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Semantic Research Grid

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					Semantic Research Grid
Open Grid Forum Web 2.0 Workshop OGF21, Seattle Washington October 15 2007

Geoffrey Fox, Aurel Cami, Ahmet Fatih Mustacoglu, Ahmet E. Topcu
Community Grids Laboratory, Indiana University Bloomington IN 47404 gcf@indiana.edu, http://www.infomall.org
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Semantic Scholars Grid
Export: RSS, Bibtex Endnote etc. Traditional Grid Cyberinfrastructure Windows Live Academic Search Google Scholar
Citeseer Bibliographic Database

Web 2.0 MySpace

Del.icio.us CiteULike
Connotea Bibsonomy

MyResearch Database
M A S H U P

Science.gov PubChem

Generic Document Tools Community Tools
Integration/ Enhancement User Interface New Document-enhanced Research Tools

Biolicious PubMed
Manuscript Central CMT Conference Management

etc. Existing User Interface

Web service Wrappers

Existing Document based Tools

Delicious Semantic Web/Grid
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http://del.icio.us purchased by Yahoo for ~$30M http://www.CiteULike.org http://www.connotea.org (Nature) Associate metadata with Bookmarks specified by URL’s, DOI’s (Digital Object Identifiers) Users add comments and keywords (called tags) Users are linked together into groups (communities) Information such as title and authors extracted automatically from some sites (PubMed, ACM, IEEE, Wiley etc.) Bibtex like additional information in CiteULike This is perhaps de facto Semantic Web – remarkable for its simplicity

Example
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Parallel Computing Collection selected on Cell Tag So far no clear “winner” in tagging space Maybe CiteUlike with different metadata better How do I preserve investment?

General Document Semantic Analysis
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Citeseer and Google Scholar scour the Internet and analyze documents for incidental metadata • Title, author and institution of documents • Citations with their own metadata allowing one to match to other documents These capabilities are sure to become more powerful and to be extended • Give “Citation Index” in real time • Tell you all authors of all papers that cite a paper that cites you etc. (Note it’s a small world so don’t go too far in link analysis) • Tell you all citations of all papers in a workshop • Helps journal editor by suggesting referees based on document analysis or by doing a “plagiarism” analysis by scoring comparison with other Internet documents

Possible challenges
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Use of Web 2.0 tools in science (and business) is very promising but adoption is currently small Which of many tools will be popular with your colleagues? What happens if tool you chose is not adopted or worse – just disappears in a industry “shake-up”? How to best integrate web-tagged document with Word and Latex citations? Need to tag URI’s – e.g. database entries, not just URL’s (did for journal control system) Is currently security model sufficient? Can we link virtual organization of tagging system with that of other Cyberinfrastructure/Web 2.0 subsystems

Roughly what we are doing
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We are NOT building a new tagging or search system We are building tools integrating and adding value to existing systems We built a mashup linking to del.icio.us, CiteULike, Connotea allowing exchange of tags between sites and between local repositories Repositories also link to local sources (PubsOnline) and Google Scholar (GS) and Windows Academic Live (WLA)
• GS has number of cited publications. • WLA has Digital Object Identifier (DOI)

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We implement a rather more powerful access control mechanism We build heuristic tools to mine “web lists” for citations We have an “event” based architecture (consistency model) allowing change actions to be preserved and selectively changed
• Supports integrating different inconsistent views of a given document and its updates on different tagging systems

del.icio.us Tags

Download to Local System

Semantic Research Grid (SRG) Architecture

Key Concepts of System Architecture
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Digital Entity (DE): a digital collection of metadata for a citation Event: a time-stamped action on a digital entity. Our event-based model consists of:
• Major Events:
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Insertion or deletion of a digital entity Modifications to an existing digital entity

• Minor Events:
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• Dataset:
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Collection of major and minor events Service-based Framework (SOAP over Http)
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Example Subsystem
CiteULike Connotea Delicous

Core Web Services

Research Database

Research Database

Research Database

Transfer  Download/Upload  Modify Digital Entity (DE)  Share DE with other users  Add/Get More info on a DE  History (as a set of events) of a DE and rollback
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SRG System Modules I
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Digital Entity (DE) Management Service
• • • • Manual DE entity into the system DE history DE versioning and flexible choices (rollback) Editing and more info tools for a DE (Update Model)

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Session and Event Management Services
• Event and dataset management • DE view options • User credentials (username/password) - cookie-based

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Annotation Tools Service
• • • • Transfer Service Download service Upload Service Extract DE and tags from web lists
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SRG System Modules II
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Search Tools Services
• Google Scholar/Windows Live Academic • Google Scholar Advanced • Local Database Search:  Via integrated PubsOnline Tool from Indiana University  My Research Database  My Research Database Advanced

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Authentication and Authorization Services
• • • • Login and Logout service DE Access rights management Database access rights management Administrative tools
User Registration Username and password recovery User’s Profile Management DE metadata view options
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Other Services
• • • •

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Technical Issues
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Event-based model
• Manipulating data and metadata • How to build event-based model ?
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Major and Minor events Datasets (collection of minor events)

• How to apply event-based model ? • How to apply modifications to a record (Digital Entity) ?
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Keep them in user’s session and let user apply them Or apply them automatically to a DE

• How to merge metadata fields of Event and Digital Entity ?

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Identification of metadata fields as dynamic or static field How to apply service-based framework as wrapper?
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Some recent Features of SRG
• Hybrid Consistency Framework Implementation – Data-centric strict consistency model – Implements primary-copy based consistency protocol – Pull-based: • Time-based consistency approach. • Communicates with Annotation Tools to collect updates periodically – Push-based: • Updates are distributed to Annotation Tools immediately once they occurred on the primary copy • Periodic Search Tools Implementation – Search, compare and apply the updates made to a Digital Entity (DE) in the system. • Unique (128 bit) UUID assignment for each Digital Entity • User Tags view in the system – Displays all tags belongs to a user – Allow easy update or more info request on a Digital Entity by tags

Hybrid Consistency Framework for Semantic Research Grid

Tool Updating Database from Web Page

Metadata Collection from CGL web pages
• The aim is to
– Eliminate duplicate data entry in different web platforms.
– Building richer metadata in SRG using base collected Digital Entities from web pages. – Share new Digital Entities with other tools and users in SRG

– Push new collected Digital Entities to other communities using web 2.0 features

Methodology for Collection
• Collect:
– Digital Entities in Community Grid Publication web pages.

• Analyze:
– Using heuristic methodology to extract metadata fields of the Digital Entities for CGL publications

• Build:
– RSS objects using collected Digital Entities. – New tags using collected Digital Entities.

• Compare:
– Collected Digital Entities from CGL web pages with the existing Digital Entities in SRG.
• If they are:
– different: Store new Digital Entities in SRG storage. – same: Option to update tags and other fields.

• Share:
– New Digital Entities with other Tools using SRG.

Security Model
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Security in Web 2.0 can be limited We implement a simple but more powerful security model around local tools that wrap Web 2.0 systems We used an access-control matrix model to provide security for our information system
• Supports multiple groups and multiple users for each object. • Similar to UNIX file system  The Unix RWX bits corresponds to Read, Write, and Execute operation for each file and directory. • In SRG, DE (Digital Entity) correspond to the file element and folder corresponds to the directory element. • For each DE and folder, there are three types of access rights defined in the systems: Read, Write, and Delete.

Security Model II
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We have a security model that supports
• Level of Authorization  Roles are defined as Super Administrator (SA) and Group Administrator (GA), User (U)  The system allows having more than one SA.  An existing SA can add other SAs to the system.  SA can assign any U to become GA, and remove GA from group.  Each group should at least one GA. GA add/remove U from group • User profile  Share user profile between Web 2.0 sites.

Current Usage of Semantic Research Grid Project
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We have used/tested Semantic Research Grid (SRG) (a prototype model) for published scientific research publications in Community Grids Lab at Indiana University In CGL 20 students ,post-docs and faculty members are testing They are using the prototype model for collecting of publication, uploading/ downloading them and sharing them with other users

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Integration • We have successfully integrated Google Scholar and Windows Live Academic search tools and CiteUlike, Delicious, and Connotea annotation tools which provide a system that allow dynamic publication. Flexibility and Extensibility • We provides flexibility allowing integration of different tools having common metadata. • Easy to add and extend service mechanism Management and Consistency Scheme of Digital Entities • Allows the manipulation of a digital entity • Applies Event-based model based on the concept of:  Major events  Minor events  Datasets • Provides a rollback feature to:  Support for history tool for a DE  Merge and change the content of a digital entity • A service-based framework for using existing annotation tools through web services Prototype project web site: http://gf6.ucs.indiana.edu:58080/SRGrid

Summary

Domain Specific Semantic Document Analysis
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It is natural to develop core document Services such as those used in Citeseer/Google Scholar but applied to “your” documents of interest that may not have been processed yet • As just submitted to a conference perhaps These tools can help form useful lists such as authors of all cited or submitted papers to a journal OSCAR3 (from Peter Murray-Rust’s group at Cambridge) augments the application independent “core” metadata (Title, authors, institutions, Citations) with a list of all chemical terms • This tool is a Service that can be applied to “your” document or to a set of documents harvested in some fashion • Luis Rocha has developed related ideas for Biology • Other fields have natural application specific metadata and OSCAR like tools can be developed for them This is another Semantic Scholar Grid Tool

OSCAR3 Chemistry Document analysis
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It detects “magic” chemical strings in text and then
• Stores them as metadata associated with document

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Queries ChemInformatics repositories to tell you lots of information about identified compounds Tells you which other documents have this compound

Initial Results from OSCAR on PubMed
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We have a small sample (100) of full text Chemistry papers selected at random from 15 years of PubMed with over 5 million abstracts • OSCAR3 generates 4.17 compound names per abstract • and 36.7 compound names per full text • 555,007 PubMed abstracts of 2005 – 2006 (part) used for Abstracts (on Big Red) Illustrates how much knowledge journal publishers are hiding from us

CICC Chemical Informatics Cyberinfrastructure Collaboratory
Integrating document (OSCAR) and conventional services on the IU Big Red Supercomputer
MOAD Database

PubMed Database

OSCAR Text Analysis

Cluster Grouping

Toxicity Filtering

Docking

PubChem Database

Initial 3D Structure Calculation NIH PubChem Database

Molecular Mechanics Calculations

NIH PubChem Database

Quantum Mechanics Calculations

POV-Ray Parallel Rendering

IU’s Varuna Database

Product databases are wrapped with Web service interfaces and are suitable for inclusion in Taverna workflows.


				
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