tooluniverse-gene-disease-association

Resolve the gene symbol to Ensembl and HGNC identifiers, then query DisGeNET, OpenTargets, Monarch, OMIM, GenCC, and Orphanet for associations. Merge results into a unified table and rank diseases by how many databases support each link.

Resolve the disease name to a MONDO or UMLS identifier using MonarchV3_search, then query DisGeNET disease genes and Monarch gene-to-disease associations. Rank candidate genes by cross-database concordance and GenCC validity classifications.

Yes, DisGeNET tools require a DISGENET_API_KEY environment variable, obtainable free for academic use at disgenet.org. Without it, use OpenTargets and Monarch Initiative, which are free and cover much of the same data.

OMIM_get_gene_map requires the gene MIM number, not the phenotype MIM number. If OMIM calls fail, Monarch Initiative causal gene-disease associations include OMIM data without requiring an API key.

Strength is graded by concordance: count how many of the six databases support each association, then weigh evidence hierarchy. Mendelian segregation and GenCC Definitive classifications outrank GWAS hits and text-mining results.

GenCC handles gene renames automatically, but other tools require the current HGNC symbol. Use MyGene_query_genes to confirm the canonical symbol before querying DisGeNET, OpenTargets, or Monarch.