RGD Reference Report - OMIA Disease Annotation Pipeline - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)

OMIA Disease Annotation Pipeline

Authors: RGD automated, PIPELINES 
Citation: OMIA Disease Annotation Pipeline
RGD ID: 12801476
Web Url: http://omia.angis.org.au/download/

Gene-disease and gene-phenotype annotations are created for RGD genes based on associations imported from the Online Mendelian Inheritance in Animals (OMIA) database. OMIA "phene" terms are manually matched to RGD Disease Ontology (RDO) and Mammalian Phenotype Ontology (MP) terms by RGD curators and stored as alternative IDs (alt_ids) for the corresponding ontology terms in RGD. The causal_mutations/gene_table and omia.xml.zip files are downloaded from OMIA (http://omia.angis.org.au/download/) and species-specific lines (e.g. for dog) are extracted. Genes in the file are matched to RGD genes via the NCBI Gene ID and "phenes" are matched via the alternate IDs as detailed above. Since the downloaded data was not reviewed by RGD curators before making assignments, the evidence code assigned to these annotations is "IEA", that is, "inferred by electronic annotation". The PubMed ID(s) for the original associations are stored/presented in the XREF_SOURCE/"Original References" field. The pipeline is run and annotations updated on a weekly basis.