| Why was the NetPath project started? |
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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 License. |
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| What are the various features that are annotated in every pathway? |
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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". |
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| What are your criteria for selecting a gene as up or down regulated by a ligand? |
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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. |
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| Is all the data contained in NetPath strictly from humans? |
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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. |
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| How can I use the Semantic Web Application Programming Interface (API) for querying NetPath? |
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The API is available as a web service and can be accessed through the URL - http://203.200.58.139:8080/PROJECTS/NetPath_SPARQL/sparqlAPI. The API contains two URL parameters: 'sparql_query' containing the SPARQL syntax and 'patwhay_id' specifying the pathway to be queried. The 'pathway_id' for all pathways in NetPath is avalable here. |
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