaml Could not get id columns: /home/james/upheno-dev/src/scripts/../curation/patterns-for-matching/apoptoticAnatomicalEntity.yaml Could not get id columns: /home/james/upheno-dev/src/scripts/../curation/patterns-for-matching/functionalAnatomicalEntity.yaml Could not get id columns: /home/james/upheno-dev/src/scripts/../curation/patterns-for-matching/lesionInAnatomicalEntity.yaml

matentzn commented 8 months ago

we have obsoleted all the corresponding ids