# IGVF Catalog

## Docs

- [What is IGVF Catalog?](https://docs.catalog.igvf.org/introduction.md): IGVF Catalog allows you to query and visualize data from the IGVF Consortium
- [Main Search](https://docs.catalog.igvf.org/using-search.md): Use the main search bar to navigate the catalog
- [Gene](https://docs.catalog.igvf.org/nodes/gene.md)
- [Transcript](https://docs.catalog.igvf.org/nodes/transcript.md)
- [Variant](https://docs.catalog.igvf.org/nodes/variant.md)
- [Protein](https://docs.catalog.igvf.org/nodes/protein.md)
- [Motif](https://docs.catalog.igvf.org/nodes/motif.md)
- [Phenotype](https://docs.catalog.igvf.org/nodes/phenotype.md)
- [Drug](https://docs.catalog.igvf.org/nodes/drug.md)
- [Pathway](https://docs.catalog.igvf.org/nodes/pathway.md)
- [GO Term](https://docs.catalog.igvf.org/nodes/go-term.md)
- [Complex](https://docs.catalog.igvf.org/nodes/complex.md)
- [PMID](https://docs.catalog.igvf.org/nodes/pmid.md)
- [Ontology Terms](https://docs.catalog.igvf.org/nodes/ontologies.md)
- [Disease](https://docs.catalog.igvf.org/nodes/disease.md)
- [Study](https://docs.catalog.igvf.org/nodes/study.md)
- [Region](https://docs.catalog.igvf.org/nodes/region.md)
- [Variant Dashboard](https://docs.catalog.igvf.org/region/variant-dashboard.md)
- [Region Ancestry](https://docs.catalog.igvf.org/region/ancestry.md)
- [Home](https://docs.catalog.igvf.org/pages/home.md)
- [Search](https://docs.catalog.igvf.org/pages/search.md)
- [Lexical Search](https://docs.catalog.igvf.org/pages/lexical.md)
- [Browse Data](https://docs.catalog.igvf.org/pages/browse.md)
- [Catalog Apps](https://docs.catalog.igvf.org/pages/apps.md)
- [Cypher Query Runner](https://docs.catalog.igvf.org/pages/cypher.md)
- [Files and Filesets](https://docs.catalog.igvf.org/pages/files.md)
- [Chat Assistant](https://docs.catalog.igvf.org/pages/chat.md)
- [Glossary](https://docs.catalog.igvf.org/pages/glossary.md)
- [Data Sources](https://docs.catalog.igvf.org/pages/sources.md)
- [Settings](https://docs.catalog.igvf.org/pages/settings.md)
- [Data Sources Index](https://docs.catalog.igvf.org/data-sources/index.md): IGVF and ENCODE portal files referenced by the Catalog
- [Files & Filesets](https://docs.catalog.igvf.org/data-sources/files-filesets.md): How files_fileset links Catalog data to IGVF and ENCODE portal files
- [Field Lineage](https://docs.catalog.igvf.org/data-sources/field-lineage/index.md): Portal file columns through adapters to Catalog API fields
- [API Introduction](https://docs.catalog.igvf.org/api-reference/introduction.md): IGVF Catalog REST API — development environment
- [Variants](https://docs.catalog.igvf.org/api-reference/variants.md): Retrieve genetic variants.
- [Variants Frequency](https://docs.catalog.igvf.org/api-reference/variants-frequency.md): Retrieve genetic variants within a genomic region by frequencies.
- [Variants Genes](https://docs.catalog.igvf.org/api-reference/variants-genes.md): Retrieve variant-gene pairs including eQTLs & splice QTLs from AFGR and eQTL Catalogue, and CRISPR screen and Variant-EFFECTS from IGVF, by variants.
- [Variants Drugs](https://docs.catalog.igvf.org/api-reference/variants-drugs.md): Retrieve drugs associated with the query variants from pharmGKB.
- [Variants Summary](https://docs.catalog.igvf.org/api-reference/variants-summary.md): Retrieve genetic variants summary.
- [Variants Proteins](https://docs.catalog.igvf.org/api-reference/variants-proteins.md): Retrieve allele-specific transcription factor binding events from ADASTRA in cell type-specific context,
- [Variants Diseases](https://docs.catalog.igvf.org/api-reference/variants-diseases.md): Retrieve diseases and genes associated with the query variant from ClinGen.
- [Variants Variant Linkage Disequilibrium](https://docs.catalog.igvf.org/api-reference/variants-variant-linkage-disequilibrium.md): Retrieve genetic variants in linkage disequilibrium (LD).
- [Variants Phenotypes](https://docs.catalog.igvf.org/api-reference/variants-phenotypes.md): Retrieve variant-trait pairs from GWAS, SGE, and cV2F by variants.
- [Variants Biosamples](https://docs.catalog.igvf.org/api-reference/variants-biosamples.md): Retrieve data from STARR-seq, BlueSTARR, and MPRA for a given variant.
- [Variants Predictions](https://docs.catalog.igvf.org/api-reference/variants-predictions.md): Retrieve element gene predictions associated with a given variant.
- [Variants Genes Summary](https://docs.catalog.igvf.org/api-reference/variants-genes-summary.md): Retrieve a summary of associated genes from GTEx eQTLs & splice QTLs by internal variant ids.
- [Variants Nearest Genes](https://docs.catalog.igvf.org/api-reference/variants-nearest-genes.md): Retrieve a list of human genes if region is in a coding variant. Otherwise, it returns the nearest human genes on each side.
- [Variants Genes Proteins](https://docs.catalog.igvf.org/api-reference/variants-genes-proteins.md): Retrieve genes and proteins associated with a variant matched by ID.
- [Variants Region Summary](https://docs.catalog.igvf.org/api-reference/variants-region-summary.md): Retrieve a summary count of all methods reporting variants in a given region.
- [Variants gnomAD Alleles](https://docs.catalog.igvf.org/api-reference/variants-gnomad-alleles.md): Retrieve GNOMAD alleles for variants in a given region.
- [Variants Coding Variants](https://docs.catalog.igvf.org/api-reference/variants-coding-variants.md): Retrieve coding variants from dbSNFP associated with a variant.
- [Variants Genomic Elements](https://docs.catalog.igvf.org/api-reference/variants-genomic-elements.md): Retrieve genomic elements associated with a given variant.
- [Variants Predictions Count](https://docs.catalog.igvf.org/api-reference/variants-predictions-count.md): Retrieve counts of element gene predictions and cell types associated with a given variant.
- [Variants Variant Linkage Disequilibrium Summary](https://docs.catalog.igvf.org/api-reference/variants-variant-linkage-disequilibrium-summary.md): Retrieve a summary of genetic variants in linkage disequilibrium (LD).
- [Variants Phenotypes Score Summary](https://docs.catalog.igvf.org/api-reference/variants-phenotypes-score-summary.md): DEPRECATED. Please use coding-variants/phenotypes/summary.
- [Variants Genomic Elements Cell Gene Predictions](https://docs.catalog.igvf.org/api-reference/variants-genomic-elements-cell-gene-predictions.md): Retrieve predicted associated genes and cell types for a given variant.
- [Coding Variants](https://docs.catalog.igvf.org/api-reference/coding-variants.md): Retrieve coding variants annotations.
- [Coding Variants Variants](https://docs.catalog.igvf.org/api-reference/coding-variants-variants.md): Retrieve variants associated with a coding variant.
- [Coding Variants Phenotypes](https://docs.catalog.igvf.org/api-reference/coding-variants-phenotypes.md): Retrieve phenotypes associated with the query coding variant.
- [Coding Variants Phenotypes Count](https://docs.catalog.igvf.org/api-reference/coding-variants-phenotypes-count.md): Retrieve counts of coding variants associated with phenotypes.
- [Coding Variants Phenotypes Score Summary](https://docs.catalog.igvf.org/api-reference/coding-variants-phenotypes-score-summary.md): Retrieve scores of variants or coding_variants associated with phenotypes. Via coding variants edges.
- [Genes](https://docs.catalog.igvf.org/api-reference/genes.md): Retrieve genes.
- [Genes Genes](https://docs.catalog.igvf.org/api-reference/genes-genes.md): Retrieve coexpressed gene pairs from CoXPresdb and genetic interactions from BioGRID.
- [Genes Proteins](https://docs.catalog.igvf.org/api-reference/genes-proteins.md): Retrieve proteins from genes.
- [Genes Variants](https://docs.catalog.igvf.org/api-reference/genes-variants.md): Retrieve variant-gene pairs including eQTLs & splice QTLs from AFGR and eQTL Catalogue, and CRISPR screen and Variant-EFFECTS from IGVF, by Ensembl gene ids.
- [Genes Diseases](https://docs.catalog.igvf.org/api-reference/genes-diseases.md): Retrieve disease-gene pairs from Orphanet, GenCC and ClinGen by genes.
- [Genes Pathways](https://docs.catalog.igvf.org/api-reference/genes-pathways.md): Retrieve pathways from genes.
- [Genes Structure](https://docs.catalog.igvf.org/api-reference/genes-structure.md): Retrieve genes structure.
- [Genes Transcripts](https://docs.catalog.igvf.org/api-reference/genes-transcripts.md): Retrieve transcripts from genes.
- [Genes Genomic Elements](https://docs.catalog.igvf.org/api-reference/genes-genomic-elements.md): Retrieve genomic elements and gene pairs by querying genes.
- [Genes Proteins Variants](https://docs.catalog.igvf.org/api-reference/genes-proteins-variants.md): Retrieve variants associated with genes or proteins that match a query.
- [Genes Coding Variants Scores](https://docs.catalog.igvf.org/api-reference/genes-coding-variants-scores.md): Retrieve scores and predictions of associated coding variants for one specific gene.
- [Genes Proteins Genes Proteins](https://docs.catalog.igvf.org/api-reference/genes-proteins-genes-proteins.md): Retrieve genes or proteins associated with either genes or proteins that match a query.
- [Genes Coding Variants All Scores](https://docs.catalog.igvf.org/api-reference/genes-coding-variants-all-scores.md): Retrieve a list of all numeric scores of associated coding variants for a gene and a dataset.
- [Gene Products GO Terms](https://docs.catalog.igvf.org/api-reference/gene-products-go-terms.md): Retrieve GO terms from either proteins or transcripts.
- [Transcripts](https://docs.catalog.igvf.org/api-reference/transcripts.md): Retrieve transcripts.
- [Transcripts Genes](https://docs.catalog.igvf.org/api-reference/transcripts-genes.md): Retrieve genes from transcripts.
- [Transcripts Proteins](https://docs.catalog.igvf.org/api-reference/transcripts-proteins.md): Retrieve proteins from transcripts.
- [Proteins](https://docs.catalog.igvf.org/api-reference/proteins.md): Retrieve proteins.
- [Proteins Genes](https://docs.catalog.igvf.org/api-reference/proteins-genes.md): Retrieve genes from proteins.
- [Proteins Motifs](https://docs.catalog.igvf.org/api-reference/proteins-motifs.md): Retrieve motifs for proteins.
- [Proteins Variants](https://docs.catalog.igvf.org/api-reference/proteins-variants.md): Retrieve allele-specific transcription factor binding events from ADASTRA in cell type-specific context,
- [Proteins Proteins](https://docs.catalog.igvf.org/api-reference/proteins-proteins.md): Retrieve protein-protein interactions.
- [Proteins Complexes](https://docs.catalog.igvf.org/api-reference/proteins-complexes.md): Retrieve complexes by querying from protein participants. Each record includes protein and complex.
- [Proteins Transcripts](https://docs.catalog.igvf.org/api-reference/proteins-transcripts.md): Retrieve transcripts from proteins.
- [Genomic Elements](https://docs.catalog.igvf.org/api-reference/genomic-elements.md): Retrieve genomic elements.
- [Genomic Elements Genes](https://docs.catalog.igvf.org/api-reference/genomic-elements-genes.md): Retrieve genomic elements and gene pairs by querying genomic elements.
- [Genomic Elements Variants](https://docs.catalog.igvf.org/api-reference/genomic-elements-variants.md): Retrieve variants associated with genomic elements.
- [Genomic Elements Biosamples](https://docs.catalog.igvf.org/api-reference/genomic-elements-biosamples.md): Retrieve MPRA experiments by querying positions of genomic elements.
- [Diseases Genes](https://docs.catalog.igvf.org/api-reference/diseases-genes.md): Retrieve disease-gene pairs from Orphanet and GenCC by diseases.
- [Diseases Variants](https://docs.catalog.igvf.org/api-reference/diseases-variants.md): Retrieve variants and genes associated with the query disease from ClinGen.
- [Phenotypes Variants](https://docs.catalog.igvf.org/api-reference/phenotypes-variants.md): Retrieve variant-trait pairs from GWAS, SGE, and cV2F by phenotypes.
- [Phenotypes Coding Variants](https://docs.catalog.igvf.org/api-reference/phenotypes-coding-variants.md): Retrieve coding variants associated with the query phenotype.
- [Ontology Terms](https://docs.catalog.igvf.org/api-reference/ontology-terms.md): Retrieve ontology terms.
- [Ontology Terms Parents](https://docs.catalog.igvf.org/api-reference/ontology-terms-parents.md): Retrieve all parent nodes of an ontology term.
- [Ontology Terms Children](https://docs.catalog.igvf.org/api-reference/ontology-terms-children.md): Retrieve all child nodes of an ontology term.
- [Ontology Terms Transitive Closure](https://docs.catalog.igvf.org/api-reference/ontology-terms-transitive-closure.md): Retrieve all paths between two ontology terms (i.e. transitive closure).
- [GO Terms Gene Products](https://docs.catalog.igvf.org/api-reference/go-terms-gene-products.md): Retrieve annotations associated with a GO term.
- [Motifs](https://docs.catalog.igvf.org/api-reference/motifs.md): Retrieve transcription factor binding motifs from HOCOMOCO.
- [Motifs Proteins](https://docs.catalog.igvf.org/api-reference/motifs-proteins.md): Retrieve proteins and complexes for motifs.
- [Studies](https://docs.catalog.igvf.org/api-reference/studies.md): Retrieve studies from GWAS.
- [Complexes](https://docs.catalog.igvf.org/api-reference/complexes.md): Retrieve complexes.
- [Complexes Proteins](https://docs.catalog.igvf.org/api-reference/complexes-proteins.md): Retrieve protein participants for complexes. Each record includes complex and protein.
- [Drugs](https://docs.catalog.igvf.org/api-reference/drugs.md): Retrieve drugs (chemicals).
- [Drugs Variants](https://docs.catalog.igvf.org/api-reference/drugs-variants.md): Retrieve variants associated with the query drugs from pharmGKB.
- [QTLs](https://docs.catalog.igvf.org/api-reference/qtls.md): Retrieve QTLs from gene, variant, or region.
- [Health](https://docs.catalog.igvf.org/api-reference/health.md): Health check endpoint for the API service
- [Pathways](https://docs.catalog.igvf.org/api-reference/pathways.md): Retrieve pathways from Reactome.
- [LLM Query](https://docs.catalog.igvf.org/api-reference/llm-query.md): Ask a question that interests you. This API is password protected.
- [Autocomplete](https://docs.catalog.igvf.org/api-reference/autocomplete.md): Autocomplete names for genes and proteins based on prefix search.
- [Pathways Genes](https://docs.catalog.igvf.org/api-reference/pathways-genes.md): Retrieve genes from pathways.
- [Files Filesets](https://docs.catalog.igvf.org/api-reference/files-filesets.md): Retrieve data about a specific dataset.
- [Pathways Pathways](https://docs.catalog.igvf.org/api-reference/pathways-pathways.md): Retrieve related pathway pairs from Reactome.
- [Biosamples Variants](https://docs.catalog.igvf.org/api-reference/biosamples-variants.md): Retrieve data from STARR-seq, BlueSTARR, and MPRA for a given biosample.
- [Gene Regulatory Network](https://docs.catalog.igvf.org/api-reference/gene-regulatory-network.md): Retrieve regulatory or response genes for a given regulatory gene. The network is modeled as: (regulators) -> (responses).
- [Enhancer Gene Predictions](https://docs.catalog.igvf.org/api-reference/enhancer-gene-predictions.md): Retrieve genomic elements and gene pairs by querying genomic elements.
- [Biosamples Genomic Elements](https://docs.catalog.igvf.org/api-reference/biosamples-genomic-elements.md): Retrieve MPRA expriments by querying cell ontology terms.

## OpenAPI Specs

- [catalog-dev.openapi](https://docs.catalog.igvf.org/openapi/catalog-dev.openapi.json)


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