Building a Database Semanticizer for Task Computing

-Anubhav SonthaliaMS Thesis Defense, 12/06/04

Overview Basics Introduction Task Computing Database Semanticizer BioGrid Task Computing – An

application Conclusion Demo

What is the Semantic Web

The Semantic Web is an extension of the current Web, in which data is given a well-defined meaning by representing it in RDF and linking it to commonly accepted ontologies. – Tim Berners Lee, October 2002

Task Computing

Our answer for ubiquitous computing challenges based on the Semantic Web

What are Semantics – A Task Computing Definition

“Semantics” is a set of “clues and glues” for resources (information, services) to be used in different systems (computers and humans) and contexts.

“Semantics” is: Interoperability-enabler/enhancer Measured by extent of interoperability it

enables

Problem

Most Structured data is stored in relational databases.

We need to map it to OWL in order to use it in the semantic context.

Solution

Developed a semi automatic approach to create a map between relational databases and semantic objects.

Goal of Task Computing User wants to do “Tasks”

“Services” offer means Web services, UPnP services etc.

Filling the gap

Task Computing - Definition is a user-oriented framework that lets non-

expert users accomplish complex tasks in application-, device-, and service-rich environments.

provides a myriad of ways for users to interact with and through ubiquitous environments.

TC in eHome

TC in a Car

GPS Navigator (or PDA) to control

TC Voice Menu:Do you want to …(1) Navigate to an

address in PDA(2) Play Music from

Digital Audio Player(3) …

TC in an Office

TC at an Airport

TC at a Coffee Shop

Task Computing Technology Major components are:

Service Discovery Service Composition Service Execution Service Publishing

Task Computing Architecture

DeviceApplication

E-service

Service ServiceService

Semantic Service

Description

Semantic Service

Description

DiscoveryEngine

Execution & Execution Monitoring

Engine

ServiceComposition

Engine

ManagementTools

Task Computing

ClientApplications

ServiceLayer

MiddlewareLayer

PresentationLayer

Content

Web-basedClient

Service

Semantic Service

Description

Task Computing Environment

User

Web Service API

Semantic Service

Description

RealizationLayer

Grasping the Environment

Discover services through UPnP Acquire Semantic Service Description (SSD) using

UPnP requests.

Business card metaphor: With a business card (SSD), you can put

the person (service) in a social context (Web ontology)

Then you can interact with the person (service)

Semantic Service Compositions

Route from FLA to Addr

Add into Outlook Cont

Addr: AddressCont: ContactWP: Web Page

Discovered Services

View Locally File

View on Projector File

My FavoriteWP

My FileFile

Business Address of ContAddr

Dulles AirportCont

Contact from OutlookCont

Weather Info of AddrWP

Task Execution

“My Contact”OWL-S

Grounding

Web Service Callwith no input

Contact

“My Contact” Web Service

“Business Address of”

OWL-S

Grounding

Result(OWL String)

Address

“Route fromFLA to”OWL-S

Grounding

“Route from FLA to” UPnP

STEER

Result(None)

UPnP Callwith a string

Route from FLA to Business Address of My Contact

<rdf:RDF …> …<Contact rdf:ID="Contact_Ryusuke_Masuoka"><hasBusinessAddress> <Address> <Country>USA</Country> <StreetAddress>8400 Baltimore Ave </StreetAddress> <City>College Park</City> <State>MD</State> <ZipCode>20740<ZipCode> </Address> <hasBusinessAddress> <hasHomeAddress>… </hasHomeAddress> <FirstName>Ryusuke</co:FirstName> <LastName>Masuoka<LastName>… </Contact …> …</rdf:RDF>

Semantic Contact Instance Semantic Address Instance

<soapenv:Envelope …><soapenv:Body> <GetWeather …> <zip type="xsd:string" …> 20740</zip> </GetWeather> </soapenv:Body></soapenv:Envelope>

“Weather Info of”Web Service

<soapenv:Envelope …><soapenv:Body> <GetPhoto …> <street type="xsd:string" …> 8400 Baltimore Ave</street> <city type="xsd:string" ….> College Park</city> <state type="xsd:string" …>MD</state> <zip type="xsd:string" …>20740</zip> </GetPhoto> </soapenv:Body></soapenv:Envelope>

“Aerial Photo of” Web Service <soapenv:Envelope …>

<soapenv:Body> <InitService …> <address type="xsd:string" …> 8400 Baltimore Ave, College Park, MD 20740 </address> </InitService> </soapenv:Body></soapenv:Envelope>

“Route fromFLACP”

UPnP Service

“Business Address of”

OWL-S

“Weather Info of”OWL-S

“Aerial Photo of”OWL-S

“Route fromFLACP”OWL-S

<rdf:RDF …><Address …> <Country>USA</Country> <StreetAddress>8400 Baltimore Ave </StreetAddress> <City>College Park</City> <State>MD</State> <ZipCode>20740</ZipCode> </Address></rdf:RDF>

TC Service Execution (Instance View)

Service Publishing

Lets the user “publish” services from OS/App/OWL objects, and OWL-S

Publish service = Make service’s OWL-S through UPnP

Numerous ways of publishing services White hole, bank service, multimedia publisher, image generator, etc.

Semantic

-ization

Create a web service withWSDL to publish the object instance, and generate an OWL-S file to describe the

web service

OS/Applicationobjects

NoProcessing

NoProcessing

Semanticobjects

Semantic ServiceDescription

Publish the OWL-Sdescription file

Semantic objects

OWL-S service descriptionwith grounding to web service

Allow Task Computing Client to discover

White Hole

PIPE

NoProcessing

White Hole and PIPE

PIPE- A Service Management Tool

Web Service API

Revisit the Problem Most Structured data is stored in relational

databases.

We need to map it to OWL in order to use it in the semantic context.

Important in Bio-Grid Task Computing domain

Database Semanticizer We have created a tool which enables easy

mappings between the databases and commonly accepted ontologies.

It creates the semantic instance objects.

It can publish the object as a service in order to enable us to pick it up from TCC.

Process Overview

Modules

Database Web Service Wrapper Application Service and Control UI.

System Architecture

Web Service Wrapper Connects to a remote database or a remote

Grid.

Uses the OLE DB interface.

In grid environments, we may not be able to directly connect to a database. Hence this wrapper is a way of getting around the problem.

contd…

Provides various Web methods GetTables GetTableDetails ExecuteNonQuery ExecuteQuery

Application Body

Contd… GUI Interface

Displays the various Tables and Columns with details. Helps the user grasp the schema of the database before he makes any SQL queries

Execute SQL queries to reach the final object tuples we want to use and convert to semantic objects

Enter Ontology URI using which semantic objects need to be created.

Mapping Editor

Mapping Editor Parses the ontology and creates a tree view of the

objects in the ontology. Also shows the various datatype and object

properties. Shows the various attribute elements for the selected

SQL query. User can create a mapping using simple clicks. Save these mappings if desired. Use saved mapping.

Contd… The mapping editor has been written using C#.

There is no OWL parser for C#. C# OWL Parser built on top of the Drive RDF Parser from

CMU.

OWL Parser provides us a programmatic API to parse OWL ontologies.

Service Control UI Web page interface

giving the user control over the application or accepting user input.

In our case, displays the query results in the form of a table allows the user pickup an object.

write semantic object file, publish through PIPE pass semantic object as output

Contd…

Related Work MIT Simile Project

Java2rdf Flat2rdf

Mindswap Lab Excel2rdf csv2rdf

Contd… D2R Map –

declarative, XML-based language to describe mappings between databases and

ontology

Limitations can create RDF, not OWL objects. also user expected to learn the new constructs user is expected to be well versed with XML

OWL-S Service Descriptions Service Profile – used for discovering the

service

Service Model – contains all functional properties.

Service Grounding – interface to plugin to WSDL description. Provides XSLT for transforming between XML

and RDF/OWL.

Example Fax Service available on the

Web.

<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:contactOnt="http://www.flacp.fujitsulabs.com/tce/ontologies/2004/03/object.owl" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" contactOnt:dummy=""><xsl:template match="/"><xsl:variable name="X1" select="//contactOnt:number" /><obj><xsl:value-of select="$X1"/></obj></xsl:template></xsl:stylesheet>

Bio-STEER- Application of Task Computing

Bio-informatics Databases and sequence matching:

Find similar proteins Phylogenetic analysis

sampling properties of sequence data Comparative genomics

genome content genome structure genome evolution

Motivation Problems in Bioinformatics

Lots of tools: I/O Lots of data: structure, formats Lots of interaction b/w data and tools: workflow Computationally expensive Wide range of skills for Biologists

Motivation contd… Technologies:

Semantic Web Interactive composition of semantic web services

(workflows) Search and information extraction

Grid Computing Computational power

TCE Web Services Composition Usability Issues

Services for Bio-STEER We have semanticized some services

available on the web. For e.g. – BLAST service, Clustal-W.

Other services like Muscle, Phyml are being semanticized.

DB

Semanticizer

Demo

DBDB

DBDB WS

Access DB through WS

Map to ontology

Semantic Instances

Future Work

Mapping Object Properties directly to multivalued attributes.

Link to RDF data stores like the Kowari Metastore to assert the instances.

Conclusion Task Computing environments are now able

to access legacy databases and create semantic instances from the same.

Extremely important in the evolution of task computing applications like Bio Grid Task Computing.

Thank You

Questions ?