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2026-03-16 EFO 3.88.0

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@ar-ibrahim ar-ibrahim released this 16 Mar 17:47
· 216 commits to master since this release
v3.88.0
e33aab0
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Summary:

EFO 3.88.0 contains a mass replacement of EFO disease terms with Mondo terms. These terms previously have been mapped and merged with the Mondo terms since EFO version 3.0.0 but now have been replaced with the Mondo IDs directly. For a list of all terms obsoleted and their replacements (which are available via the term_replaced_by annotation on each term) please see the attached obsoleted_terms_table.tsv.

Number of classes changed: 9919
Number of classes added: 2720
Number of classes deleted: 1

Important term changes (Open Targets Therapeutic Areas)

Old ID Old Label New ID New Label
EFO:0000319 cardiovascular disease MONDO:0004995 cardiovascular disorder
EFO:0000540 immune system disease MONDO:0005046 immune system disorder
EFO:0000618 nervous system disease MONDO:0005071 nervous system disorder
EFO:0001379 endocrine system disease MONDO:0005151 endocrine system disorder
EFO:0005741 infectious disease MONDO:0005550 infectious disease
EFO:0005803 hematologic disease MONDO:0005570 hematologic disorder
EFO:0005932 animal disease MONDO:0005583 non-human animal disease
EFO:0009690 urinary system disease MONDO:0002118 urinary system disorder
EFO:0010284 hepatobiliary disorder MONDO:0002515 hepatobiliary disorder
EFO:0010285 integumentary system disease MONDO:0002051 integumentary system disorder

What's Changed

  • QC for duplicate labels/exact synonyms in EFO by @aleixpuigb in #2628
  • Import MONDO_0004645 (cheek mucosa cancer) by @Copilot in #2600
  • Remove incorrect OMIM:266600 xref from ulcerative colitis (EFO_0000729) by @Copilot in #2610
  • Add new term: MGI DNBSEQ-T7 (EFO_0920057) by @Copilot in #2630
  • Merge duplicate beta-2 microglobulin measurement terms (EFO:0005197 ← EFO:0020180) by @Copilot in #2631
  • Add EFO term for Visium HD Spatial Gene Expression (EFO_0920058) by @Copilot in #2632
  • Add EFO_0920059: CosMx SMI (NanoString spatial molecular imager) by @Copilot in #2642
  • Replaced EFO disease terms with mapped Mondo terms and added QC by @zoependlington in #2647
  • Obsoleted EFO terms and Mondo replacements a847ce1
  • EFO release 3.88.0 by @ar-ibrahim in #2648

Full Changelog: v3.87.0...v3.88.0

Contributors

zoependlington, aleixpuigb, and ar-ibrahim
Assets 11
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