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acquiring and integrating data from a wide variety of sources into the database helps to deliver new capabilities, which is the top priority for release 2.1. this important release will bring together the following components: a query service that will translate biopax and psi-mi queries into database queries based on lucent’s original work on biopax import; a data service for importing biopax and psi-mi records; and a new biopax viewer for creating bngl-formatted use cases (summary files) to drive new analytics. biopax -based queries can be used to deliver and display this information. the new psi-mi 2.5 import and display capabilities provide an alternative way to discover and analyze pathway data. the biopax query service will also display pathways created by pathway tools [ 7 ] -based tools. the biopax query service will provide users access to the content of biopax level 3.0 files and biopax-based use cases.
in addition, we will provide a pathway visualization service based on maude [ 8 ], which is derived from cytoscape [ 9 ], for displaying pathway content. this tool includes built-in biopax and psi-mi validators to ensure that the displayed pathways are valid biopax and psi-mi-formatted representations of the underlying data.
a common question posed by many of our customers is, “what is out of reach?” as most of them are now familiar with the capabilities of the open source software contained in the lucent software repository, they want to know what we are currently working on. we have found that the psi-mi community consists of several independent working groups, each with a clearly defined vision and mission. we have decided not to become a member of any of these groups and to concentrate on delivering our own set of solutions. the first of these is cpath. currently under development, cpath will provide an integrated analytical solution to lucent from a single perspective, although other future projects are envisioned as well, such as allowing users to create their own workflows, containing multiple compatible analytic views that can be queried individually or combined into a single workflow. the goal of cpath is to move from a single tool to a suite of complementary tools that will allow users to solve a wide variety of problems, in addition to providing more advanced capability to data import and analysis.
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