RGD Reference Report - RGD HPO Phenotype Annotation Pipeline - Rat Genome Database

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RGD HPO Phenotype Annotation Pipeline

Citation: RGD automated import pipeline for human HPO-to-gene-to-disease annotations
RGD ID: 8699517
Web Url: http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt

The RGD human phenotype annotation pipeline imports associations between the Human Phenotype Ontology (HPO) and human genes. The file genes_to_phenotype.txt (http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt) provided by the HPO group at The Jackson Laboratory is downloaded and genes in the file are matched to RGD records via the shared NCBI Gene ID. Annotations are made using the IAGP or "Inferred from Association of Genotype to Phenotype", evidence code based on the genetic nature of the original diseases/phenotypes. Additionally, the association of the gene and phenotype relationship to a specific disease is designated via the corresponding OMIM and Orphanet IDs (ORPHA, http://www.orpha.net/) found in the last ("disease_id") column of the download file. These IDs are loaded into the "Original reference" field of the RGD annotation and link back in each case to the corresponding database.