Documentation Index
Fetch the complete documentation index at: https://docs.catalog.igvf.org/llms.txt
Use this file to discover all available pages before exploring further.
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 page showing the relationship path between the current term and the one you entered
Each table can be sorted by clicking on the column headers. You can also use the search box above each table to filter the results.
Associated Variants (Disease terms)
Variant-Disease-Genes annotations are loaded from the ClinGen database, also found on the Variant pages
Genes (Disease terms)
Disease-Gene edges are loaded in the IGVF Catalog from [Orphanet](https://www.orpha.net/, also found on the Gene pages
Protein - GO Annotations
Proteins (technically gene products) are annotated by the Gene Ontology project GAF files;
these are represented as edges between proteins and ontology (GO) terms. These are displayed in on the Protein
