CiliaHub Data API

Programmatic access to the CiliaHub ciliary gene and ciliopathy disease database. All endpoints return JSON and are free to use for research purposes.

Research use: These endpoints serve the CiliaHub web application and are available for research and bioinformatics use. Please cite CiliaHub if you use this data in publications. Rate limit: 60 requests/minute.

Ciliary Gene Endpoints

GET /data/genes/ciliary_genes.json
Full ciliary gene database — 2,615 genes with localization, LoF effects, functional categories, orthologs and phenotypes.
fetch('https://ciliahub.org/data/genes/ciliary_genes.json') .then(r => r.json()) .then(data => { const gene = data.genes['CEP290']; console.log(gene.lof_effect_on_cilia_length); // "Decrease" console.log(gene.localization); // ["transition zone", "basal body"] });
GET /data/genes/ciliary_genes.json → genes[SYMBOL]
Single gene lookup — access any gene by symbol key.
// Example: get IFT88 data fetch('https://ciliahub.org/data/genes/ciliary_genes.json') .then(r => r.json()) .then(data => console.log(data.genes['IFT88']));

Ciliopathy Disease Endpoints

GET /data/ciliopathy/ciliopathy_by_gene.json
Curated ciliopathy gene-disease associations — 579 genes with classifications (Primary/Motile/Idio-ciliary), diseases, and references.
fetch('https://ciliahub.org/data/ciliopathy/ciliopathy_by_gene.json') .then(r => r.json()) .then(data => { const gene = data.genes['ARL13B']; console.log(gene.classifications); // ["Primary Ciliopathies"] console.log(gene.diseases); // ["Joubert Syndrome"] });
GET /data/ciliopathy/ciliopathy_by_class.json
Genes indexed by ciliopathy classification — Primary, Motile, Idio-ciliary, Secondary.
fetch('https://ciliahub.org/data/ciliopathy/ciliopathy_by_class.json') .then(r => r.json()) .then(data => { const primary = data.by_classification['Primary Ciliopathies']; console.log(primary.length); // 165 genes });

Data Schema

ciliary_genes.json → genes[SYMBOL]:
gene · ensembl_gene_id · description · omim_id
lof_effect_on_cilia_length (Decrease/Increase/No effect)
overexpression_effect_on_cilia_length
effect_on_ciliated_cell_percentage
localization (array) · functional_category (array)
functional_summary · references (PMID array)
orthologs {mouse, c_elegans, xenopus, zebrafish, drosophila}
phenotypes {mouse_ciliopathy, mouse, human_ciliopathy, human}

ciliopathy_by_gene.json → genes[SYMBOL]:
gene · omim_id · localization
classifications (array) · diseases (array)
disease_refs (PMID array) · functional_summary
candidate (boolean, omitted if false)

Citation

If you use CiliaHub data in your research, please cite:

CiliaHub: A curated database of ciliary genes and ciliopathy disease associations. ciliahub.org

For ciliopathy disease data, also cite CiliaMiner: ciliaminer.com ↗