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EFO - Release Notes
Experimental Factor Ontology version 3.76.1
Date Released: 28th March 2025
Class Count: 63,628
Summary:
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: 51
Number of classes added: 126
Number of classes deleted: 0
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1. Changes to URIs
2. Changes to EFO
3. Obsolete Classes in EFO
4. Scope of the Ontology
5. External Ontology and Resource Mapping List
6. Known OWL to OBO Conversion Issues
7. Contact Details
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1. Changes to URIs
@Classes new to this version
Class: http://purl.obolibrary.org/obo/MONDO_0004286
Label(s): pancreatic intraductal papillary-mucinous neoplasm
+ 'pancreatic intraductal papillary-mucinous neoplasm' SubClassOf 'malignant exocrine pancreas neoplasm'
Class: http://purl.obolibrary.org/obo/OBA_2045258
Label(s): susceptibility to urinary tract infection
+ 'susceptibility to urinary tract infection' SubClassOf 'susceptibility to infectious disease measurement'
+ 'susceptibility to urinary tract infection' SubClassOf 'inheres in part of' some 'anatomical entity'
Class: http://purl.obolibrary.org/obo/OBA_2045257
Label(s): susceptibility to strep throat
+ 'susceptibility to strep throat' SubClassOf 'susceptibility to infectious disease measurement'
+ 'susceptibility to strep throat' SubClassOf 'inheres in part of' some 'anatomical entity'
Class: http://purl.obolibrary.org/obo/OBA_2050119
Label(s): gene expression attribute
+ 'gene expression attribute' SubClassOf 'metabolism trait'
Class: http://purl.obolibrary.org/obo/OBA_2050118
Label(s): helping behavior trait
+ 'helping behavior trait' SubClassOf 'behavior trait'
Class: http://purl.obolibrary.org/obo/MONDO_0034820
Label(s): cleft lip and palate-craniofacial dysmorphism-congenital heart defect-hearing loss syndrome
+ 'cleft lip and palate-craniofacial dysmorphism-congenital heart defect-hearing loss syndrome' SubClassOf 'syndromic disease'
+ 'cleft lip and palate-craniofacial dysmorphism-congenital heart defect-hearing loss syndrome' SubClassOf 'genetic disorder'
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2. Changes to EFO3
@Classes modified from previous
Class: http://www.ebi.ac.uk/efo/EFO_1001394
Label(s): Peritoneal Fibrosis
+ 'Peritoneal Fibrosis' SubClassOf 'digestive system neoplasm'
Class: http://www.ebi.ac.uk/efo/EFO_1001228
Label(s): ureterolithiasis
- 'ureterolithiasis' SubClassOf 'kidney disease'
Class: http://www.ebi.ac.uk/efo/EFO_1001227
Label(s): ureterocele
- 'ureterocele' SubClassOf 'kidney disease'
Class: http://www.ebi.ac.uk/efo/EFO_1001100
Label(s): peritoneal neoplasm
+ 'peritoneal neoplasm' SubClassOf 'digestive system neoplasm'
Class: http://www.ebi.ac.uk/efo/EFO_0008490
Label(s): ampulla of Vater adenocarcinoma
+ 'ampulla of Vater adenocarcinoma' SubClassOf 'pancreatic adenocarcinoma'
Class: http://purl.obolibrary.org/obo/MONDO_0021960
Label(s): ureteritis
- 'ureteritis' SubClassOf 'kidney disease'
- 'ureteritis' SubClassOf 'inflammatory disease'
+ 'ureteritis' SubClassOf 'nephritis'
Class: http://www.orpha.net/ORDO/Orphanet_98685
Label(s): Oculomotor palsy
- 'Oculomotor palsy' SubClassOf 'palsy'
+ 'Oculomotor palsy' SubClassOf 'facial paralysis'
Class: http://purl.obolibrary.org/obo/MONDO_0000921
Label(s): ampulla of vater neoplasm
+ 'ampulla of vater neoplasm' SubClassOf 'pancreatic neoplasm'
Class: http://purl.obolibrary.org/obo/MONDO_0000919
Label(s): ampulla of vater cancer
+ 'ampulla of vater cancer' SubClassOf 'Malignant Pancreatic Neoplasm'
Class: http://purl.obolibrary.org/obo/MONDO_0003553
Label(s): ampulla of vater adenosquamous carcinoma
+ 'ampulla of vater adenosquamous carcinoma' SubClassOf 'pancreatic adenosquamous carcinoma'
Class: http://www.ebi.ac.uk/efo/EFO_1000513
Label(s): Salivary Gland Acinic Cell Carcinoma
- 'Salivary Gland Acinic Cell Carcinoma' SubClassOf 'digestive system disease'
+ 'Salivary Gland Acinic Cell Carcinoma' SubClassOf 'Digestive System Carcinoma'
Class: http://purl.obolibrary.org/obo/MONDO_0003490
Label(s): ampulla of vater squamous cell carcinoma
+ 'ampulla of vater squamous cell carcinoma' SubClassOf 'squamous cell carcinoma of pancreas'
Class: http://www.ebi.ac.uk/efo/EFO_1000355
Label(s): Malignant Mesothelioma
+ 'Malignant Mesothelioma' SubClassOf 'digestive system cancer'
Class: http://www.ebi.ac.uk/efo/EFO_1000317
Label(s): Lacrimal Gland Adenoid Cystic Carcinoma
+ 'Lacrimal Gland Adenoid Cystic Carcinoma' SubClassOf 'cutaneous adenocystic carcinoma'
Class: http://www.ebi.ac.uk/efo/EFO_1000304
Label(s): Intestinal Type Adenocarcinoma
+ 'Intestinal Type Adenocarcinoma' SubClassOf 'Digestive System Carcinoma'
Class: http://www.ebi.ac.uk/efo/EFO_1000270
Label(s): Gastric Diffuse Large B-Cell Lymphoma
+ 'Gastric Diffuse Large B-Cell Lymphoma' SubClassOf 'gastrointestinal lymphoma'
+ 'Gastric Diffuse Large B-Cell Lymphoma' SubClassOf 'lymphatic system cancer'
Class: http://www.ebi.ac.uk/efo/EFO_1000224
Label(s): Duodenal Gastrin-Producing Neuroendocrine Tumor
+ 'Duodenal Gastrin-Producing Neuroendocrine Tumor' SubClassOf 'digestive system neoplasm'
Class: http://www.ebi.ac.uk/efo/EFO_1000058
Label(s): nasopharyngeal squamous cell carcinoma
- 'nasopharyngeal squamous cell carcinoma' SubClassOf 'digestive system disease'
+ 'nasopharyngeal squamous cell carcinoma' SubClassOf 'Digestive System Carcinoma'
Class: http://www.ebi.ac.uk/efo/EFO_1000049
Label(s): pulmonary tuberculosis
+ 'pulmonary tuberculosis' SubClassOf 'respiratory tract infectious disorder'
Class: http://purl.obolibrary.org/obo/MONDO_0004517
Label(s): ureter tuberculosis
- 'ureter tuberculosis' SubClassOf 'bacterial urinary tract infection'
+ 'ureter tuberculosis' SubClassOf 'renal tuberculosis'
Class: http://www.ebi.ac.uk/efo/EFO_1000921
Label(s): endomyocardial fibrosis
+ 'endomyocardial fibrosis' SubClassOf 'neoplasm of thorax'
Class: http://purl.obolibrary.org/obo/MONDO_0002087
Label(s): peritoneum cancer
+ 'peritoneum cancer' SubClassOf 'digestive system cancer'
Class: http://purl.obolibrary.org/obo/MONDO_0002113
Label(s): peritoneal carcinoma
+ 'peritoneal carcinoma' SubClassOf 'Digestive System Carcinoma'
Class: http://purl.obolibrary.org/obo/OBA_2045256
Label(s): multiple keratinocyte carcinoma susceptibility
- 'multiple keratinocyte carcinoma susceptibility' SubClassOf 'characteristic of' some 'keratinocyte'
Class: http://purl.obolibrary.org/obo/OBA_2045220
Label(s): immunoglobulin isotype switching attribute
+ 'immunoglobulin isotype switching attribute' SubClassOf 'part_of' some http://purl.obolibrary.org/obo/OBA_2050119
Class: http://www.ebi.ac.uk/efo/EFO_0007536
Label(s): vesicoureteral reflux
- 'vesicoureteral reflux' SubClassOf 'kidney disease'
Class: http://www.ebi.ac.uk/efo/EFO_0007169
Label(s): biliary dyskinesia
+ 'biliary dyskinesia' SubClassOf 'pancreas disease'
Class: http://purl.obolibrary.org/obo/MONDO_0021953
Label(s): tuberculous fibrosis of lung
- 'tuberculous fibrosis of lung' SubClassOf 'respiratory tract infectious disorder'
Class: http://purl.obolibrary.org/obo/OBA_1000110
Label(s): bone density
- 'bone density' SubClassOf 'part_of' some 'bone mineral mass'
Class: http://purl.obolibrary.org/obo/MONDO_0002401
Label(s): malignant tenosynovial giant cell tumor
+ 'malignant tenosynovial giant cell tumor' SubClassOf 'Malignant Bone Neoplasm'
Class: http://purl.obolibrary.org/obo/PR_000013872
Label(s): regenerating islet-derived protein 3-gamma
- 'regenerating islet-derived protein 3-gamma' SubClassOf 'protein'
+ 'regenerating islet-derived protein 3-gamma' SubClassOf http://www.w3.org/2002/07/owl#Thing
Class: http://www.ebi.ac.uk/efo/EFO_0007143
Label(s): alveolar soft part sarcoma
- 'alveolar soft part sarcoma' SubClassOf 'digestive system disease'
+ 'alveolar soft part sarcoma' SubClassOf 'digestive system cancer'
Class: http://purl.obolibrary.org/obo/OBA_VT0005007
Label(s): bone mineral mass
- 'bone mineral mass' SubClassOf 'characteristic of' some 'bone element'
- 'bone mineral mass' SubClassOf 'measurement'
+ 'bone mineral mass' SubClassOf 'amount'
Class: http://www.ebi.ac.uk/efo/EFO_1001940
Label(s): basaloid squamous cell carcinoma
- 'basaloid squamous cell carcinoma' SubClassOf 'digestive system disease'
+ 'basaloid squamous cell carcinoma' SubClassOf 'Digestive System Carcinoma'
Class: http://www.ebi.ac.uk/efo/EFO_0009913
Label(s): ossifying fibroma of the jaw
+ 'ossifying fibroma of the jaw' SubClassOf 'digestive system neoplasm'
Class: http://purl.obolibrary.org/obo/OBA_2043233
Label(s): level of regenerating islet-derived protein 3-gamma in blood serum
- 'level of regenerating islet-derived protein 3-gamma in blood serum' SubClassOf 'characteristic of' some
('protein' and ('part_of' some 'blood'))
Class: http://purl.obolibrary.org/obo/MONDO_0003425
Label(s): ophthalmoplegia
+ 'ophthalmoplegia' SubClassOf 'facial paralysis'
Class: http://www.ebi.ac.uk/efo/EFO_0006566
Label(s): dysplastic oral keratinocyte
+ 'dysplastic oral keratinocyte' SubClassOf 'digestive system neoplasm'
Class: http://www.ebi.ac.uk/efo/EFO_0000637
Label(s): osteosarcoma
- 'osteosarcoma' SubClassOf 'bone neoplasm'
- 'osteosarcoma' SubClassOf 'musculoskeletal system cancer'
+ 'osteosarcoma' SubClassOf 'Malignant Bone Neoplasm'
Class: http://www.ebi.ac.uk/efo/EFO_0009029
Label(s): Central precocious puberty
+ 'Central precocious puberty' SubClassOf 'precocious puberty in female'
Class: http://purl.obolibrary.org/obo/MONDO_0021804
Label(s): silicotuberculosis
- 'silicotuberculosis' SubClassOf 'respiratory tract infectious disorder'
Class: http://www.ebi.ac.uk/efo/EFO_0003016
Label(s): collecting duct carcinoma
+ 'collecting duct carcinoma' SubClassOf 'Kidney Medullary Carcinoma'
Class: http://purl.obolibrary.org/obo/MONDO_0001926
Label(s): ureteral disorder
+ 'ureteral disorder' SubClassOf 'kidney disease'
Class: http://www.ebi.ac.uk/efo/EFO_1001769
Label(s): carcinoid heart disease
+ 'carcinoid heart disease' SubClassOf 'neoplasm of thorax'
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3. Obsolete Classes in EFO
@Classes deleted from this version
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4. Scope of the Ontology
The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue and Centre for Therapeutic Target Validation. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. We also add terms for external users when requested.
Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. The factors are modelled as classes (i.e. types) within the ontology and properties are used to add information about each type such as a textual definition and synonyms for that term label as well as axiomatic class descriptions such as whether the entity being described is part_of another entity or a subclass of it.
As an application focused ontology, we attempt to import and reuse classes where they exist in external, reference ontologies.
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5. External Ontology and Resource Mapping List
The full list of ontologies and external resources currently imported or mapped into EFO is as follows:
The Monarch Disease Ontology (MONDO)
Orphanet Rare Disease (version 2.0)
UBERON anatomy ontology
Chemical entities of biological interest (CHEBI)
Cell type ontology (CL)
Cell Line Ontology (CLO)
Mammalian phenotype (MP) ver1.309
Human Phenotype (HP)
Medical Subject Headings (MSH) ver2009_2009_02_13
International Classification of Diseases (ICD-9) ver9
Phenotypic quality (PATO) ver1.188
CRISP Thesaurus Version 2.5.2.0
Mosquito gross anatomy (TGMA) ver1.10
Human disease (DOID) ver1.88
Drosophila gross anatomy (FBbt) ver1.30
Foundational Model of Anatomy (FMA) ver3.0
The Arabidopsis Information Resource (TAIR) (various dates)
The Jackson Lab mouse database (various dates)
SNOMED Clinical Terms (SNOMEDCT) ver2009_01_31
Ontology for Biomedical Investigations (OBI)
Units of measurement (UO) ver1.21
Microarray experimental conditions (MO) ver1.3.1.1
Plant structure (PO)
Minimal anatomical terminology (MAT) ver1.1
NIFSTD (nif) ver1.4
NCI Thesaurus (NCIt) ver09.07
Zebrafish anatomy and development (ZFA) ver1.23
BRENDA tissue / enzyme source (BTO) ver1.3
Relation Ontology
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6. Known OWL to OBO Conversion Issues
We are using the OORT library to convert the OWL inferred view of the ontology into OBO. This is a lossy process and works only for the is_a axis. We discard much of the richness that is available in the OWL version of the EFO. We always recommend you use the OWL version of EFO as the primary resource if possible. More information can be obtained from www.ebi.ac.uk/efo or you can download the EFO OWL file directly from www.ebi.ac.uk/efo/efo.owl
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7. Contact Details
For questions and comments and to report any usage issues please visit the www.ebi.ac.uk/efo website, or e-mail efo-users@ebi.ac.uk