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Babel 1.6 #279

Merged
merged 30 commits into from
Sep 23, 2024
Merged

Babel 1.6 #279

merged 30 commits into from
Sep 23, 2024

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gaurav
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@gaurav gaurav commented May 20, 2024 •
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This PR collects some changes that were necessary for the Translator "Fugu" release.

  • Upgraded:
    • Biolink Model: 4.1.6 -> 4.2.1
    • UMLS version: 2023AB -> 2024AA
    • RxNorm version: 03042024 -> 07012024
    • PANTHER sequence: PANTHER_Sequence_Classification_files/PTHR18.0_human -> PANTHER_Sequence_Classification_files/PTHR19.0_human
    • PANTHER pathways: SequenceAssociationPathway3.6.7 -> SequenceAssociationPathway3.6.8
  • Added a manual Disease concord connecting MONDO:0005799 "hookworm infectious disease" and MESH:D006725 "Hookworm Infections" (as per Assets 52-54: adjust ID for hookworm infectious disease NCATSTranslator/Tests#92)
  • Reduced the number of warnings generated by the Publications compendium generator, so that we only warn of a duplicate title for a publication if the subsequent title actually differs from the original one.
  • Added a check for the disease manual concord: an error is raised if a file does not have three tab-separated columns (such as if the tabs were silently converted into spaces).
  • Fixed bug in FRINK call, added improved error checking.

Should be merged after PR #297.

@gaurav gaurav mentioned this pull request Jun 12, 2024
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@gaurav gaurav mentioned this pull request Jul 1, 2024
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@gaurav gaurav mentioned this pull request Aug 10, 2024
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@gaurav gaurav changed the base branch from master to improve-biomart August 13, 2024 05:09
@gaurav gaurav requested a review from cbizon August 13, 2024 05:26
@gaurav gaurav marked this pull request as ready for review August 13, 2024 05:26
@gaurav gaurav changed the title Babel 1.6 Babel 1.6 for "Fugu" release Aug 13, 2024
@gaurav gaurav changed the title Babel 1.6 for "Fugu" release Babel 1.6 for Translator "Fugu" release Aug 13, 2024
@gaurav gaurav changed the title Babel 1.6 for Translator "Fugu" release Babel 1.6 Aug 13, 2024
Base automatically changed from improve-biomart to master September 23, 2024 18:15
@gaurav gaurav merged commit 02505bb into master Sep 23, 2024
@gaurav gaurav deleted the babel-1.6 branch September 23, 2024 18:15
gaurav added a commit that referenced this pull request Sep 26, 2024
@gaurav
Merge pull request #335 from TranslatorSRI/fix-drugbank-bug
e6cc26d 
This PR adds DrugBank labels (from DrugBank v5.1.12). Somehow closes #332, but I'm not sure how (it might be a previous change in PR #279 that really closed this).
@gaurav gaurav restored the babel-1.6 branch November 23, 2024 16:44
@gaurav gaurav deleted the babel-1.6 branch November 23, 2024 16:45
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@cbizon cbizon cbizon approved these changes

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@gaurav @cbizon