Semantic Research Grid

1. 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 1

2. MyResearchDatabase Bibliographic Database Web serviceWrappers Web 2.0 Semantic Scholars Grid MySpace Windows Live Academic Search Traditional GridCyberinfrastructure Export:RSS, 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

3. 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 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

4. 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?

5. 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 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

6. 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 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

7. 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

8. del.icio.us Tags Download to Local System del.icio.us Tags

9. Semantic Research Grid (SRG) Architecture

10. Key Concepts of System Architecture 10 12/20/2019 • 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)

11. Example Subsystem CiteULike Connotea Delicous Core Web Services Research Database Research Database Research Database 12/20/2019 11 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

12. SRG System Modules I 12/20/2019 12 • 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

13. 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 • User’s Profile Management • DE metadata view options 12/20/2019 13

14. Technical Issues 12/20/2019 14 • 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 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 ? • Identification of metadata fields as dynamic or static field • How to apply service-based framework as wrapper?

15. 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

16. Hybrid Consistency Framework for Semantic Research Grid

18. Tool Updating Database from Web Page

20. 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

21. 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.

22. 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.

23. 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.

25. 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

26. 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.edu:58080/SRGrid

27. Domain Specific Semantic Document Analysis • It is natural to develop core document Servicessuch 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

28. 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

29. 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

30. CICC Chemical Informatics Cyberinfrastructure Collaboratory MOAD Database Integrating document (OSCAR) and conventional services on the IU Big Red Supercomputer PubMed Database OSCAR Text Analysis Cluster Grouping Toxicity Filtering 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 IU’s Varuna Database POV-Ray Parallel Rendering