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Category Cross-Omics>Pathway Knowledge Bases/Databases/Tools Abstract PathCase is an integrated software system for storing, managing, analyzing, and querying biological pathways at different levels of genetic, molecular, biochemical and organismal detail. At the computational level, PathCase allows users to visualize pathways in multiple abstraction levels, and to pose predetermined as well as ad hoc queries using a graphical user interface. Pathways are represented as graphs, and implemented as a relational database. PathCase has multiple levels, with multiple tools at each level. The PathCase web client is a web-based interface to the PathCase Database, and provides a web-based toolset via a Java applet loaded within a browser window. It is designed as an intuitive and easy-to-use tool, with No need to study user manuals. The PathCase Desktop Client is a desktop application for browsing and interacting with the PathCase database. The desktop client is discontinued, but the latest version can still be found under the "Legacy Software" link on the manufacturer’s web-site. PathCase currently runs on two different data sets: (1) PathCase featuring KEGG pathways, and (2) PathCase featuring sample pathways from literature. Products main components are as follows: (Note: Some of these components are only available in the desktop client). Pathway Browser -- The Pathway Browser provides a tree-structured view of the metabolic pathways, and signaling pathways available in the database. Metabolic pathways, processes, and molecular entities can be browsed in different orders, and a set of useful queries can be specified about pathways, processes and molecular entities, from predefined simple queries to parameterized path selection and neighborhood queries. Similarly, for signaling pathways, signaling steps, and signaling and signaled molecules and their components can be browsed; a set of useful queries for signaling pathways are presently being developed. Pathway Viewer -- The Pathway Viewer presently visualizes a single metabolic pathway or multiple metabolic pathways in an organism-specific or organism- independent manner, provides a large number of functionalities including collapsing-zooming, hiding-expanding, editing, and node property-setting. The tool supports ad-hoc querying of the pathways data as well as menu-driven queries. It also provides a seamless transition from metabolic pathways to signaling pathways, and from signaling steps that belong to metabolic pathway processes into the relevant pathways. Pathway viewer for signaling pathways is currently under construction. Pathway Explorer (Advanced Query Interface) -- Pathway Explorer provides a generic user interface for posing a large class of queries about pathways using tree-structured views. Entities involved in the pathways database can be better viewed by generalization/specialization hierarchies, e.g., classes of pathways, super pathways, functional classifications in arbitrary granularities, etc. In addition, pathway components, i.e., processes in a pathway, and molecular entities involved in each process can naturally be viewed in the form of a tree-structured (hierarchical) view. Motivated by this observation, Pathways Explorer is a query interface which allows users to query the database using tree-structured views. As an example, consider the tree- structured (hierarchical) schema Pathways-Process-Molecular entity, where a pathway consists of several processes, and each process is associated with several molecular entities. This may also be visualized as a logical schema of a nested relation (Pathways (Process (Molecular_Entity)*)*), or an XML view. Thus, Pathways Explorer can also be considered as a query interface for querying tree-structured views for a relational database. Pathway Editor -- (Note: This component is currently functional for metabolic pathways). Pathway Editor provides a set of tools for the end users to access and edit the data residing in the database. Pathway Editor has a wizard style interface, similar to an installation program. Through the main wizard forms and various pop-up dialog forms, users can browse, edit, and create pathways, processes and molecules. The key features of Pathway Editor are: 1) Creating new pathways, processes, molecular entities and storing them in the database server; 2) Editing pathways by adding or removing processes; 3) Editing processes by adding or removing molecular entities; 4) Changing a molecular entity’s name, entering synonyms; 5) Changing molecular entity’s role in a process; 6) Adding or editing external links to local pathways, processes or molecular entities; 7) Verifying pathways; 8) Deleting pathways, processes, and molecules. Pathway Web Services -- The Pathway web services component provides many querying functions that are available over the Internet. This component has a function for each query it implements. Pathway tools in any machine connected to the Internet can use SOAP (Simple Object Access Protocol) to invoke these functions, and receive query results. The manufacturer has implemented over forty (40) functions. Querying functions are categorized into five (5) types: molecular entity queries, reaction (process) queries, pathway queries, organism queries and path computations. J-Viewer -- A Java version of the graphical tool to view pathway graphs -- The J-Viewer of the Pathway Database System consists of two components: J-Pathway Browser and J-Pathway Viewer. The J-Pathway Browser Tool is a tool that hierarchically lists the pathways, processes, and molecular entities in the database, and allows users to (a) view textual information, and (b) launch the J- Pathway Viewer that visualizes pathway graphs. The J-Pathway Viewer of the Pathway System provides a visual interface to biochemical pathways stored in the underlying database. The Pathway Viewer is basically a graph drawing and manipulation tool. J- Pathway Viewer provides an intuitive and highly visual means for biochemists to study, query, and curate biological pathways. The tool supports ad-hoc querying of the pathways data as well as menu-driven queries. Note: J-Viewer has lesser functionality than the Pathway Browser (.net version), and the data comes from the older database with 38 pathways. System Requirements You must have version 1.6 or later of the Java browser plug-in installed on your system to view pathway graphs. To download the latest version of the free plug-in, go to Sun's JRE 1.6 (also known as version 6.0) download page.
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Pathways Database System Group Department of Electrical Engineering and Computer Science, Olin 506 10900 Euclid Ave. Cleveland, Ohio 44106 E-mail: pathcase@case.edu Manufacturer's Web Site http://nashua.case. edu/PathwaysWeb/Default.aspx Price PathCase is an academic research tool, and we would be more than happy to share our knowledge with other researchers who could benefit from it. Please contact us at pathcase@case.edu with your name, organization, and your request.
from KEGG as we are not licenced to do so (to download KEGG pathways data, please directly use the KEGG site), and (b) PathCase sample pathways database as this data is collected from and available in the literature. The installation and use of the (legacy) PathCase desktop client system needs a Tom Sawyers Software licence as well as the Microsoft SQLServer database system license. G6G Product Number 20104 G6G Manufacturer Number 100490 |
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