2026-09-15 EFO 3.94.0

What's Changed

• Deterministic release-notes generation with a CI consistency gate (refs #2826) by @jamesamcl in #2827
• Run-stable basic-report and edges reports (refs #2826) by @jamesamcl in #2828
• Added 2 new terms to test ID allocation workflow by @ar-ibrahim #2786
• Import MONDO_0100100, replacement for obsoleted MONDO_0019398 (fixes check_mondo_obsoletes on master) by @jamesamcl #2816
• EFO Release 3.94.0 by @ar-ibrahim in #2824

Full Changelog: v3.93.0...v3.94.0

2026-08-17 EFO 3.93.0

What's Changed

• Import 156 MONDO/HP terms for EVA-EFO (#2684) by @ar-ibrahim in #2760
• obsolete: Orphanet_570 (Moebius syndrome), replaced by MONDO_0008006 by @ar-ibrahim in #2761
• add: slide ID term (refs #2639) by @ar-ibrahim in #2763
• Add 10x GEM-X Epi Multiome and 10x Next-GEM Multiome terms by @ar-ibrahim in #2764
• EFO Release 3.93.0 by @ar-ibrahim in #2765

Full Changelog: v3.92.0...v3.93.0

2026-07-15 EFO 3.92.0

What's Changed

• Solve unsatisfiable classes by @aleixpuigb in #2716
• Added in subset annotation for #2707 by @zoependlington in #2718
• Add Claude Code multi-agent curation workflow by @aleixpuigb in #2719
• Fix allocate-definitive-ids by using ODK system robot wrapper by @aleixpuigb in #2717
• Add term: systemic inflammation (#2721) by @aleixpuigb in #2722
• Import HP:0006292 'Abnormality of dental eruption' (#2723) by @aleixpuigb in #2724
• Fix allocate-definitive-ids workflow (use ODK system robot for kgcl) by @aleixpuigb in #2725
• Stop allocate-definitive-ids self-trigger loop by @aleixpuigb in #2726
• efo-ticket: branch from an up-to-date master by @aleixpuigb in #2728
• Import 12 UBERON GTEx tissue terms (#2727) by @aleixpuigb in #2729
• Import head size trait (OBA_VT0000002) (#2705) by @aleixpuigb in #2730
• Add esterified, free, and total desmosterol measurement terms (EFO_0920097–0920099) by @jamesamcl with @Copilot in #2694
• docs: require hasDbXref provenance on synonyms by @aleixpuigb in #2732
• import: MONDO dermatophytosis subtypes (refs #2649) by @aleixpuigb in #2733
• Added files for EFO website by @zoependlington in #2736
• add: biparietal distance and amniotic fluid index (refs #2526) by @aleixpuigb in #2734
• docs: flag temporary agent-generated EFO IDs in PRs by @aleixpuigb in #2741
• fix: two MONDO-import CI failures (nolabels + check_mondo_obsoletes) by @aleixpuigb in #2743
• add: 26 spatial/imaging/omics assay terms + 9 OBI imports (refs #2735) by @aleixpuigb in #2742
• Add portable EFO PR-reviewer across Claude, Copilot, and Codex (#2746) by @aleixpuigb in #2749
• Add apnea-hypopnea index & cigarette smoking status measurement terms (#2747) by @aleixpuigb in #2748
• Import OBI:0003099 matrix assisted laser desorption ionization imaging mass spectrometry assay by @zoependlington with @Copilot in #2745
• Import terms from OBA fro GWAS by @aleixpuigb in #2751
• Import oba terms for GWAS bulk by @aleixpuigb in #2752
• Release 3.92.0 by @ar-ibrahim in #2753

Full Changelog: v3.91.0...v3.92.0

2026-06-15 EFO 3.91.0

What's Changed

• [NTR] Add myocardial strain (EFO:0920101) by @Copilot in #2706
• Add MONDO_1060213 to imports and dependencies by @ar-ibrahim in #2710
• Added assay terms for #2707 by @zoependlington in #2712
• EFO release 3.91.0 by @ar-ibrahim in #2714

Full Changelog: v3.90.0...v3.91.0

2026-05-18 EFO 3.90.0

Summary:

EFO 3.90.0 contains terms to cater for users, such as the GWAS Catalog, Open Targets, and more.

Number of classes changed: 95
Number of classes added: 60
Number of classes deleted: 3

What's Changed

• Fix ROBOT QC label_whitespace violations and duplicate label in efo-edit.owl by @Copilot in #2675
• Added 3 new response to terms by @ar-ibrahim in #2687
• Fix 4 EquivalentClass axioms causing EFO unsatisfiable classes by @Copilot in #2686
• Import OBI:0002197 (tissue section thickness) under EFO:0001444 (measurement) by @Copilot in #2691
• Add EFO term: imaging protocol (EFO_0920094) by @Copilot in #2692
• Add new ontology term fixation protocol (EFO_0920095) under OBI protocol by @Copilot in #2695
• Add new EFO term: permeabilization time (EFO_0920096) by @Copilot in #2696
• Add EFO_0920096: sample ID by @Copilot in #2671
• Add temporary EFO IDs and automated definitive ID allocation by @Copilot in #2698
• Obsolete 34 duplicate EFO measurement terms (v3.90) by @Copilot in #2693
• Fix label typo in EFO_0022979: lipiodomic → lipidomic by @Copilot in #2700
• Import OBA, CHEBI, and UBERON terms for kidney and mineral measurements by @ar-ibrahim in #2701
• Use checkout v6 and push action in workflow by @aleixpuigb in #2702
• EFO release 3.90.0 by @ar-ibrahim in #2703

Full Changelog: v3.89.0...v3.90.0

2026-04-15 EFO 3.89.0

Summary:

EFO 3.89.0 contains terms to cater for users, such as the GWAS Catalog, Open Targets, and more.

Number of classes changed: 130
Number of classes added: 33
Number of classes deleted: 0

What's Changed

• Added import for immunocytochemistry for #2651 by @zoependlington in #2660
• Add UniProt-to-EFO/OBA protein measurement mapping table by @Copilot in #2659
• Add EFO_0920060 premenopausal by @Copilot in #2658
• Add EFO_0920061 perimenopausal by @Copilot in #2657
• Disable uv cache pruning in copilot setup steps by @Copilot in #2663
• Add EFO:0920062 phenotyping as subclass of experimental process by @Copilot in #2661
• Add EFO_0920063: TeloHAEC cell line by @Copilot in #2664
• Add 22 new terms for nucleic acid delivery methods and integration states by @Copilot in #2666
• NTR: Add 10x Flex versioned terms (v1/v2 hierarchy) by @Copilot in #2667
• Rename EFO_0920089 to "10x Flex Apex"; add "10x GEM-X Flex v2" as exact synonym by @Copilot in #2668
• Import pupil size trait (OBA:VT0001321) by @Copilot in #2669
• Add EFO term: anatomical region (EFO_0920090) by @Copilot in #2670
• EFO release 3.89.0 by @zoependlington in #2677

Full Changelog: v3.88.0...v3.89.0

2026-03-16 EFO 3.88.0

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

2026-02-16 EFO 3.87.0

EFO 3.86.0 contains terms to cater for users, such as the GWAS Catalog, Open Targets, and more.

Number of classes changed: 23
Number of classes added: 177
Number of classes deleted: 1

What's Changed

• Imported and created terms for CMPDKP #2313 by @zoependlington in #2611
• Added new terms for #2614 by @zoependlington in #2616
• Imported term for #2603 by @zoependlington in #2621
• Imported HP term for #2617 by @zoependlington in #2622
• Removed duplicate diseases for #2615 by @zoependlington in #2623
• EFO 3.87.0 Release by @zoependlington in #2625

Full Changelog: v3.86.0...v3.87.0

2026-01-15 EFO 3.86.0

EFO 3.86.0 contains terms to cater for users, such as the GWAS Catalog, Open Targets, and more.

Number of classes changed: 249
Number of classes added: 14
Number of classes deleted: 1

What's Changed

• Improve handoffs by @aleixpuigb in #2587
• Add sample volume term (EFO_0920055) by @Copilot in #2593
• Add buffer volume term (EFO_0920056) by @Copilot in #2594
• Added assay terms for #2383 by @zoependlington in #2602
• Added sequencing term for #2137 by @zoependlington in #2604
• Added extraction protocol for #2330 by @zoependlington in #2605
• EFO Release 3.86.0 by @zoependlington in #2608

Full Changelog: v3.85.0...v3.86.0

2025-12-15 EFO 3.85.0

EFO 3.85.0 contains terms to cater for users, such as the GWAS Catalog, Open Targets, and more. There is now a dynamic import for FBBI, with the 'recorded image' branch imported into EFO.

Number of classes changed: 206
Number of classes added: 132
Number of classes deleted: 3

What's Changed

• Modify agentic workflow by @aleixpuigb in #2560
• Add description to EFO ontology for proper OLS display by @Copilot in #2470
• Update agentic workflow by @aleixpuigb in #2566
• Add has_primary_input (RO:0004009) axioms linking response terms to CHEBI entities by @Copilot in #2561
• Add critical checks and synonym rules to EFO agent docs by @aleixpuigb in #2568
• Add selenium deficiency term (EFO_0920016) by @Copilot in #2573
• Add adiposity index terms (EFO_0920017-0920020) by @Copilot in #2576
• Update lipid amount parent from protein measurement to lipid measurement by @Copilot in #2580
• Add 13 metabolomics terms for cholesteryl esters and lipoprotein particle concentrations by @Copilot in #2578
• Add EFO_0920034: age at high-grade serous ovarian cancer diagnosis by @Copilot in #2581
• Add bronchiectasis inflammatory endotype terms (fixes #2546) by @Copilot in #2582
• Add new term 'functional assay in yeast' (EFO_0920043) by @Copilot in #2583
• Imported recorded image branch from FBBI creating dynamic import for … by @zoependlington in #2585
• Add 8 drug response terms for GWAS catalog (issue #2562) by @Copilot in #2584
• EFO release 3.85.0 by @zoependlington in #2589

Full Changelog: v3.84.0...v3.85.0