Thursday, March 24, 2011

Are You Being Served?

A table of pathways with omics data.
(click to enlarge)
This post will provide a brief survey of the Pathway Tools Web Services.  These services can be used to access any site running the latest version (15.0) of Pathway Tools.  Thus, you can invoke them for any of the 1000+ PGDBs served by the BioCyc website without installing the Pathway Tools software locally, or you can install and run the software yourself in order to create queries (or allow other users to create queries) that access your own PGDBs.

XML Data Retrieval Web Services

With the release of Pathway Tools 14.5 last fall, we unveiled a set of XML-based web services designed to allow users to programmatically query and retrieve data from a Pathway Tools web server.

If you know the object identifier of any Pathway Tools object (such as a gene, compound, reaction, protein, transcription unit, etc.), you can retrieve its data (at low or full detail) in ptools-xml format, an XML format that maps closely to the underlying Pathway Tools schema.  For pathways, you have the choice of retrieving data in ptools-xml format or in BioPAX format. If you don't know the object identifier of the object(s) you want, you can issue a query using a subset of the BioVelo query language. See the BioCyc Web Services page for details, including query syntax, a description of the ptools-xml format, and multiple examples of BioVelo queries.

How might you use this?  One terrific example is Scooter Morris' new bioCycPlugin for Cytoscape. He uses our ptools-xml interface to query a Pathway Tools website (which defaults to BioCyc) to first determine the list of available organisms, and then to return a list of pathways matching a user query. When the user selects a pathway of interest, the plugin retrieves its data in BioPAX format and loads it into Cytoscape.

Data Upload Web Services
A pathway drawn with omics data.
(click to enlarge)

Other types of services allow you to manipulate some of the pages generated by Pathway Tools to add your own omics and other data.  Details of how to specify this information can be found in sections 4.13-4.16 in the Pathway Tools Website User Guide. The following operations, some of which are brand new in the just-released Pathway Tools version 15.0, are available:
  • Specify a set of highlights for the Cellular Overview Diagram.  Indicate as part of the URL a set of reactions, pathways, genes, enzymes or compounds.  The diagram will be generated with the appropriate objects pre-highlighted.
  • Upload omics data to show on the Cellular Overview Diagram.  This can be done using either the GET or POST method.
  • Generate a table of pathway diagrams for a specified set of pathways, either with or without omics data.  You can request either a list of specific pathways (by object identifier), or all pathways whose omics data exceeds some threshold.  This can be done using either the GET or POST method.
  • Show a regular pathway page, but superimpose the pathway diagram with omics data from a URL you supply (GET method only).
One possible application of these services is for a site with access to an omics data repository to add value to that data by linking it to our views of the data's metabolic context (either the full overview, or specific pathways of interest).  I'm sure our users can come up with other ideas!

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