Workshops

VIVO & Eagle-i @ IU Workshop

Date:

September 27-29, 2010


Meeting Place:

School of Library and Information Science, Indiana University
1320 E. 10th St., School of Library and Information Science (SLIS), LI043, LI036, and LI043A
Bloomington, IN 47405

Organizers:

Katy Börner

Victor H. Yngve Professor of Information Science, School of Library and Information Science, Indiana University, Bloomington;
Director, Cyberinfrastructure for Network Science Center; Curator, Places & Spaces: Mapping Science exhibit
katy@indiana.edu

Ying Ding

Assistant Professor, Information Science, School of Library and Information Science, Indiana University, Bloomington; Core Faculty of Cognitive Science; Co-Director, Semantic Web Lab
dingying@indiana.edu

Workshop Goals & Agenda:

This 3-day workshop brings together VIVO & Eagle-i ontology and development teams to discuss the potential alignment of ontologies and systems and seek long-term sustainability.

The goals of the meeting are:

  • Present and discuss current status of VIVO & Eagle-i ontologies and systems.
  • Identify synergistic collaboration opportunities and challenges.
  • Outline a course of activities over the next 5 years.

Schedule:

Monday, September 27, 2010

9:00am Welcome by Organizers (Katy Börner and Ying Ding)
9:15am Quick round of introductions, modification of agenda as needed
9:30am Feedback from experience at IU creating and populating a research instance

  • Improving manual data entry
  • Rolling out self editing at IU authentication, permissions, policies
  • Data provenance and update policies/workflow
  • Features and schedules for upcoming releases
11:00am

VIVO Visualizations

  • How can VIVO visualization tools become more general so that they can be adopted for other projects, using other LOD data?
  • How should we interact with other semantic web programmers?
12:00pm Lunch break (lunch buffet at Samira, 100 W 6th St., 812-331-3761)
12:30pm Integrating Yuyin Sun’s work into the development features and release timeline
1:00pm

Ontology team preparation for meetings with Eagle-i

  •  Review of Eagle-i ontology
  • Compiling a list of classes and properties we would like to import
  • Preparing for discussions on future directions, expertise, and interoperability
2:00pm

VIVO & Eagle-i development overviews (once Daniela Bourges arrives)

  •  Overview of VIVO including current visualizations, theming at different sites, and the research instance at IU
  • Discussions of technology choices and how they reflect the respective project goals, data sources, and support models
  • Discussion of commonalities based on use of ontologies and triple stores
3:30pm

Search in Eagle-i and VIVO

  • Overall requirements and goals at the individual institution and national level
  • Opportunities for semantic search leveraging controlled vocabularies and other classes and properties in our respective ontologies
  • Exploration of development perspectives on using ontologies for application configuration and/or search interface contextualization
4:30pm

Development directions focusing on visualization and interoperability

  • Most likely areas of collaboration
  • Considering how to engage wider communities in a hackathon event?
5:30pm Adjourn
6:00pm Jon Corson-Rikert and Brian Loew's presentation at the Networks and Complex Systems Talk Series (open for public)
7:00pm Joint dinner (Eagle-i ontology team arrives) at Taste of India (316 E. 4th St., 812-333-1399)

Tuesday, September 28, 2010

9:00am Introduction of new participants, and current status of the ontology development for two projects)
9:30am Details and directions for the Eagle-i ontology
10:00am Details and directions for the VIVO ontology
10:30am Overview of the University of Michigan M-Cores system and data model (Mary Hill)
11:00am

Brainstorming with development and ontology teams on goals and means for interoperability among VIVO, Eagle-i, and M-Cores

  • At the data modeling/ontology level
  • At the search level
  • At the core facility level – how can VIVO and Eagle-i provide tools for both researcher and resource networking without requiring duplicated effort?
12:30pm Joint Lunch at the Tudor Room (IMU, 900 E 7th St.)
1:30pm Continued discussions between VIVO and eagle-i teams on topics including but not limited to:
  •  Ontology alignment and interoperability through direct imports of classes and properties in both directions
  • eagle-i and Vivo usage of OWL axioms. similarities, differences, best practices (usage of equivalent classes, class restrictions etc)
  • referencing external taxonomies and ontologies such as genes
  • resolving person URIs and interoperabilty between eagle-i and vivo
  •  Common points of intersection and overlap with other ontologies
  • Design of ontologies for application configuration and search interfaces
  •  Opportunities for sharing data and exploring direct interoperability between VIVO and Eagle-i installation at OHSU
  •  Referencing individuals across triple stores -- approaches for sharing and/or linking instance data
  • Possible collaborations on visualization and data analysis
3:30pm Break
4:00pm

Topics and outline generation for a joint paper on Eagle-i and VIVO ontologies

  • How the goals and requirements of the two projects have influenced the two ontologies – how are they similar and how are they different
  • Common principles and best practices
  • Establishing intereoperability
  • What this will mean for sustainability
5:00pm Preparation for Wednesday meetings, including preliminary discussion of joint funding opportunities
6:00pm Adjourn
7:00pm Joint Dinner at Turkuaz Cafe (301 E. 3rd St., 812-333-7908)

Wednesday, September 29, 2010

9:00am Introductions and discussion of goals and desired outcomes for the day
9:15am

Approaches to discovering expertise

  • Discussion of use cases and examples of the type of inferencing that we'd like to be able to do (homework prior to the meeting)
  • Approaches -- textual, network and semantic analysis, composites of both
  • Usage of text/data mining to validate ontology (could also go elsewhere in agenda)
  • Relationships to controlled vocabularies
10:30am Break
11:00am

Representing expertise

  • Existing tools and relevant projects (e.g., OpenCalais, OpenAmplify, Gridworks Suggest)
  • What would be different about a semantic approach?
12:30pm Joint Lunch
1:30pm Visualization options for direct and derived expertise, including basemaps of science work
2:00pm Funding opportunities and proposal plan
3:00pm Break
3:15pm VIVO team members meet with IU Library VIVO implementation team
4:00pm Next steps in our collaboration
4:30pm Looking ahead to a 5-year plan
6:30pm Adjourn

Participants Attending:

Jon Corson-Rikert

Jon Corson-Rikert

Head of Information Technology Services (VIVO Implementation Team)

Brian Lowe

Brian Lowe

Programmer/Analyst III, Cornell University (VIVO Implementation Team)

Stella Mitchell

Stella Mitchell

Semantic Applications Programmer, Cornell University (VIVO Development Team)

Melissa Haendel

Melissa Haendel

Lead Data Curator, Oregon Health & Science University (Eagle-i Ontology Team)

Carlo Torniai

Carlo Torniai

Scientific Data Curator, Oregon Health & Science University (Eagle-i Ontology Team)

Barry Smith

Barry Smith

SUNY Distinguished Professor; Julian Park Chair; Adjunct Professor of Neurology; Adjunct Professor of Computer Science, University at Buffalo (Ontology)

William Barnett

William Barnett

Sr. Manager, Life Sciences, Indiana University, Bloomington; Director, Indiana CTSA; School of Medicine, IUPUI, Indianapolis

Lilith Reeves

Lilith Reeves

Associate Professor of Clinical Medical and Molecular Genetics, Department of Medical and Molecular Genetics and Chief Scientific Officer, IU Clinical and Translational Sciences Institut, Indiana University School of Medicine

Michael Warden

Michael Warden

Knowledge Solutions Leader, Collexis, Inc.

Bing He

Bing He

PhD Student, School of Library and Information Science, Indiana University, Bloomington; Researcher, Semantic Web Lab

Yuyin Sun

Yuyin Sun

VIVO System Development Lead; Researcher, Semantic Web Lab

Mansoor Ahmed

Mansoor Ahmed

PostDoc, School of Library and Information Science, Indiana University, Bloomington; Researcher, Semantic Web Lab

Shanshan Chen

Shanshan Chen

VIVO Ontology Development Lead; Researcher, Semantic Web Lab

Daniela Bourges-Waldegg

Daniela Bourges-Waldegg

Teach Lead and Architect, Center for Biomedical Informatics, Harvard Medical School (Eagle-i Consortium)

Hildreth Robert Frost

Hildreth Robert Frost

Research Associate in Biomedical Informatics, Harvard Medical School (Eagle-i Consortium)

Interested But Cannot Attend:

Melanie Wilson

Melanie Wilson

Scientific Data Curator, Oregon Health & Science University (Eagle-i Ontology Team)

Joanna Brownstein

Joanna Brownstein

Program Manager, Center for Biomedical Informatics, Harvard Medical School (Eagle-i Consortium)

Jeff Krause

Brian Athey

Collegiate Professor, Computational Medicine and Bioinformatics; Professor, Departments of Psychiatry and Internal Medicine; Chair (Designate), Computational Medicine and Bionomics; Director, Academic Informatics; Associate Director, Informatics and IT, Michigan Institute for Clinical Health Research (MICHR), University of Michigan Medical School

Travel/Housing:

Please contact Mark Price at 812/855.5120 or maaprice@indiana.edu to arrange travel.


Room blocks have been set aside for attendees of this workshop at the Biddle Hotel at the Indiana Memorial Union (IMU), located on the Indiana University Bloomington campus. If booking yourself, please use group code "VIVO" when booking the room to receive the discounted rate of $99.00 per night (plus tax).


Hotel Address:
Biddle Hotel and Conference Center
900 E. 7th St.
Bloomington, IN 47405


Hotel Contact Information:
Toll-Free: 800/209.8145
Main IMU Switchboard: 812/856.6381

Directions:

Please visit http://cns.slis.indiana.edu/contact.html for directions and maps, or you may also contact Mark Price at 812/855.5120 or maaprice@indiana.edu.

Acknowledgments:

Information coming soon.

Thank you to our generous sponsors: