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Remove CHEBI:CHEBI:41423 from PUBCHEM.COMPOUND:2662 results #69

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gaurav opened this issue Sep 23, 2022 · 2 comments · Fixed by #78
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Remove CHEBI:CHEBI:41423 from PUBCHEM.COMPOUND:2662 results #69

gaurav opened this issue Sep 23, 2022 · 2 comments · Fixed by #78
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@gaurav
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Babel September R...

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@gaurav
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gaurav commented Sep 23, 2022

Querying PUBCHEM.COMPOUND:2662 returns CHEBI:CHEBI:41423 as an equivalent ID, which is wrong: https://nodenormalization-sri.renci.org/1.3/get_normalized_nodes?curie=PUBCHEM.COMPOUND%3A2662&conflate=true

Note also that MESH:C105934 is labeled as [OBSOLETE] celecoxib -- are we definitely identifying obsolete MESH terms correctly?
@gaurav gaurav added this to the Babel September Release 2022 milestone Sep 23, 2022
@gaurav gaurav self-assigned this Sep 23, 2022
@gaurav gaurav mentioned this issue Sep 23, 2022
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@colleenXu
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A similar issue: @cbizon noticed that in this screenshot, there is a CHEBI:CHEBI: ID but no correct CHEBI ID. I noticed that the top synonym seemed to be the UNII ID rather than a human-readable name (vitamin b12)

Screen Shot 2022-09-23 at 1 48 56 PM

@colleenXu colleenXu mentioned this issue Sep 23, 2022
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@gaurav
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gaurav commented Sep 27, 2022

The CHEBI:CHEBI: bug seems to be coming from pull_drugcentral in drugcentral.py, which creates an xref file whose second column is expected to be an identifier only; however, for CHEBI (and only CHEBI) this column includes the CHEBI: prefix, and so we double-concatenate it later on. Working on a fix now.

gaurav added a commit that referenced this issue Oct 11, 2022
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Attempt to fix CHEBI:CHEBI: bug (#69)
ff97578
@gaurav gaurav mentioned this issue Oct 11, 2022
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gaurav added a commit that referenced this issue Oct 13, 2022
@gaurav
Merge pull request #78 from TranslatorSRI/fix-chebi-chebi-bug
7536b25 
The CHEBI:CHEBI: bug is caused by DrugCentral adding a `CHEBI:` prefix to its identifier. This PR checks for that prefix and removes it so the rest of our code can work correctly. Since it only works on `CHEBI` entries with the prefix, it should be fairly safe to leave in even if DrugCentral removes the prefix at a later date. Fixes #69.

This also deletes the non-functional `get_drugcentralx` target, which refers to a function that no longer exists in this repository. Closes #77.
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Fix CHEBI:CHEBI: bug (#69) TranslatorSRI/Babel
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