Ontology Terms
The IGVF Catalog uses a set of ontologies to represent biological and experimental concepts and identities that are useful in annotation entities and contexts.| Ontology | URL | Description | Usage |
|---|---|---|---|
| CHEBI | http://www.ebi.ac.uk/chebi | Chemical Entities of Biological Interest | Drugs and Chemicals |
| Cellosaurus | https://www.cellosaurus.org/ | A knowledge resource on cell lines | Biosamples |
| NCIT | https://github.com/ncit-obo-org/ncit-obo-edition | NCI Thesarus (OBO edition) | Phenotypes and others |
| EFO | http://www.ebi.ac.uk/efo | Experimental Factor Ontology | Assays and others |
| CLO | https://github.com/CLO-Ontology/CLO | Cell Line Ontology | Biosamples |
| GO | http://geneontology.org/ | Gene Ontology | Functional Annotations |
| MONDO | https://monarch-initiative.github.io/mondo | Merge of multiple Disease Ontologies | Diseases and Phenotypes |
| HPO | http://www.human-phenotype-ontology.org/ | Human phenotypic abnormalities | Phenotypes |
| CL | https://obophenotype.github.io/cell-ontology/ | Cell types | Biosamples |
| ORPHANET | https://www.orpha.net/ | Rare diseases | Diseases |
| UBERON | http://uberon.org/ | Integrated cross-species anatomy ontology | Biosamples |
| Oncotree | https://oncotree.mskcc.org/ | Community-led cancer classification system | Diseases |
| VARIO | https://obofoundry.org/ontology/vario | Description of effects, consequences, and mechanisms of variations | Genetic entites |
| ENCODE | https://encodeproject.org | Special terms created for the ENCODE project | Biosamples |
| BAO | http://bioassayontology.org/ | Bioassay Ontology | Assays targets |
| OBA | https://github.com/obophenotype/bio-attribute-ontology | Ontology of Biological Attributes | Assay targets |
Disease-Gene Association Network
A graph showing the Disease and Genes it’s linked to (only Disease ontologies)Ontology Term Parents Table
This table shows the parent terms of the current ontology term you’re viewing.| Column | Description |
|---|---|
| Relationship Type | Describes how this term relates to its parent |
| Term ID | Unique identifier for the parent term (click to view its page) |
| Name | Name of the parent term (hover to see full text if it’s long) |
| Description | Description of the parent term (hover to see full text if it’s long) |
| Source | Origin of the term information (click for more details) |
| Subontology | Subgroup of the ontology this term belongs to |
| Synonyms | Alternative names for the term (click to expand if there are many) |
Ontology Term Children Table
This table displays the child terms of the current ontology term.| Column | Description |
|---|---|
| Relationship Type | Describes how this term relates to its child |
| Term ID | Unique identifier for the child term (click to view its page) |
| Name | Name of the child term (hover to see full text if it’s long) |
| Description | Description of the child term (hover to see full text if it’s long) |
| Source | Origin of the term information (click for more details) |
| Subontology | Subgroup of the ontology this term belongs to |
| Synonyms | Alternative names for the term (click to expand if there are many) |
Transitive Closure
At the bottom of the page, you’ll see a link labeled “Enter Closure End”. This feature allows you to explore the relationship between the current term and any other term in the ontology. To use this feature:- Click on “Enter Closure End”
- A prompt will appear asking you to enter another ontology term
- Type in the term ID (e.g., UBERON_0014892)
- Press Enter or click OK
- You’ll be taken to a new page showing the relationship path between the current term and the one you entered