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://compbio.charite.de/jenkins/job/hpo.annotations/lastSuccessfulBuild/artifact/util/annotation/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 is downloaded from the Computational Biology Group at the Institute for Medical Genetics and Human Genetics at Charité-Universitätsmedizin Berlin (http://compbio.charite.de). Genes in the file are matched to RGD records via the shared NCBI/"Entrez" Gene ID and 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 specified through the corresponding OMIM and Orphanet IDs. As of April 2017, the downloaded file contains disease associations from both OMIM and Orphanet (ORPHA, http://www.orpha.net/). These IDs are loaded into the NOTES field for the annotations and link back to the corresponding databases.