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SMPDB Annotation Import Pipeline

Authors: RGD, PIPELINES 
Citation: Pipeline to import SMPDB annotations from SMPDB into RGD

The Small Molecule Pathway Database (SMPDB) Annotation Import Pipeline. Data is imported from the Small Molecule Pathway Database (SMPDB – http://smpdb.ca/). Data is extracted from the file “Protein names linked to SMPDB pathways”. The SMPDB IDs in the file are searched for mapping to RGD Pathway ontology (PW) terms via related_synonym. The genes in the file are matched to human genes in RGD using the GenBank accession ID. The human genes are annotated to the PW term with evidence code “EXP”, ‘Inferred from Experimental Evidence”. Annotations are propagated to the orthologous rat and mouse genes with evidence code “ISO”, “inferred from Sequence Orthology”.
 
CRRD Object Information
CRRD ID: 10402751
Created: 2015-10-28
Species: All species
Last Modified: 2015-10-28
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.