RGD Reference Report - CTD Disease Automated Import and Annotation Pipeline - Rat Genome Database

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CTD Disease Automated Import and Annotation Pipeline

Authors: RGD,   PIPELINES 
Citation: RGD automated import pipeline for CTD gene-to-disease annotations
RGD ID: 11554173
Web Url: http://ctdbase.org/

Gene-to-disease associations for which direct evidence is given are downloaded from the Comparative Toxicogenomics Database at http://ctdbase.org/reports/CTD_genes_diseases.tsv.gz. NCBI GeneIDs in the incoming file are matched to NCBI Gene XDB IDs for RGD genes. MeSH IDs in the "DiseaseID" column from the source file are matched to RGD Disease Ontology (RDO/MEDIC) terms using the RDO term synonyms in RGD and the terms are assigned to RGD gene records as RDO annotations. These annotations are given an evidence code of "EXP" or "Inferred from Experiment" for the source species and are automatically propagated to the orthologous genes with the "ISS" ("inferred from sequence or structural similarity") or "ISO" ("Inferred from Sequence Orthology") evidence code. The information in the "DirectEvidence" field in the source file is added to each annotation as a note, either "CTD Direct Evidence: therapeutic" or "CTD Direct Evidence: marker/mechanism". The reference PubMed IDs listed in the source file are loaded into the RGD "XREF_SOURCE" field and shown on RGD web pages as "Original Reference(s)". The source of the annotations is listed as "CTD".