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FAQ's
Why was the NetPath project started?
  Signaling pathways are rarely brought about by isolated reactions but rather by a cascade of events that can involve multiple subcellular compartments. Often, signaling pathways are studied with a focus on the roles of isolated members which makes it difficult to generate a comprehensive view of the pathway as a whole. There are other efforts in the public domain although they are generally not very detailed. In order to address these issues, we initiated the NetPath project. These pathways are freely available to all under the Creative Commons Attribution 2.5 License.
 
What are the various features that are annotated in every pathway?
  Each pathway has information pertaining to protein-protein interactions that occur upon ligand stimulation of a receptor, enzyme catalysis events, translocation of proteins from one subcellular compartment to another and genes which are up or downregulated by the pathway. All these events are together termed as "reactions."
 
What are your criteria for selecting a gene as up or down regulated by a ligand?
  If the differential expression of the gene is occurring in human cells/cell lines upon stimulation by the ligand, we add it to our list. This information could be derived from microarray or non-micorarray experiments.
 
Is all the data contained in NetPath strictly from humans?
  NetPath does contain data from mammals other than humans and only rarely is data from non-mammalian included provided that there was no other report that was human specific and if that molecule/reaction was widely accepted to be a component of the given signaling pathway as reported by the review articles and pathway authorities. However, the gene regulation data from microarray studies are specific to humans.
 
What does it mean when a reaction does not have an upstream enzyme?
  When a reaction does not have an upstream enzyme, it means that the upstream enzyme is unknown. Also, wherever the upstream enzyme and its substrate are mentioned in the catalytic reactions, it should also be considered as direct physical interactions.
 
How can I use the Semantic Web Application Programming Interface (API) for querying NetPath?
  The API is available as a web service and can be accessed through the URL - http://www.netpath.org/doSPARQL. The API contains two URL parameters: 'sparqlQuery' containing the SPARQL syntax and 'patwhayID' specifying the pathway to be queried. Click here to get the 'pathwayID' for all pathways in NetPath.
 
Does NetPath provide batch download?
  NetPath provides batch download of all pathway data including transcriptionally regulated genes. Click here to go the batch download page.
 


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