External Data Sources

Docs

The IGVF Catalog integrates and links out to a number of trusted, external resources. Below is a consolidated list of sources that power various data panels across the app. Where possible, each panel also provides per-row source links and consistent attribution.

Data Transformation & Filtering

To keep results fast and focused, responses returned by our internal endpoints may be normalized and filtered before display. Typical processing includes:

  • Schema mapping of raw fields into a unified model (e.g., mapping nested properties or flattening arrays).
  • Applying panel-specific filters (e.g., organism, coding vs. noncoding categories, study/source filters).
  • Optional transformations noted by pages, such as taking the first item from a list or mapping over an item field.
  • Supplemental fetches to enrich rows with additional context (when indicated).

Developers can inspect an endpoint's exact URL, applied filters, and transformation steps with the X-ray view in data panels where available.

Catalog Sources

Object TypeSourceLink
Variants
FAVOR (dbSNP155)
Visit
Genes, Proteins, Transcripts, Human
GENCODE v43
Visit
Genes, Proteins, Transcripts, Mouse
GENCODE m33
Visit
Proteins
UniProt
Visit
QTLs
EBI QTL Catalogue
Visit
QTLs
AFGR
Visit
eQTLs
GTEx
Visit
pQTLs
UK Biobank Plasma Proteomic Profiles
Visit
Motifs
HOCOMOCO v11
Visit
Allele specific binding
AdAstra
Visit
Allele specific binding
GVATdb
Visit
Protein Protein Interactions, Genetic Interactions
BioGRID
Visit
Protein Protein Interactions
IntAct
Visit
Gene Co-expression
CoXpressDB
Visit
Pathways
Reactome
Visit
GWAS studies
OpenTargets
Visit
Macromolecular Complexes
EBI Complex Portal
Visit
Varian/Gene/Drug Associations
PharmGKB
Visit
Rare Disease Genes
Orphanet
Visit
Variant-Gene-Disease Associations
ClinGen
Visit
Human-Mouse Orthologies
Mouse Genome Informatics
Visit
Coding Variants
dbNSFP 4.1
Visit
Linkage Disequilibria
TopLD
Visit
Cancer Gene Dependency
DepMap
Visit
Protein variant phenotypes
VAMP-seq
Visit