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    PathSys

    Category  Cross-Omics>Pathway Knowledge Bases/Databases/Tools

    Abstract   PathSys is a graph-based system for creating a combined
    database of biological pathways, gene regulatory networks and protein
    interaction maps. PathSys is also a general-purpose, scalable
    warehouse of biological information, complete with a graph
    manipulation and a query language, a storage mechanism and a
    generic data-importing mechanism through schema-mapping.
    PathSys integrated database consists of over 20 curated and publicly
    contributed data sources for the eight (8) representative organisms
    (see list below), as well as Gene Ontology (GO) information, which is
    structured as an acyclic graph.

    The 'organisms' are: 1) Budding Yeast (Saccharomices cerevisiae); 2)
    Schizosaccharomyces pombe; 3) Fly (Drosophila melanogaster); 4)
    Caenorhabditis elegans; 5) Arabidopsis thaliana; 6) Mouse (Mus
    musculis); 7) Human (Homo sapience); 8) Zebrafish (Danio rerio).

    PathSyS System Architecture -

    PathSys system consists of six (6) major parts: Client Side Application,
    Graph Query Engines, Data Importer, Integration Client/Manager,
    Schema Mapping Tools and Data Warehouse.

    The Client Side Application implements all business logic and a
    significant part of the user interface. Two (2) novel Graph Query
    Engines store and query the molecular interaction network and direct
    acyclic graphs such as ontologies and taxonomies, using specialized
    algorithms customized for each kind of graph. The Data Importer can
    accept data from an external data source, validate it against the
    schema, and then store the new data in the data warehouse. The
    Integration Client/Manager is used to specify a new database that
    needs to be integrated into the system. The end-user provides the
    system with the schema of a new source, and the schema is validated
    and stored in the Schema Library.

    Database Schema -

    The PathSys database was designed to represent generic network
    data. The current implementation defines three (3) classes of vertices
    – primary nodes (primary objects), connector nodes (events of
    interaction or regulation between primary objects) and graph nodes
    [complex objects (protein complexes, cell processes) that might
    contain graphs]. Connector nodes are identified by mechanism and
    effect type. Vertices are stored in the table Nodes. Nodes themselves
    can be of several types (Proteins, Small Molecules, Cell Processes,
    Expression Controls, Binding, Protein Modification etc.), which are
    recorded in the table NodeType.

    The current implementation also supports three (3) classes of links
    between vertices– directed and non-directed (as defined by the field
    Direction in the table Edges) and membership (as defined by the field
    Relation in the table Edges). Directed links can describe biological
    notions of regulation, such as “protein A activates protein B”; non-
    directed links are used to describe binding events: “protein A binds to
    protein B”; membership links describe situations such as “protein
    complex P contains protein A”. The database structure does Not limit
    the number of different classes of nodes and edges. Also, there can
    be any number of node types and attribute types.

    Data Integration -

    While the logical model of information in PathSys is graph based,
    there are in reality a variety of information sources that provide different
    components of the integrated graph. PathSys uses a very generic
    internal model to accommodate different kinds of sources, such that a
    'new source', providing a new set of nodes, edges, or node/edge
    properties can be dynamically incorporated into an existing integrated
    database.

    Source Definition -

    Currently, the external data source(s) can be: 1) a relational database
    schema; 2) a tree-structured Extensible Markup Language  (XML)
    document; 3) an Resource Description Framework (RDF)-styled triplet
    that describes an edge set of a graph; 4) a Directed Acyclic Graph
    (DAG) structured Web Ontology Language (OWL) document.

    Data Visualization -

    PathSys data visualization is done through the Client Side Application,
    BiologicalNetworks (see G6G Product Number 20067), which
    implements all business logic and a significant part of the user
    interface.

    System Requirements  BiologicalNetworks pathways analysis
    software supports Windows 2000 and XP, Linux and Macintosh
    operating systems.

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