Pipeline to import Pathway Interaction Database annotations from NCI into RGD
The Pathway Interaction Database (PID) Annotation Import Pipeline:
Data was originally imported from the Pathway Interaction Database (PID - http://pid.nci.nih.gov/). Data was extracted from the file "NCI-Nature Curated Pathway--> UniProt mapping". The RGD Pathway Ontology (PW) was searched for mappings between RGD pathway terms and the internal PID IDs in the file via related_synonyms. Genes in the PID pathway were then matched to RGD human genes using the UniProt protein ID. The human genes were annotated to the appropriate PW terms with evidence code "EXP" or "inferred from experimental evidence" Annotations were propagated to the rat and mouse orthologs with evidence code "ISO" or "inferred from sequence orthology". NCBI retired the PID database in September of 2013. At that time the existing annotations to RGD genes were retained but "frozen" (i.e., they will no longer be updated). Links to PID became non-functional with the retirement of the database and have been removed.