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RGD HPO Phenotype Annotation Pipeline

Authors: RGD,   AUTOMATED, PIPELINES 
Citation: RGD automated import pipeline for human HPO-to-gene-to-disease annotations
Web Url: http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt

The RGD human phenotype annotation pipeline imports associations between the Human Phenotype Ontology (HPO) and human genes. The file ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.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/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt). Genes in the file are matched to RGD records via the shared NCBI/"Entrez" Gene ID and annotations are made using the IEA or "Inferred from Electronic Annotation", evidence code. Additionally, the association of the gene and phenotype relationship to a specific disease is specified through the addition of an RDO (RGD Disease Ontology) term/ID to the HPO-gene annotation where that is possible. Disease IDs from column 1 of the input file are matched to the corresponding OMIM IDs in the RDO in order to present the correct disease association. As of April 2017, the downloaded file contained disease associations from both OMIM and ORPHANET (ORPHA, http://www.orpha.net/) in column 1. OMIM and ORPHA IDs which do not match XDB IDs on any RDO terms are added to the annotations as notes (i.e. loaded into the NOTES field for the annotation).
 
CRRD Object Information
CRRD ID: 8699517
Created: 2014-08-13
Species: All species
Last Modified: 2014-08-13
Status: ACTIVE



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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.