Releases: EBISPOT/efo
2025-09-15 EFO 3.82.0
EFO 3.82.0 contains terms to cater for users, such as the GWAS Catalog, Open Targets, and more.
Number of classes changed: 1718
Number of classes added: 21041
Number of classes deleted: 9
What's Changed
- Update copilot-setup-steps.yml with odk test by @aleixpuigb in #2451
- Add normalize_src in makefiles by @aleixpuigb in #2455
- Update copilot instructions based on previous performance by @aleixpuigb in #2456
- Add bead-based spatial transcriptomics term and update Slide-seq hierarchy by @Copilot in #2453
- Import OBA body fat mass and tissue mass terms with correct hierarchy by @Copilot in #2457
- Update copilot instructions to follow instructions for importing terms by @aleixpuigb in #2459
- Fixes #2441 Import HP:0009916 Anisocoria by @aleixpuigb in #2461
- Add two new Curio Biosciences Seeker spatial transcriptomics terms by @Copilot in #2460
- Fix obsolete term replacement: Update EFO_0600087 to use HP_0000593 instead of OBA_2045283 by @Copilot in #2471
- NTR abdominal age by @aleixpuigb in #2473
- imported OBA terms-1 by @ar-ibrahim in #2474
- Added single-cell RNA sequencing term for #2458 by @zoependlington in #2476
- Imported Mondo term for #2435 by @zoependlington in #2477
- PR duplicate label violation fix 1 by @ar-ibrahim in #2479
- imported OBA terms-2 by @ar-ibrahim in #2480
- EFO release 3.82.0 by @zoependlington in #2481
New Contributors
- @Copilot made their first contribution in #2453
Full Changelog: v3.81.0...v3.82.0
Contributors
Assets 10
2025-08-18 EFO 3.81.0
EFO 3.81.0 contains terms to cater for users, such as the GWAS Catalog, Open Targets, and more, as well as the foundations of documentation to assist implementing AI tooling into the EFO term creation and obsoletion process. Many duplicate terms have also been rectified, obsoleting the EFO term in favour of the imported term.
Number of classes changed: 845
Number of classes added: 670
Number of classes deleted: 29
What's Changed
- Updated get_mirrors to include GSSO by @zoependlington in #2429
- NTR particle-templated instant partition sequencing by @aleixpuigb in #2430
- Import '3,3',5-triiodo-L-thyronine amount' and update obsoleted term by @aleixpuigb in #2439
- #2244 NTR NGS assay kits by @aleixpuigb in #2433
- Imported terms for EVA ticket #2428 and updated EFO imports by @zoependlington in #2440
- Removed incorrect parentage and disease location for #832 by @zoependlington in #2447
- Setting up copilot by @aleixpuigb in #2446
- Obsoleted EFO duplicates of imported terms for #2278 by @zoependlington in #2448
- EFO release 3.81.0 by @zoependlington in #2449
Full Changelog: v3.80.0...v3.81.0
Contributors
Assets 10
2025-07-15 EFO 3.80.0
EFO 3.80.0 contains a new dynamic import for GSSO to cover gender, sex and sexuality terms. New terms have also been added to cater for GWAS and Open Targets as well as new assays and some improvements to previously created terms.
Number of classes changed: 10
Number of classes added: 25
Number of classes deleted: 0
What's Changed
- Issue templates by @zoependlington in #2406
- Add EFO ID range for new editor by @aleixpuigb in #2407
- Alzheimers term added for #2350 by @zoependlington in #2408
- Imported HP terms for #2361 by @zoependlington in #2409
- Added income term for #2370 by @zoependlington in #2410
- Added eczema term for #2248 by @zoependlington in #2411
- Updated glucose tolerance test definition for #2276 by @zoependlington in #2412
- Added chronic pain term for #2287 by @zoependlington in #2414
- Moved amyloid-beta measurements terms under parent for #2340 by @zoependlington in #2415
- Added import for GSSO and imported sexuality terms for #2416 by @zoependlington in #2417
- Added mutation term for #2404 by @zoependlington in #2418
- EFO release 3.80.0 by @zoependlington in #2427
New Contributors
- @aleixpuigb made their first contribution in #2407
Full Changelog: v3.79.0...v3.80.0
Contributors
Assets 10
2025-05-15 EFO 3.79.0
EFO 3.79.0 contains new assay terms, assay related terms and relationships between exposure measurements and exposure terms imported from ECTO.
Number of classes changed: 20
Number of classes added: 15
Number of classes deleted: 0
2025-05-15 EFO 3.78.0
EFO 3.78.0 contains many more OBA measurement terms replacing EFO measurement terms, a new ECTO import, and terms for FinnGen mapping at Open Targets.
Number of classes changed: 8319
Number of classes added: 675
Number of classes deleted: 0
Below are the EFO terms that have been obsoleted and replaced with OBA terms:
| EFO ID | EFO label | OBA ID | OBA label | Matched label |
|---|---|---|---|---|
| EFO:0008197 | killer cell immunoglobulin-like receptor 2DL4 measurement | OBA:2045330 | killer cell immunoglobulin-like receptor 2DL4 level | killer cell immunoglobulin like receptor 2dl4 |
| EFO:0010612 | kit ligand measurement | OBA:2050260 | kit ligand amount | kit ligand |
| EFO:0020788 | "troponin i, cardiac muscle measurement" | OBA:2045369 | "troponin I, cardiac muscle level" | "troponin i,cardiac muscle" |
| EFO:0008365 | heart amyloid deposition measurement | OBA:2045377 | heart amyloid deposition | heart amyloid deposition |
| EFO:0008045 | C-C motif chemokine 17 measurement | OBA:2050205 | C-C motif chemokine 17 amount | c c motif chemokine 17 |
| EFO:0021421 | spleen iron measurement | OBA:VT0008739 | spleen iron amount | spleen iron |
| EFO:0020470 | inhibin beta A chain:inhibin beta B chain heterodimer measurement | OBA:2045354 | activin/inhibin beta subunit level | inhibin beta a chain:inhibin beta b chain heterodimer |
| EFO:0008248 | neutrophil collagenase measurement | OBA:2045339 | neutrophil collagenase level | neutrophil collagenase |
| EFO:0020311 | cytotoxic and regulatory t-cell molecule measurement | OBA:2045351 | cytotoxic and regulatory T-cell molecule level | cytotoxic and regulatory t cell molecule |
| EFO:0004846 | serotonin measurement | OBA:1000977 | serotonin amount | serotonin |
| EFO:0004741 | blood urea nitrogen measurement | OBA:VT0005265 | blood urea nitrogen amount | blood urea nitrogen |
| EFO:0010118 | sphingomyelin measurement | OBA:1001014 | sphingomyelin amount | sphingomyelin |
| EFO:0010118 | sphingomyelin measurement | OBA:2040182 | level of sphingomyelin | sphingomyelin |
| EFO:0020312 | cytotoxic t-lymphocyte protein 4 measurement | OBA:2045352 | cytotoxic T-lymphocyte protein 4 level | cytotoxic t lymphocyte protein 4 |
| EFO:0004529 | lipid measurement | OBA:VT0001547 | lipid amount | lipid |
| EFO:0007002 | luteinizing hormone measurement | OBA:1001009 | Luteinizing hormone amount | luteinizing hormone |
| EFO:0010790 | monocyte chemotactic protein-4 measurement | OBA:2045300 | C-C motif chemokine 13 level | monocyte chemotactic protein 4 |
| EFO:0004569 | brain serotonin transporter measurement | OBA:2045374 | brain serotonin transporter level | brain serotonin transporter |
| EFO:0008222 | macrophage scavenger receptor types I and II measurement | OBA:2045337 | macrophage scavenger receptor types I and II level | macrophage scavenger receptor types i and ii |
| EFO:0020195 | C-C motif chemokine 13 measurement | OBA:2045300 | C-C motif chemokine 13 level | c c motif chemokine 13 |
| EFO:0010628 | natriuretic peptides B measurement | OBA:2045303 | natriuretic peptides B level | natriuretic peptides b |
| EFO:0020605 | neutrophil elastase measurement | OBA:2045363 | neutrophil elastase level | neutrophil elastase |
| EFO:0004739 | circulating cell free DNA measurement | OBA:2045375 | circulating cell free DNA level | circulating cell free dna |
| OBA:2045375 | circulating cell free DNA level | OBA:2045375 | circulating cell free DNA level | circulating cell free dna |
| EFO:0020518 | killer cell immunoglobulin-like receptor 3DL2 measurement | OBA:2045355 | killer cell immunoglobulin-like receptor 3DL2 level | killer cell immunoglobulin like receptor 3dl2 |
| EFO:0004735 | serum alanine aminotransferase measurement | OBA:2050062 | serum alanine aminotransferase amount | serum alanine aminotransferase |
| EFO:0004735 | alanine aminotransferase measurement | OBA:2045399 | alanine aminotransferase level | alanine aminotransferase |
| EFO:0009413 | CCL15 measurement | OBA:2045344 | C-C motif chemokine 15 level | ccl15 |
| EFO:0010230 | phosphatidylinositol measurement | OBA:2040181 | level of phosphatidylinositol | phosphatidylinositol |
| EFO:0020761 | t-lymphocyte activation antigen CD80 measurement | OBA:2045367 | CD80 molecule level | t lymphocyte activation antigen cd80 |
| EFO:0020657 | proliferating cell nuclear antigen measurement | OBA:2045366 | proliferating cell nuclear antigen level | proliferating cell nuclear antigen |
| EFO:0007807 | erythrocyte cadmium measurement | OBA:2045316 | erythrocyte cadmium level | erythrocyte cadmium |
| EFO:0004631 | vitamin D measurement | OBA:1000968 | vitamin D amount | vitamin d |
| EFO:0004857 | vitamin A measurement | OBA:1000996 | vitamin A amount | vitamin a |
| EFO:0008059 | C-X-C motif chemokine 6 measurement | OBA:2045346 | C-X-C motif chemokine 6 level | c x c motif chemokine 6 |
| EFO:0010624 | tumor necrosis factor receptor superfamily member 1B measurement | OBA:2050309 | tumor necrosis factor receptor superfamily member 1B amount | tumor necrosis factor receptor superfamily member 1b |
| EFO:0020171 | B-cell receptor CD22 measurement | OBA:2045350 | B-cell receptor CD22 level | b cell receptor cd22 |
| EFO:0803546 | lymphocyte measurement | OBA:0003352 | lymphocyte amount | lymphocyte |
| EFO:0009703 | red blood cell folate measurement | OBA:2045373 | red blood cell folate amount | red blood cell folate |
| EFO:0009703 | Red Blood Cell Folate | OBA:2045373 | red blood cell folate amount | red blood cell folate |
| EFO:0009703 | Red Blood Cell Folate Measurement | OBA:2045373 | red blood cell folate amount | red blood cell folate |
| EFO:0008209 | leukocyte immunoglobulin-like receptor subfamily B member 2 measurement | OBA:2045332 | leukocyte immunoglobulin-like receptor subfamily B member 2 level | leukocyte immunoglobulin like receptor subfamily b member 2 |
| EFO:0010231 | sterol measurement | OBA:1000973 | sterol amount | sterol |
| EFO:0020547 | macrophage colony-stimulating factor 1 receptor measurement | OBA:2045361 | macrophage colony-stimulating factor 1 receptor level | macrophage colony stimulating factor 1 receptor |
| EFO:0020540 | lymphocyte activation gene 3 protein measurement | OBA:2045359 | lymphocyte activation gene 3 protein level | lymphocyte activation gene 3 protein |
| EFO:0020539 | lymphatic vessel endothelial hyaluronic acid receptor 1 measurement | OBA:2045358 | lymphatic vessel endothelial hyaluronic acid receptor 1 level | lymphatic vessel endothelial hyaluronic acid receptor 1 |
| EFO:0803201 | tumor necrosis factor receptor superfamily member 1A measurement | OBA:2050272 | tumor necrosis factor receptor superfamily member 1A amount | tumor necrosis factor receptor superfamily member 1a |
| EFO:0005134 | amino acid measurement | OBA:1001001 | amino acid amount | amino acid |
| EFO:0022204 | blood N(1)-acetylspermidine measurement | OBA:2050393 | level of N(1)-acetylspermidine in blood | blood n(1) acetylspermidine |
| EFO:0020075 | urine glucose measurement | OBA:VT0001758 | urine glucose amount | urine glucose |
| EFO:0010913 | eosinophil cationic protein measurement | OBA:2045348 | eosinophil cationic protein level | eosinophil cationic protein |
| EFO:0020644 | platelet factor 4 measurement | OBA:2045364 | platelet factor 4 level | platelet factor 4 |
| EFO:0007578 | blood copper measurement | OBA:2045323 | blood copper level | blood copper |
| EFO:0020546 | macrophage colony-stimulating factor 1 measurement | OBA:2045302 | macrophage colony-stimulating factor 1 level | macrophage colony stimulating factor 1 |
| EFO:0800665 | bradykinin measurement | OBA:1000953 | bradykinin amount | bradykinin |
| OBA:VT0000237 | blood cell count | OBA:VT0000237 | blood cell quantity | blood cell count |
| EFO:0802869 | pituitary adenylate cyclase-activating polypeptide measurement | OBA:2050199 | pituitary adenylate cyclase-activating polypeptide amount | pituitary adenylate cyclase activating polypeptide |
| EFO:0008208 | leukocyte immunoglobulin-like receptor subfamily B member 1 measurement | OBA:2045331 | leukocyte immunoglobulin-like receptor subfamily B member 1 level | leukocyte immunoglobulin like receptor subfamily b member 1 |
| EFO:0004622 | sphingolipid measurement | OBA:1000965 | sphingolipid amount | sphingolipid |
| EFO:0004731 | eye measurement | OBA:2060173 | eye amount | eye |
| EFO:0010789 | monocyte chemotactic protein-2 measurement | OBA:2045347 | C-C motif chemokine 8 level | monocyte chemotactic protein 2 |
| EFO:0010789 | monocyte chemotactic protein 2 measurement | OBA:2045347 | C-C motif chemokine 8 level | monocyte chemotactic protein 2 |
| EFO:0020620 | oxidized low-density lipoprotein receptor 1 measurement | OBA:2050235 | oxidized low-density lipoprotein receptor 1 amount | oxidized low density lipoprotein receptor 1 |
| EFO:0008069 | carboxypeptidase B2 measurement | OBA:2050320 | carboxypeptidase B2 amount | carboxypeptidase b2 |
| EFO:0004747 | protein measurement | OBA:VT0010120 | protein amount | protein |
| EFO:0005267 | serum copper measurement | OBA:2045376 | serum copper level | serum copper |
| EFO:0010972 | blood phosphate measurement | OBA:VT0001565 | blood phosphate amount | blood phosphate |
| EFO:0010972 | blood phosphate level | OBA:VT0001565 | blood phosphate amount | blood phosphate |
| EFO:0008220 | macrophage metalloelastase measurement | OBA:2045335 | macrophage metalloelastase level | macrophage metalloelastase |
| EFO:0004502 | adiponectin measurement | OBA:1000967 | adiponectin amount | adiponectin |
| EFO:0004639 | phospholipid measurement | OBA:1001011 | phospholipid amount | phospholipid |
| EFO:0800618 | sphingosine measurement | OBA:1000970 | sphingosine amount | sphingosine |
| EFO:0004867 | vitamin E measurement | OBA:1000955 | vitamin E amount | vitamin e |
| EFO:0004768 | follicle stimulating hormone measurement | OBA:1000992 | Follicle stimulating hormone amount | follicle stimulating hormone |
| EFO:0004768 | follicle stimulating hormone level | OBA:1000992 | Follicle stimulating hormone amount | follicle stimulating hormone |
| EFO:0008142 | granulocyte colony-stimulating factor measurement | OBA:2045329 | granulocyte colony-sti... |
2025-04-15 EFO 3.77.0
EFO 3.77.0 contains many more OBA measurement terms replacing EFO measurement terms and a new PR import for protein terms.
Number of classes changed: 4198
Number of classes added: 2692
Number of classes deleted: 0
2025-03-28 EFO 3.76.1
EFO 3.76.1 fixes a few issues that have arisen due to the measurement branch replacement and updates to the EFO pipeline.
Number of classes changed: 44
Number of classes added: 6
Number of classes deleted: 0
2025-03-17 EFO 3.76.0
EFO 3.76.0 further alignments between EFO and MONDO as well as terms required for Open Targets projects, HCA, Array Express/Expression Atlas and the GWAS Catalog. We have also impleneted temprary measures to fix some issues with the new measurement replacements. All terms should now sit below the parent class of 'measurement' (EFO:0001444).
Number of classes changed: 51
Number of classes added: 126
Number of classes deleted: 0
PLEASE NOTE: The Open Targets specific files do not have this fix due to issues with the generation pipeline. This will be hopefully fixed in an upcoming patch release.
2025-02-17 EFO 3.75.0
EFO 3.75.0 further alignments between EFO and MONDO as well as terms required for Open Targets projects, HCA, Array Express/Expression Atlas and the GWAS Catalog. We have also updated the tools used in the EFO creation pipeline.
Number of classes changed: 5
Number of classes added: 0
Number of classes deleted: 0
2025-01-15 EFO 3.74.0
Experimental Factor Ontology version 3.74.0
Date Released: 15th January 2025
Class Count: 63,495
Summary:
EFO 3.74.0 includes a major change to the measurement branch with many EFO measurement terms being replaced by OBA terms. This release also further alignments between EFO and MONDO as well as terms required for Open Targets projects, HCA, Array Express/Expression Atlas and the GWAS Catalog.
Number of classes changed: 7603
Number of classes added: 5618
Number of classes deleted: 0