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_at_indiana.edu, http//www.infomall.org

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Semantic Scholars Grid
Web 2.0
MySpace
Windows Live Academic Search
Traditional GridCyberinfrastructure
ExportRSS, BibtexEndnote etc.
Del.icio.us
Google Scholar
CiteULike
Citeseer
Connotea
Science.gov
Bibsonomy
PubChem
Biolicious
Generic Document Tools
MASHUP
PubMed
CMT ConferenceManagement
Manuscript Central
Community Tools
Integration/Enhancement User Interface
etc.
Existing User Interface
New Document-enhanced Research Tools
Existing Documentbased Tools
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Delicious Semantic Web/Grid

• http//del.icio.us purchased by Yahoo for 30M
• http//www.CiteULike.org
• http//www.connotea.org (Nature)
• Associate metadata with Bookmarks specified by
  URLs, DOIs (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

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Example

• 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?

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General Document Semantic Analysis

• 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 its a small
  world so dont 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

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Possible challenges

• 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 URIs e.g. database entries, not
  just URLs (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

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Roughly what we are doing

• 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)
• 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

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del.icio.us Tags
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Semantic Research Grid (SRG) Architecture
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Key Concepts of System Architecture

• 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
• Insertion or deletion of a digital entity
• Minor Events
• Modifications to an existing digital entity
• Dataset
• Collection of major and minor events
• Service-based Framework (SOAP over Http)

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Example Subsystem
CiteULike
Delicous
Connotea

• 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

Core Web Services
Research Database
Research Database
Research Database
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SRG System Modules I

• 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)
  
• Session and Event Management Services
• Event and dataset management
• DE view options
• User credentials (username/password) -
  cookie-based
  
• Annotation Tools Service
• Transfer Service
• Download service
• Upload Service
• Extract DE and tags from web lists

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SRG System Modules II

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

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Technical Issues

• Event-based model
• Manipulating data and metadata
• How to build event-based model ?
• Major and Minor events
• Datasets (collection of minor events)
• How to apply event-based model ?
• How to apply modifications to a record (Digital
  Entity) ?
  
• Keep them in users session and let user apply
  them
  
• Or apply them automatically to a DE
• How to merge metadata fields of Event and Digital
  Entity ?
  
• 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

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Hybrid Consistency Framework for Semantic
Research Grid
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Tool Updating Database from Web Page
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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

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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.
  

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Security Model

• 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.
  

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Security Model II

• 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.

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Current Usage of Semantic Research Grid Project

• 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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Summary

• 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
  .edu58080/SRGrid
  

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Domain Specific Semantic Document Analysis

• 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-Rusts 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

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OSCAR3 Chemistry Document analysis

• It detects magic chemical strings in text and
  then
  
• Stores them as metadata associated with document
• Queries ChemInformatics repositories to tell you
  lots of information about identified compounds
  
• Tells you which other documents have this compound

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Initial Results from OSCAR on PubMed

• 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

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CICC Chemical Informatics Cyberinfrastructure
Collaboratory
MOAD Database
Integrating document (OSCAR) and conventional
services on the IU Big Red Supercomputer
PubMed Database
OSCAR Text Analysis
Toxicity Filtering
Cluster Grouping
Docking
PubChem Database
Initial 3D Structure Calculation
NIH PubChem Database
NIH PubChem Database
Molecular Mechanics Calculations
Product databases are wrapped with Web service
interfaces and are suitable for inclusion in
Taverna workflows.
Quantum Mechanics Calculations
IUs Varuna Database
POV-Ray Parallel Rendering