Tools for Repositories Microsoft Research & the Scholarly Information Ecosystem

1. Tools for Repositories Microsoft Research & the Scholarly Information Ecosystem Tony Hey Corporate Vice President Microsoft Research

2. presents… • – v.1.0 Article Authoring Add-in for Word 2007 – 2.0

3. Microsoft External Research Organization within Microsoft Research that engages in strong partnerships with academia, industry and government to advance computer science, education, and research in fields that rely heavily upon advanced computing Initiatives that focus on the research process and its role in the innovation ecosystem, including support for open access, open tools, open technology, and interoperability Developers of advanced technologies and services to support every stage of the research process

4. Worldwide External Research Themes Community and Geographic Outreach Advanced Research Tools and Services

5. Tomorrow … Today … Research tools can help… data andinformation Be able to automatically the world’s knowledge

6. A world where all data is linked … • A knowledge ecosystem: • A richer authoring experience • An ecosystem of services • Semantic storage • Open, Collaborative,Interoperable, and Automatic • Data/information is inter-connected through machine-interpretable information (e.g. paper Xis about star Y) • Social networks are a special case of ‘data meshes’ Attribution: Chris Bizer

7. …and stored/processed/analyzed in the Cloud visualization and analysis services scholarly communications Vision of Future Research Environment with both Software + Services domain-specific services search books citations blogs &social networking Reference management instant messaging identity mail Project management notification document store storage/data services knowledge management The Microsoft Technical Computing mission to reduce time to scientific insights is exemplified by the June 13, 2007 release of a set of four free software tools designed to advance AIDS vaccine research. The code for the tools is available now via CodePlex, an online portal created by Microsoft in 2006 to foster collaborative software development projects and host shared source code. Microsoft researchers hope that the tools will help the worldwide scientific community take new strides toward an AIDS vaccine. See more. compute services virtualization knowledge discovery

8. Open access Open source Open data Open Collaboration “In order to help catalyze and facilitate the growth of advanced CI, a critical component is the adoption of open access policy for data, publications and software.” NSF Advisory Committee on Cyberinfrastructure (ACCI) • Microsoft Interoperability Principles • Open Connections to Microsoft Products • Support for Standards • Data Portability • Open Engagement http://www.microsoft.com/interop/

9. Partnership: Working Openly with Others to Foster Choice, Innovation Novell and Microsoft collaboration allows Linux users to watch inauguration video stream with Moonlight • Open source is burgeoning at Microsoft • 77,000 of 147,000 projects on SourceForge run on Windows • 30,000 run on Windows only EMC, IBM, Microsoft, Oracle, SAP collaborate on a standard to help migrate content between systems Microsoft and Google make moves in identity management Red Hat and Microsoft expand server virtualization interoperability Sun and Microsoft expand investment in interoperability with new lab

10. Rich Authoring Experience Intent Data Services Relationships Provenance Structure Intelligence

11. Creative Commons Add-in for Office 2007 Intent: Insert Creative Commons licenses from within Office 2007 Services: Integrates with Creative Commons Web API to create new licenses Relationships: license information stored as RDF XML within the document OOXML Source code and binary: http://ccaddin2007.codeplex.com

12. Ontology Add-in for Word 2007 Services: Ontology download web service • John Wilbanks • Phil Bourne • Lynn Fink Intent: Term recognition & disambiguation Relationships: Ontology browser Source code and binary: http://research.microsoft.com/ontology/

13. Article Authoring Add-in for Word 2007 Services: repository deposit via SWORD Structure: Read, convert, and author NLM XML documents Relationships: ORE Resource Map creation Structure: Client-side XML validation Binary (version 2.0): http://research.microsoft.com/authoring/ This work is licensed under a Creative Commons Attribution 3.0 United States License.

14. Chem4Word - Chemistry Drawing in Word Author/edit 1D and 2D chemistry. Change chemical layout styles. • Peter Murray-Rust • Joe Townsend • Jim Downing Intent: Recognizes chemical dictionary and ontology terms Relationships: Navigate and link referenced chemistry Data: Semantics stored in Chemistry Markup Language <?xmlversion="1.0" ?> <cmlversion="3" convention="org-synth-report" xmlns="http://www.xml-cml.org/schema"> <moleculeid="m1"> <atomArray> <atomid="a1" elementType="C" x2="-2.9149999618530273" y2="0.7699999809265137" /> <atomid="a2" elementType="C" x2="-1.5813208400249916" y2="1.5399999809265137" /> <atomid="a3" elementType="O" x2="-0.24764171819695613" y2="0.7699999809265134" /> <atomid="a4" elementType="O" x2="-1.5813208400249912" y2="3.0799999809265137" /> <atomid="a5" elementType="H" x2="-4.248679083681063" y2="1.5399999809265137" /> <atomid="a6" elementType="H" x2="-2.914999961853028" y2="-0.7700000190734864" /> <atomid="a7" elementType="H" x2="-4.248679083681063" y2="-1.907348645691087E-8" /> <atomid="a8" elementType="H" x2="1.0860374036310796" y2="1.5399999809265132" /> </atomArray> <bondArray> <bondatomRefs2="a1 a2" order="1" /> <bondatomRefs2="a2 a3" order="1" /> <bondatomRefs2="a2 a4" order="2" /> <bondatomRefs2="a1 a5" order="1" /> <bondatomRefs2="a1 a6" order="1" /> <bondatomRefs2="a1 a7" order="1" /> <bondatomRefs2="a3 a8" order="1" /> </bondArray> </molecule> </cml> Intelligence: Verifies validity of authored chemistry Available soon: http://research.microsoft.com/chem4word/

15. An Ecosystem of Services Conversion Peer Review Translation Discovery Cloud Storage

16. Supports conference workflow Bidding Author Feedback Camera Ready Submissions Paper Submission Paper Assignment Paper Decision Making Time Reviewing Author Notification Discussions Sessions and Presentations Peer Reviewing Conference Capture & Online Publishing CMT - A Service for Academic Conference Management Provides: • Peer-reviewing of academic conferences/workshops • Conference capture and online publishing • Interoperability with other scholarly publication services • Web based service for managing academic conference workflows • Hosted, free, sponsored by MSR • Started in 1999 • http://cmt.research.microsoft.com

17. Usage Statistics • 240+ conferences used CMT in the past 12 months • Includes large conferences such as CVPR, VLDB, ACM SIGMOD • 40K+ distinct users from 90+ different countries • ~15K papers managed 5/20/2009 17 TCI

18. Microsoft Translator Query-time translation Embeddable widget Bilingual side-by-side viewer http://www.microsofttranslator.com/AddIn.aspx http://www.microsofttranslator.com/dev/ajax/

19. Microsoft Electronic Journals ServiceA Hosted Offering for the Scholarly Community Hosted editorial and peer review management tool Targeted at scholarly societies and small to medium-sized publishers Support and tracks online collaboration between authors Simplifies self-publishing of workshop/conferenceproceedings and small journals Alpha version available at: http://research.microsoft.com/ejournal/

20. Document Conversion Service Convert to and from Word, ODF, Word Perfect , RichText, and UOF View documents in various formats Compare original and converted documents http://odf-converter.sourceforge.net/

21. Open Document Standards May 18th announcement • New project seeks to eliminate Open XML confusion and build interoperability • Microsoft working with the Fraunhofer Institute for Open Communication Systems FOKUS in Berlin • Building a document format test library and validation tool • Tools will ease the effective exchange of data and improve the long-term benefits for data archiving • At the Document Interoperability Initiative (DII) global forum in London, release of a number of products to support interoperable files: • Open XML Document Viewer v1.0, a plug-in for the Opera browser to help users access documents via the web or across mobile devices • The Apache POI 3.5 software development kit, includes a Java API to access information in the Open XML Format. • The Open XML-ODF translator, has support for .XLS and .PPT file formats, improved ability to translate between ODF and Open XML formats.

22. oreChem – The Chemical Semantic Web • Geoffrey Fox • Carl Lagoze • Jeremy Frey • Simon Coles • Peter Murray-Rust • Jim Downing • Nico Adams • Lee Giles • Karl Mueller • PrasenjitMitra Semantic storage Mash-up (re-use) data experiments scientists documents molecules text data molecules data Compound document authoring measurements

23. Semantic Storage Conversion Peer Review Relationships Services Cloud Storage

24. Zentity – a Research Output Repository Platform Native support for RSS, OAI-PMH, OAI-ORE, AtomPub and SWORD Default web UI with CSS support and custom ASP.Net controls Flexible data model enables many scenarios and can be easily extended over time A semantic computing platform to store and expose relationships between digital assets Binary (version 1.0): http://research.microsoft.com/zentity/

25. Zentity – Goals Quick • Easy to install • ‘Scholarly Works’ data model • Authors, Papers, Data, Videos, Code, Lectures, Books, etc. • Default Web UI Extensible • UI Toolkit • Intuitive programming experience • Extensible Data Model (entities, relationships) • RDFs for new data models Interoperable • BibTeX Import • RSS/Atom Syndication • METS support • OAI-PMH Provider • OAI-ORE • Simple Search API • Atom Publishing Protocol • SWORD Free & Open • Freely available • Based on open standards • SQL Server and Developer tools available via Dreamspark

28. Research Output Repository Platform PDF file Lecture on 2/19/2008 contains is representation of PowerPoint presentation authored by organized by tony presented by Elizabeth, Sebastien, Matthew, Norman, Brian, Sarah, George, Roy

29. Zentity 1.0 DEMO

30. Further Information and Resourceshttp://research.microsoft.com • The site contains access and downloads of relevant tools and resources for the worldwide academic research community. A small set of examples include: • Research Output Repository: building blocks, tools, and services for developers who are tasked with creating and maintaining an organization’s repository ecosystem. http://research.microsoft.com/zentity • Tools and Services for Research Collaboration: http://research.microsoft.com/en-us/collaboration/tools/default.aspx

32. Additional slides

33. GenePattern? Should we include this? --AW