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phenotype_to_genes.txt

The phenotype_to_genes.txt file displays the HPO identifier and term name, the NCBI Gene identifier, the gene symbol, and the disease identifier. This file shows each HPO term that has at least one gene associated with it. In contrast to the genes_to_phenotypes.txt file, this file includes the ancestor classes of each associated phenotype. For example given that:

  • HP_1 subclass_of HP_3
  • HP_1 subclass_of HP_3

then genes_to_phenotypes.txt would have:

  • geneA annotated to HP_1
  • geneB annotated to HP_2

then phenotype_to_genes.txt contains:

  • HP_3 annotates geneA and geneB

File format

Here is a sample of the file format.

hpo_id hpo_name ncbi_gene_id gene_symbol disease_id
HP:0003300 Ovoid vertebral bodies 1280 COL2A1 OMIM:184255
HP:0003300 Ovoid vertebral bodies 1280 COL2A1 OMIM:271700
HP:0003300 Ovoid vertebral bodies 1280 COL2A1 OMIM:151210
HP:0003300 Ovoid vertebral bodies 1280 COL2A1 ORPHA:
HP:0003300 Ovoid vertebral bodies 1280 COL2A1 OMIM:183900
HP:0003300 Ovoid vertebral bodies 1280 COL2A1 ORPHA:1856
HP:0003300 Ovoid vertebral bodies 2335 FN1 OMIM:184255
HP:0003300 Ovoid vertebral bodies 2335 FN1 ORPHA:93315
HP:0003300 Ovoid vertebral bodies 126792 B3GALT6 ORPHA:536467
HP:0003300 Ovoid vertebral bodies 126792 B3GALT6 OMIM:271640
HP:0003300 Ovoid vertebral bodies 4882 NPR2 OMIM:602875