VIVO

December 20, 2011

Overview

VIVO 1.4 introduces two significant new features as well as extending development begun in previous releases. Proxy editing allows any VIVO user to designateanother user as his or her proxy for review or update, a much-requested feature, and VIVO 1.4 also includes the ability to annotate VIVO entries with terms from controlled vocabularies using external terminology services.

Proxy editing

VIVO now allows anyone with a VIVO profile to delegate editing privileges for his or her entry to another user, or proxy. Proxy-based editing facilitates adoption and updating of VIVO in settings where researchers do not have the time to maintain their own entries and wish to delegate editing to specific persons. Proxy editing also supports granting a VIVO user the rights to edit other entities such as specific organizations, furthering sustainability by controlled distribution of editing responsibility. Proxy privileges can be managed by VIVO administrators on behalf of multiple users or by an individual user on his or her own behalf.

Linking to external vocabularies

Many people have requested support for associating terms from established controlled vocabularies with people, publications, grants, organizations, and other types of data in VIVO. While small taxonomies or vocabularies may most easily be imported in their entirety into VIVO, a number of the more popular controlled vocabularies are very large in proportion to the number of terms likely to be referenced within a single VIVO instance. Incorporating terms by reference helps keep terms in sync as these vocabularies continue to evolve and is more consistent with linked data principles.

Stony Brook University's Department of Medical Bioinformatics, led by Dr. Moisés Eisenberg, hosts an RDF version of the National Library of Medicine's Unified Medical Language System or UMLS (http://www.nlm.nih.gov/research/umls/). Through a 2011 VIVO mini-grant, Stony Brook has developed a web service that accepts incoming term requests from VIVO and returns one or more matching UMLS concepts with stable URIs. VIVO displays the label associated with the UMLSconcept but the concept's URI ensures that references remain unambiguous, even across multiple VIVO instances at different institutions.

The interface from VIVO to the UMLS service has been implemented to allow linking to additional vocabulary services such as GEMET (http://www.eionet.europa.eu/gemet), and we will offer additional choices in upcoming releases.

Visualizations

The VIVO 1.4 release features a novel science maps visualization that supports the comparison of publication profiles of up to three organizations.

All science map visualizations also now feature the updated basemap of science that uses 10 years of publication data (2001-2010) from Elsevier's Scopus and Thomson Reuters' Web of Science. The UCSD map was originally created by theRegents of the University of California and SciTech Strategies in 2008. It was updated by SciTech Strategies, L'Observatoire des sciences et des technologies, and Indiana University's Cyberinfrastructure for Network Science Center (CNS) in 2011.

Ontology changes

Ontology changes from 1.3 to 1.4 were relatively minor, including an update to the Geopolitical Ontology and changes to support linking to external vocabularyreferences as described above. Changes for each release are documented on the VIVO wiki on Sourceforge at http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology.

With version 1.4, the VIVO ontology^! will be submitted to the Bioportal (http://www.bioontology.org/bioportal), an open repository of ontologies hosted by the National Center for Biomedical Ontology, to facilitate access and dissemination.

Freemarker conversion

VIVO 1.4 continues the major effort begun with version 1.2 and continued in 1.3 to convert VIVO's entire user-facing code base from Java Server Pages (JSPs) to FreeMarker, the Java template engine library (http://freemarker.sourceforge.net/). FreeMarker more cleanly separates internal application programming logic from page display, making the VIVO application more understandable and extensible, especially for developers new to VIVO. The entire user-facing editing system has been refactored for VIVO 1.4 to simplify the configuration of custom forms and allow more rigorous code testing and data verification.

Improved diagnostics

VIVO 1.4 features improved diagnostic messages to help with configuration issues. As VIVO starts up, it runs a series of tests looking for common configuration errors. If VIVO finds a problem it will display an error or warning message in the browser, instead of the VIVO home page. These start-time diagnostics and prominent display make it even easier to install VIVO.

Vitro as a standalone application

VIVO extends the underlying Vitro open-source semantic web^! application with the VIVO ontology, software customizations specific to the VIVO ontology, and visualtheming. With version 1.4 of VIVO, the underlying Vitro software has been packaged for use independently of the VIVO ontology. Vitro supports ontology creation and editing as well as importing existing ontologies, and is an excellent tool for populating ontologies with instance data, for publishing RDF as linked data, and for hands-on teaching about ontologies and semantic webconcepts.

Acknowledgements

This release represents the work of the entire VIVO team and contributions from the larger VIVO open source^! community, including feedback from adopting sites within and beyond the VIVO project, feedback from outreach efforts in the biomedical and library communities, ontology improvements and collaborations, and multiple forms of user and application testing.
 
The files are currently available on SourceForge and linked on the downloads page at http://vivoweb.org/download. Congratulations to all involved!

The VIVO project is funded by the National Institutes of Health, U24 RR029822, "VIVO: Enabling National Networking of Scientists".

The Board of euroCRIS and the Leaders of the VIVO Project team are delighted to announce their intention to cooperate in the development of international systems for research information.

euroCRIS is mandated by the European Commission to maintain, develop and promote CERIF (Common European Research Information Format) a European Union Recommendation to member states.  A not-for-profit association since 2002 – although existing as an unofficial association since 1991 – euroCRIS has members in almost all continents and has encouraged CERIF to be a national standard in 8 countries and utilised in many organisations in more than 30 countries.  CERIF is a data model which can be implemented as a CRIS (Current Research Information System) or used for interoperation.

VIVO is an open source^! ontology^! and software system designed at Cornell University for researchers and used in many universities in the USA that has attracted interest more widely internationally.  It is based on the Semantic Web / Linked Open Data concept.  Recent development has been supported by the U.S. National Institutes of Health, U24 RR029822, through a consortium of universities led by the University of Florida and including Cornell University, Indiana University, Ponce School of Medicine, The Scripps Research Institute, Washington University School of Medicine in St. Louis, and Weill Cornell Medical College.

Recently euroCRIS has developed a technology to interoperate the formalised database structure of CERIF with linked open data / semantic web^! constructs thus this cooperation is timely.

We propose to structure the cooperation in three aspects:

1.  Interoperation and convergence of semantics in the two systems;
2. Interoperation of the systems to allow homogeneous access over heterogeneous research information systems;
3. Exploring utilising the VIVO user interface for researchers as a ‘front-end’ to the CERIF research information storage environment;

This cooperation will add to the existing strategic partnerships that euroCRIS has with ALLEA (All European Academies), APA (Alliance for Permanent Access to the Records of Science, CASRAI (The Consortia Advancing Standards in Research Administration Information), EARMA (European Association of Research Managers and Administrators), ERCIM (European Research Consortium for Informatics and Mathematics), ESF (European Science Foundation), EUA (European Universities Association), ICSU-CODATA , JISC (Joint Information Systems Committee), and the euroCRIS member organisations including CRIS systems suppliers and publishers of scholarly works.

This partnership will further facilitate a diverse collection of activities associate with the VIVO project, across federal agencies, professional societies, data providers, and a variety of efforts with the Semantic Web and ontology development communities. Exploring the interoperabilities between the activities of euroCRIS and VIVO will also serve to enhance the efforts at VIVO implementations across the United States and around the world as scholars look to share their research efforts and promote their expertise. Significant partners of the VIVO project include: the USDA (United States Department of Agriculture), the ORCID (Open Researcher and Contributor ID) Initiative, the American Psychological Association and the Publish Trust Project, Symplectic Limited, Wellspring Worldwide, and the Australian-based ANDS VIVO project, a collaboration of the University of Melbourne, Queensland University of Technology, and Griffith University. The cooperation will strengthen the VIVO team’s international links and provide many opportunities for joint developments to the benefit of the worldwide research community.

CTSA Informatics KFC meeting

Many of us will be at the CTSA Informatics KFC meeting October 12-13 at Natcher Conference Center on the NIH campus. The meeting will provide a number of opportunities to interact with colleagues and learn about various related topics, including: the VIVO ontology^!, researcher networking efforts at a number of sites and within the CTSA consortium, Semantic Web-based initiatives and more.

A discussion about the VIVO Ontology

There will be a comprehensive discussion of the VIVO ontology at the CTSA Research Networking Affinity Group meeting, scheduled for 8:00 AM to noon on October 12. Ying Ding of Indiana University and Stella Mitchell of Cornell University will represent the VIVO team on these discussions where they will go over the VIVO ontology with representatives from CTSAs from around the country. Please email Kristi Holmes at holmeskr@wustl.edu if you would like to receive the materials that were sent out to the RNA group in anticipation of this discussion.

A sample of IKFC Presentations of interest

Demonstrations:

• #15: eagle-i: development and expansion of a scientific resource discovery network
• #17: The Human Studies Database (HSDB) Project
• #19: Harvard Catalyst Profiles: Research networking, bibliometric analysis, and social network analysis based on linked open data and VIVO ontology
• #23: A Research Participant Tracking System that Supports Business Process through System Integration

Posters:

• #27: VIVO: A tool for collaboration and research discovery (presented by Mike Conlon – come hear about the latest news/features from the VIVO team!)
• #30: DIRECT2Experts – Distributed Interoperable Research Experts Collaboration Tool
• #36: Finding Collaborators: Towards Interactive Tools for Research Social Networks (Chuck Borromeo, more information below!)
• #61: ResearchIQ: Semantic Search for the Research Community
• #51 & #52 will both address VIVO in addition to their main topics

This is just a small sample of the content that will be covered. Please take a look at the abstracts for the full listing of accepted submissions.

New Research Study

Here’s some information about a research study at Pittsburgh that is currently recruiting participants. Many of you might have met Chuck at the VIVO conference in Washington this past August. I encourage you to contact Chuck about participation and also if you have any questions about the study.

Chuck Borromeo is a Master's student at the University of Pittsburgh in the Department of Biomedical Informatics (DBMI). He is recruiting participants for a study gathering requirements for collaborator search
systems. The study will determine the functionality best suited to  inding potential collaborators. Each participant will be interviewed via WebEx and asked to evaluate two wireframe mock-ups. The interviews should last approximately one hour. When completed, the study will provide validated design requirements to the research networking community for inclusion in their software applications. For more information, Chuck will be presenting a poster about the project at the CTSA IKFC meeting Oct. 12-13 at the NIH (poster #36). If you wish to participate, please contact Chuck Borromeo at chb69@pitt.edu.

The 2011 VIVO Conference was simply amazing!  We'd like to thank everyone for attending and contributing to the conference and we'd especially like to thank our keynote and invited speakers. The sessions were top-notch and there were many interesting discussions in the hallways between sessions and the scholarly exchange continued throughout the evenings. We'd also like to thank our outstanding sponsors! Your kind support of the conference was essential for its success. We would also like to express our sincere appreciation to our session chairs and to the conference and program committees for tirelessly working behind the scenes to enable such a fantastic event.  

We'll be pulling together detailed information in the coming weeks, including links to the national networking applications that were part of our "apps contest" and we'll also make conference materials available online. Watch this space for updates about this process.

If you were a presenter (talk, poster, or panel), please send your final materials to Kristi at kristi@vivoweb.org.  We'll add the content to a 2011 VIVO Conference website and we'll let everyone know when the materials are available.

Thanks again - we look forward to seeing you August 22-24 in Miami, Florida for the 2012 VIVO Conference!