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System Evolvability Features of the SenseLab Project

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Title: System Evolvability Features of the SenseLab Project


1
  • System Evolvability Features of the SenseLab
    Project
  • Luis Marenco, MD
  • Center for Medical Informatics
  • Yale University School of Medicine

2
Outline
  • The nature of some bioscience applications (e.g.
    Neuroscience) where domain knowledge is in
    constant revision requires an application
    infrastructure capable to evolve over time.
  • The reasons and one possible solution to this
    problem will be reviewed in the following
    topics
  • Motivation The SenseLab project
  • Background issues of standard applications
  • Evolvable applications goals
  • Some Possible solution scenarios
  • EAV/CR - features for evolvable applications
  • EAV/CR derived methodologies for evolvable
    applications
  • EAV/CR application demo (SenseLab)
  • EAV/CR Solution Framework

3
Motivation The SenseLab Project
  • The SenseLab project is a ongoing effort to
    integrate multidisciplinary sensory data using
    the olfactory system as model domain.
  • The process involves the development of
    neuroinformatics databases and tools in support
    of neuroscience research.
  • SenseLab web-portal contains the following
    web-databases
  • Neuronal research NeuronDB, ModelDB, and
    CellPropDB
  • Olfactory research ORDB, OdorDB, and OdorMapDB
  • The fundamental problem statement is the
    maintenance burden due
  • Constant domain evolution
  • Research of not well understood process like
    olfaction involves constant factoring-in of new
    variables or disciplines

4
Background Issues of Standard Applications
  • Standard database applications are characterized
    with code entwined with metadata descriptors from
    back-end databases. The limitations to this
    approach are
  • Increased coding as database complexity grows
  • Limited code reusability
  • Lack of robust data interoperability (messages
    mirror the schema)
  • Complexity derived by use of multiple tools to
    maintain schema data editing, and security
  • To advance knowledge represented as metadata, the
    necessary schema changes will lead to
  • Downtime and application breakdown
  • Interface redesign (GUI and Inter-application
    recoding)
  • Increased code complexity
  • Increased probability of coding errors

5
Background Issues of Standard Applications (2)
  • Traditional Web-database applications
  • Data entry and security Cumbersome, expensive
    and non-portable to other applications
  • Searching mechanisms Limited, difficult to
    standardize and expensive to create. The hidden
    web remains an issue
  • Site-wide architectures are cumbersome to adapt
    to new web formats (e.g. Semantic-web types)
  • Metadata maintenance
  • Data dictionary Incomplete
  • Complex, non centralized, and requires more than
    one tool
  • Requires specific database expertise. Non
    portable knowledge
  • Tools and software libraries are specific to
    every vendor database

6
Evolvable Application Goals
  • PRIMARY
  • Create a programmatic approach capable to allow
    databases structural changes without disrupting
    the existing data and code
  • Minimize codemetadata dependency focusing on
    automated interface generation (GUI Inter App.)
  • Improve code simplification as project matures
    Extreme Programming principles
  • SECONDARY
  • Facilitate system integration to a Web platform
  • Accessibility from common web browsers.
  • Incorporate role-based security with public and
    private data
  • Create generic interfaces and formats for data
    exchange
  • Improve code reusability leveraging previous
    approach
  • Foresee robust interoperability with standardized
    protocols

7
Possible Solution Scenarios (some)
  • Use of object oriented or object relational
    databases Immature and unsupported
  • Leverage other application approaches (e.g.
    Protégé) The part that is related with flexible
    data structures Lack of features (e.g.
    non-distributed or web-based, no security
    implied). Future version will possibly cover
    these features.
  • Built a new ground-up solution to provide
    needed features The EAV/CR Application Framework
    (Combination of data storage approach software
    practices)

8
EAV/CR Storage Approach
  • EAV/CR (Entity-Attribute-Value with Classes and
    Relationships) data storage system is derived
    from the EAV row based data modeling approach
    widely used in Electronic Patient Record Systems
    and MS Windows Registry, among others.

9
Relational (left) to EAV/CR (right) Comparison
EAV/CR uses a limited number of tables to
represent any amount of tables from a relational
DB. EAV/CR treats data (VALUES) and metadata
(CLASSES, ENTITIES, and ATTTRIBUTES) as
relational data allowing flexible domain
representation.
10
EAV/CR Storage Approach (2)
  • EAV/CR augments standard EAV by
  • Grouping entities in Classes C
  • Using strong data typing for value storage
  • Allowing computed attributes (functions)
  • Allowing entity relationships R (related and
    hierarchical attribs.)
  • Including implicit data and metadata versioning
    and timestamp
  • Including Web oriented features Metadata have
    been enriched with web parameters to automate
    web-interface generation (Web forms, XML, )
  • Assisting ontological representation Mapping
    standardized vocabulary and semantic
    relationships identifiers to data and metadata
    elements

11
EAV/CR Features for Evolvable Applications
  • Automatic system adaptability to DB structural
    changes
  • Generic metadata-driven database navigation
  • Robust data-entry and schema-maintenance web
    forms generation
  • Ability to create database portals to present
    different subsets of the data to users with a
    particular research focus
  • Centralized role-based security. Uses a
    compartmentalized distributed administration
    model to minimize dedicated administration costs
  • Monitoring tools

12
EAV/CR Features for Evolvable Applications (2)
  • Expandable system architecture Allows parallel
    processing by scaling-out. Parallel web servers
    can connect to the same EAV/CR database
    preserving security, data and metadata
    concurrency
  • Delegated user profile management Users are
    responsible of their own profiles, administrators
    provide access to users to specific database
    resources. (Web portal model)

13
EAV/CR derived methodologies for evolvability
  • Data Services Creation of the EDSP InfoSet
    protocol to allow description of database
    ontology, metadata, and data in a simple XML
    format. (It brings the EAV/CR approach to the XML
    world).
  • The following processes depend on EDSP
  • Data transference
  • Middle tier components
  • Automated Ad-hoc query interface generation
  • Using EDSP as the source for these processes
    improves software components stability and
    reusability

14
EAV/CR Application Framework
  • Programming model
  • Component programmer
  • Domain programmer
  • EAV/CR Framework Toolkit (version1. Codename?)
  • Database Component Encapsulates EAV/CR logic
    presenting interfaces for domain programmers.
    Created in MS C.NET
  • Plumbing code Generic Web portal scripts.
    IIS-ASP-VBScript

15
Summary
  • EAV/CR and Evolvability
  • High data integration
  • Flexibility in database schema evolution /
    maintenance
  • Code reuse and increased reliability
  • Extensible application architecture
  • Disadvantages
  • Querying complexity
  • Multi-parameterized queries performance penalty
  • Complex EAV/CR components programming

16
Demo Metadata driven Ad hoc interface generation
  • Boolean expression can be added for complex
    associations. Results can be retrieved in HTML,
    XML text and other formats.

17
Demo Metadata driven Ad hoc interface generation
(2)
  • The same generic code behind this interface is
    reused in other databases augmenting the value
    added in this robust evolvable design.

18
Demo EAV/CR Centralized Schema Management
  • The Schema Manager tool displays and allows
    edition of the database structure. This figure
    shows the database inventory of the SenseLabs
    EAV/CR data store with links to specific elements

Next gtgt After selecting CellPropDB
19
Demo EAV/CR Centralized Schema Management (2)
  • Selecting a database (e.g. ModelDB), displays
    the web database information, this can be changed
    at any time.

20
Demo EAV/CR Centralized Schema Management (3)
  • On the left, selecting Classes displays the
    list of Classes for ModelDB, on the right the
    Class Models is being edited

21
Demo EAV/CR Centralized Schema Management (4)
  • While in the class Models, selecting the
    Attributes tab shows all its attributes (left).
    On the right, the attribute neurons shows its
    relation to neuron objects from NeuronDB.

22
Demo EAV/CR Centralized Schema Management (5)
  • Similarly like in previous slides, Schema manager
    allows entering of new users and granting rights
    to specific databases. Lastly, by clicking on the
    diagram link, shows the ER representation of the
    ModelDB database.

23
Demo InfoSets and Evolvable Interoperability
  • The creation of the EDSP (EAV/CR dataset
    protocol) allows transference of database schema
    and data in a simple consistent format based upon
    the universally accepted XML format. This picture
    show a partial rendering of some olfactory
    receptors molecules from ORDB

24
Demo InfoSets and Evolvable Interoperability (2)
  • Meanwhile, exchange of data with other standard
    protocols is achieved through XML
    transformations. Below is the previous EDSP
    message transformed into Microsoft XDR, format
    used by the MS Office Suite to import into MS
    Access and MS SQL Server.

25
Demo InfoSets and Evolvable Interoperability (4)
  • A practical use of the XDR is demonstrated here
    while importing data directly from a SenseLab URL
    to an Access or SQL Server database.

26
Demo InfoSets and Evolvable Interoperability (5)
  • This example points to a particular olfactory
    receptor at
  • (http//senselab.med.yale.edu/senselab/site/dbGate
    /Xtract.asp?o1798xsledsp-officedata)

27
Demo InfoSets and Evolvable Interoperability (6)
  • Access shows the tables to be generated

28
Demo InfoSets and Evolvable Interoperability (7)
  • Next imports the tables

29
Demo InfoSets and Evolvable Interoperability (8)
  • relationships, and the data (preserving strong
    data typing )
  • All in one deEAVfication process.
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