ExFactor Ontology release notes.txt

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EFO - Release Notes
Experimental Factor Ontology version 3.75.0
Date Released: 17th February 2025
Class Count: 63,496

Summary:

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

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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





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2. Changes to EFO3

@Classes modified from previous

Class: http://purl.obolibrary.org/obo/GO_1903510
Label(s): mucopolysaccharide metabolic process 
- 'mucopolysaccharide metabolic process' SubClassOf 'macromolecule metabolic process'
- 'mucopolysaccharide metabolic process' SubClassOf 'carbohydrate derivative metabolic process'
+ 'mucopolysaccharide metabolic process' SubClassOf http://www.w3.org/2002/07/owl#Thing

Class: http://purl.obolibrary.org/obo/FBbt_00007049
Label(s): head visceral muscle primordium 
- 'head visceral muscle primordium' SubClassOf 'Drosophila developmental tissue'
+ 'head visceral muscle primordium' SubClassOf http://www.w3.org/2002/07/owl#Thing

Class: http://purl.obolibrary.org/obo/GO_0006699
Label(s): bile acid biosynthetic process 
- 'bile acid biosynthetic process' SubClassOf 'steroid biosynthetic process'
+ 'bile acid biosynthetic process' SubClassOf 'biosynthetic process'
+ 'bile acid biosynthetic process' SubClassOf 'steroid metabolic process'

Class: http://purl.obolibrary.org/obo/UBERON_0004639
Label(s): renal afferent arteriole 
- 'renal afferent arteriole' SubClassOf 'artery'

Class: http://purl.obolibrary.org/obo/GO_0019915
Label(s): lipid storage 
- 'lipid storage' SubClassOf 'biological_process'
+ 'lipid storage' SubClassOf 'cellular process'



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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