VIVO & Eagle-i @ IU Workshop


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

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Ying Ding 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

Katy Borner 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

Workshop Goals

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:


Monday, September 27, 2010 ~ Location: SLIS, LI043
9:00 am Welcome by Organizers (Katy Börner and Ying Ding)
9:15 am Quick round of introductions, modification of agenda as needed
9:30 am

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
11:00 am

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?
12:00 pm Lunch break (lunch buffet at Samira, 100 W 6th St., 812-331-3761)
12:30 pm Integrating Yuyin Sun’s work into the development features and release timeline
1:00 pm

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
2:00 pm

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
3:30 pm

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
4:30 pm

Development directions focusing on visualization and interoperability

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

Tuesday, September 28, 2010
~ Location: SLIS, LI043
9:00 am

Introduction of new participants, and current status of the ontology development for two projects)

9:30 am Details and directions for the Eagle-i ontology
10:00 am Details and directions for the VIVO ontology
10:30 am Overview of the University of Michigan M-Cores system and data model (Mary Hill)
11:00 am

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?
12:30 pm Joint Lunch at the Tudor Room (IMU, 900 E 7th St.)
1:30 pm 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
3:30 pm Break
4:00 pm

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
5:00 pm Preparation for Wednesday meetings, including preliminary discussion of joint funding opportunities
6:00 pm Adjourn
7:o0 pm Joint Dinner at Turkuaz Café (301 E. 3rd St., 812-333-7908)

Wednesday, September 29, 2010 ~ Location: SLIS, LI036 and LI043A
9:00 am Introductions and discussion of goals and desired outcomes for the day
9:15 am

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
10:30 am Break
11:00 am

Representing expertise

  • Existing tools and relevant projects (e.g., OpenCalais, OpenAmplify, Gridworks Suggest)
  • What would be different about a semantic approach?
12:30 pm Joint Lunch
Location: SLIS, LI043A
1:30 pm Visualization options for direct and derived expertise, including basemaps of science work
2:00 pm Funding opportunities and proposal plan
3:00 pm Break
3:15 pm VIVO team members meet with IU Library VIVO implementation team
4:00 pm Next steps in our collaboration
4:30 pm Looking ahead to a 5-year plan
6:30 pm Adjourn
*Agenda is subject to change

Invited Participants

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
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
Daneila Bourges-Waldegg Daniela Bourges-Waldegg
Teach Lead and Architect, Center for Biomedical Informatics, Harvard Medical School (Eagle-i Consortium)
  Hildreth Robert Frost
Research Associate in Biomedical Informatics, Harvard Medical School (Eagle-i Consortium)
[Not Confirmed]

Invited but unable to attend


Please contact Mark Price at 812/855.5120 or 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


Please visit for directions and maps, or you may also contact Mark Price at 812/855.5120 or


Information coming soon.