Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 1 Continuation Format Page VIVO: Enabling National Networking of Scientists Year 2 Progress Report: July 1, 2010 June 30, 2011 1 Summary The VIVO project has had a remarkable second year. Development has produced major new releases of the core software, as well as a new tool for general purpose data ingest, the VIVO Harvester. Ontology has matured the VIVO ontology, aligning it with signi ficant other ontologies and demonstrating the extensibility of the VIVO vocabulary for additional use cases. Implementation has progressed at all seven schools with plans to transition to sustainable operations at each. Six mini grants were funded to aug ment development and spur innovation. Over 121 presentations have been made by VIVO team members in a wide variety of venues in support of VIVO adoption Five papers are in press and an additional five conference papers have appeared. The result has bee n more than fifty VIVO projects in progress around the world. An open source community has been established to enable collaboration and on going support of the software and its use in research and scholarship discovery a nd networking. Four annual VIVO events have been established to further create and sustain community throughout each year. The goal of establishing a national network of scientists has blossomed into a world effort to partner in support of an open informa tion infrastructure for research discovery, collaboration and scholarly work. Significant challenges remain that will be addressed in future work. Significant improvements are needed in the ability to ingest data and implement VIVO. New capabilities are needed to make use of semantic data stored across the web of data. Connecting applications using this linked data will be a challenge. This report describes development, ontology, implementation, outreach, sustainability and evaluation for the period July 1, 2010 to June 30, 2011 The r eport concludes with summary assessments, challenges and prospects for the future. 2 Development With three months still to go as of this writing, the development team has addressed and is on track for achieving major development milestones for the project. The VIVO software has been updated with the major 1.2 release and two maintenance releases, and the VIVO Harvester has had four releases including the major 1.0 release in March, 2011 and additional u pdates in May and June. 2.1 Development Accomplishments Version 1.2 of the VIVO application was released in mid February after four months of development and several weeks of intensive testing. This release incorporates major visual theme and navigation change s and extends the initial co author visualizations for co investigator relationships as well as providing support for comparing temporal graphs of publications among institutions or departments. Version 1.2 also significantly reduces server memory requirem ents, as confirmed by extensive testing in production at the University of Florida, Cornell, and Washington University School of Medicine in St. Louis. page as well as site wide navigation. The new interface has been extensively informed through user testing, with priorities including simplified navigati on and configurable menu page options as well as an improv ed overall browsing experience. 2.1.1 Visualizations Visualizations now extend the user experience on individual res earcher pages as well as providing rich interactive overviews. The Figure 1 Sparkline visualizations in VIVO 1.2 showing pap ers and co autho rs over time
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 2 Continuation Format Page grant reception, and grant collaboration. We have also created several tables that show this data numerically as well (top paper collaborators, top grant collaborators, and more). The co author visualization highlights the immediate co authors of each person in a VIVO instance and has been refined to cluster authors into communities, mak ing the separation or inter various co au thors much easier to see This same interactivity has been extended in a new visualization allowing users to see and explore the grant collaboration network of each individual in a VIVO i nstance. A new temporal graph visualization also introduced with VIVO 1.2 allows users to explore and compare the publication and grant histories of schools, departments, and people side by side within a VIVO instance. The temporal graph visualization can also be used to visually check publication and grant data coverage within a VIVO instance. All visualizations and tables now include options for downloading the data that they are based on, which enables users to further explore this data using spreadsheet or network analysis tools. We have also completed a system for basic VIVO visualization data caching, which allows us to pre calculate data for visualizations and which results in significantly improved load and response time for users. 2.1.2 VIVO Ha rvester The VIVO Harvester answers the most frequent inquiry from prospective adopting institutions about VIVO -how to load institutional and publications data. The Harvester team at the University of Florida adopted an open, iterative approach to softwa re design involving extensive testing and feedback from implementation sites within and outside the project. A set of modular tools deliver the Extract, Transform, and Load (ETL) functions common in enterprise data management applications These tools are extended by functions specific to RDF and additional support for data matching and ongoing update after an initial ingest. The Harvester provides a configurable framework that supports a wide variety of input options including XML, Open Archives Initiativ e Protocol for Metadata Harvesting 1 (OAI PMH ) harvesting, direct downl oad from relational databases, and upload of spreadsheets and common bibliographic formats The Harvester design has evolved rapidly in supporting the three most commonly requested conte nt types -human resources data, grants, and publications. The Harvester team has also provided extensive consultation and training, both on line and in person, including recorded webinars. 2.1.3 Open Source Community The single biggest change to VIVO developme nt is the transition from development within the project to participation by a growing community of VIVO adopters beyond the current VIVO: Enabling National Networking of Scientists project. The Harvester has been developed and documented on SourceForge fr om the beginning, and the VIVO application itself was moved to SourceForge in early March, 2011. Documentation is transitioning from the project based Confluence wiki to the public SourceForge site with assistance from the University of Florida Library tea m. The development process has been very well served by this increased openness and visibility. An Internet Relay Chat (IRC) channel frequently provides near real time responses, and postings to the VIVO development list on SourceForge have increased stead ily, with over a dozen developers from within the project as well as a growing number of people at newly adopting sites participating in answering questions. Adoption and development list participation have been heavily influenced by the new voices at the table through the VIVO mini grants competition; these grants will be described individually later in this report, but directly engaging additional programmers outside the project has had a major benefit in bringing new ideas to the original development tea ms as well as encouraging other developers to participate. 2.1.4 National Networking Visualization We created a first version of the National Researcher Networking Visualization 2 The NRN visualization aims to visually represent the state of various national researcher networking efforts by showing the data holdings of major researcher networking systems in the U.S. The visualization allows users to see the number of people, publications, patents, funding and courses in each of the publicly accessible instances of VIVO, Elsevier SciVal
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 3 Continuation Format Page experts, Harvard Catalyst Profiles, and Stanford CAPS. Users can animate the map to see growth of these national researcher networks over time. 2.1.5 The VIVO Community Search The ability to search across multiple VIVO installations has been a key premise of the VIVO: Enabling National Networking of Scientists project since its inception, and the 2009 Recovery Act U24 Limited Competition The VIVO project has from its inception targeted a distributed approach to search that allow s each institution hosting VIVO full control over the information exposed for indexing. Managing the information at each source VIVO installation allows the indexing and search delivery functions to be independent of any single point of aggregation; any in terested party can elect to adopt the VIVO indexing tool and/or the VIVO search service across any set of participating organizations. The only requirement is that participating applications produce RDF data expressed using the VIVO ontology. Keeping the indexing and multisite search delivery software separate from VIVO itself provides a number of key advantages. We anticipate that searching the national or international VIVO network will be of significant interest beyond the VIVO community alone, and the separation of indexing and search delivery from each other and from the VIVO code base provides a modular way to participate in and leverage the resulting indexed data. The search indexing processes RDF harvested using standard linked data requests to the applications (VIVO or other) at each hosting institution, with a configurable target frequency of updating set initially at 2 4 hours. The indexing process converts the har vested RDF into an Apache Solr index; Solr is a major open source search tool that extends the Lucene search software presently used by VIVO for search indexing within a single VIVO instance. Solr offers additional options over Lucene for managing very large search indexes, including s upport for distributed index generation and for replication across multiple sites for maximum performance. While the size of the VIVO index will be small during the scope of the project, Solr provides a robust growth path for the future. The VIVO project will also make available an exemplar multisite VIVO community search application built using the Drupal open source content management system and the Apache Solr plug in module for Drupal 3 Extensions to the Apache Solr module will be contributed to the Drupal open source community to fully enable other parties wishing to implement searches that leverage any desired consortium of sites producing VIVO data. Searching across multiple institutions rather than a single one provides a number of new interfa ce requirements, especially when users wish to easily alternate between a search with a local scope and searches across an entire network. The VIVO community search interface has been tested using fully Figure 2 National Networking Visualization showing geolocation of aspects of research activity Figure 3 Development view of VIVO community search providing semantic faceted search across sites
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 4 Continuation Format Page functional prototypes with data indexed from the seven project partner sites, both as a single landing page integrating data from multiple sites and as an extension of the search capability at any single VIVO installation. Feedback has stressed the importance of clear organization a nd reinforcement of current search limits through visual cues, and the User Interface Team is working to provide as consistency between local VIVO and whole VIVO community searches. 2.1.6 Release 1.3 The development team has scheduled the release of VI VO version 1.3 for late July to allow partner sites and adopting institutions a full month for updating before the VIVO Conference in late August. The visualization team has imp lemented a Science Map visualization, which allows users to visually explore the scientific strengths of a university, school, department, or person in the VIVO instance. Users will be able to see where an organization or ajor scientific disciplines or 554 sub disciplines, and will be able to see how these disciplines and sub disciplines interrelate with one another on the map of science. Wireframes and design documentation for upcoming enhanced versions of the Science Map visualization have already been developed; the Science Map visualization will most likely be in the form of a PDF that a user can download. VIVO 1.3 will feature notable improvements to the local search, primarily to improve relevance ranking but also to boost the influence of semantic relationships in the search. This will improve recall by including text from related resources (e.g., adding a grant and p ublication titles to his or her search entry) and by boosting overall relevance ranking based on the number and nature of connections from one individual to others. Release 1.3 includes significant changes that bring the VIVO infrastructure closer to where we believe it needs to be for optimal open source community participation and contributions. In addition to a large number of bug fixes and improvements to the major changes in the 1.2 release, 1.3 provides an entirely new model of authorization within the VIVO application to allow more granular control over system configuration and editing. This work is a necessary prerequisite to the much sought after proxy editing feature, whereby one person (typically an administrative assistant) can be designated as a proxy editor for another (typically one or more faculty members or a research center or other organization). The authorization system also allows VIVO webmasters to better control editing rights to the ontology and display features of VIVO, and it provid es an internal user account for all self editors as the locus for future implementation of personal preferences for limiting display or controlling ordering of publications and other information within VIVO pages. The interface for changing and supplementi While less directly visible to the public, version 1.3 also includes additional changes focused directly on supporting open source community involvement in extending and customizing V IVO. The development team m Java Server Pages to the FreeM arker page templating system that much more cleanly separates internal application programming logic from page display, with dramati c results in version 1.2. We have seen the payoff in the success of other adopting sites, most notably the VIVO mini grant projects, who have been able to step in and modify or extend VIVO to meet their Figure 4 Science Map visualization for VIVO version 1.3
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 6 Continuation Format Page The creation of the derived graphs described above will enable the creation of various new visualizations, inc luding but not limited to an automatically generated and interactive view of a VIVO institution's organizational hiera rchy, and a visualization that will allow a user to see the strongest connections between any two VIVO users. We are also exploring a collaboration opportunity with the Gephi 5 team, which would enable VIVO users to visually explore various networks in VIVO using images generated by the Gephi network visualization tool. 2.2.2 VIVO Harvester Plans The VIVO Harvester is being tested at a number of existing and prospective adopting sites leading up to the late June Implementation Fest and beyond, and the UF team has been responding rapidly with new documentation and improved scripting interfaces that clarify the many available options, as well as more thoroughly documented examples. Members of the team attend ed the Implementation Fest and have provided one on one remote and on site assistance to additional adopting institutions. Several key areas remain for future work and will be represented in tasks proposed as development areas for the no cost extension period. Data ingest and update processes rely heavily on data matching that can be improved based on the full scope of current information in VIVO as well as information such as previous email addresses and affiliations. Individual ingest and update scripts have been enhanced to improve alignment of organization names, place names, awards, conferences and other events, and subject keywords i n addition to researchers themselves, and we propose to incorporate more sophisticated matching techniques in VIVO and the Harvester. 2.2.3 Connecting VIVO with Linked Open Data and Other Applications The direct connections established between VIVO at Cornell (I thaca) and the Weill Cornell Medical College VIVO and exploratory work at the VIVO Hackathon provide use cases for closer coupling between any two VIVO instances. Hackathon work found several examples of publications with co authors at VIVO sites and/or Ha rvard Profiles, and pointed out how information discovered in cross site searching could supplement each as well as reduce the large numbers of unknown co authors represented in VIVO. Bi directional connections in grants, faciliti es, center and institute affiliations, and degree programs, as well as co author relationships provide compelling demonstrations for linking two VIVOs, especially as these multi faceted relationships evolve over time. The ability to manage information at actively exposing and updating connections to researchers and research activities wherever else they may researcher ne tworking. The VIVO mini grants also highlight the potential of extending VIVO in ways that will require new development in the core application. Linking between VIVO instances underscores the importance of consistency in applying controlled vocabulary terms so that data harvested from multiple VIVOs will not have multiple URIs for the same term but instead leverage the UMLS work of the Stony Brook University mini grant and it relates closely to the ORCID mini grant as well. Many open challenges remain in this domain, including how to blend locally defined controlled vocabularies (e.g., university strategic goal areas) with externally defined vocabularies, and how best to establish and maintain coordinated lists of educational organizations, grant sponsors, publishers, journals, and events as well as people in ways consistent with several emerging efforts at global authority databases and services. The VIVO Tec hnical Advisory Board has already been helpful in discussions on URI proliferation and identity management, and project members are actively participating in international workshops on researcher identity and attribution (e.g., the IRISC 2011 workshop 6 ). T he Duke VIVO widgets, Digital Vita Documents, and HUBzero mini grant projects have also highlighted the need for more flexible and extensible ways to query VIVO and share content directly with other applications. VIVO developers have already provided speci alized application responses to return the equivalent of several individual linked data requests through a single request response and the evolving VIVO community search indexing will likely offer additional options for previewing available content, ident ifying or following semantic linkages, and providing useful dynamic data compilations such as recent publications by individual, group, or
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 7 Continuation Format Page center. This area of work has many benefits for repurposing VIVO data in other applications as well as dynamic report generation, whether for biosketches, CVs, or recommender systems. 3 Ontology 3.1 Ontology Team Structure and Activities The VIVO Ontology Team has been organized around three activities initiated in the first year of the project : 1) ongoing evolution of the ontology feature set in response to new data sources identified at Florida and needs expressed by implementation sites. 2) The Cor nell Semantic Applications group coordinates the production of ontology updates and new ontology modules, implements reasoning improvements and makes other changes in the VIVO application to support ontology editing and management, including ontology impor ts and exports. 3) SPARQL query builder, while also supporting ontology documentation and evaluation. Each of the seven VIVO project sites has a designated representative on the ontology implementation team, the sites have provided insights on new requirements for the VIVO ontology, such as representing clinical ac tivities, as well as discussing implications of the ontology on data representation and practice. Depending on the upcoming release schedule, the three primary ontology team sub groups meet weekly or biweekly via GoToMeeting to discuss ontology i ssues submitted through the VIVO tracking system or conveyed through biweekly implementation calls and to prioritize improvements for each release. This eagle i ontology team and the larger Resource Represent ation Coordination group coordinated by Dr. Melissa Haendel at the Oregon Health and Science University. The JIRA issue tracking system has been instrument al in tracking ontology related problems and questions, proposing and discussing new functionalities or improvements, tracking user case studies, disseminating summaries of policy discussions, and providing documentation in the context of feature development During the second year of the project the issue tracking system has been opened for broader participation through links from the VIVO open source development site on SourceForge 7 3.2 Accomplishments We have released VIVO ontology versions 1.1 and 1.2, with the releas e of version 1.3 expected in late July. Version 1.2 of the VIVO ontology includes two significant new modules developed through ongoing collaborations with the eagle i Project 8 The two ontology teams held face to face meetings at Indiana Univer s ity in September, 2010, and have continued to meet at regular intervals since then. We first worked jointly to modify the VIVO ontology for alignment with the Basic Formal Ontology (BFO), an upper ontology providing a high level organizing structure de signed for information representation and that can also for use in support of domain ontologies developed for scientific research. An optional VIVO ontology module encapsulates the alignment to BFO and will help inform further alignment efforts. The BFO alignment work guided the implementation of a Scientific Research module combining the top level eagle i classes and a number of associated properties to link research resources to people and organizations. The goal of this module is to allow an institution hosting VIVO to capture and store information on research reso urces within the institution in order to demonstrate the potential value of implementing the full eagle i application, represent a subset of research resources available for broad use, or permit direct interoperability with eagle I or other semantic platforms for search or data reuse within the institution. This module is now part of a default VIVO installation. Significant progress has been made on ontology documentation with the immediate goal of submitting the VIVO core ontology to the Bioportal in association with the VIVO 1.3 release. The ontology documentation is being developed on the public SourceForge wiki, and the Indiana team has prepared standard format OWL Doc HTML pages for the VIVO ontology to link from SourceForge The Florida team is preparing diagrams of
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 8 Continuation Format Page key sections of the ontology to help with data acquisition planning and Harvester configuration at existing and newly adopting VIVO institutions. The Indiana team tested Cornell data (v 1. 1) and UF data (v1.2) with a set of SPARQL queries to identify consistently the ontology has been populated at those two institutions. The Ind iana team is also developing semantic web components to facilitate knowledge discovery, including the SPARQL Query Builder included in VIVO 1.2 and a search tool to discover associations between two people in VIVO. The SPARQL Query Builder help s VIVO data curators to semi automatically build complicated SPARQL queries by choosing candidate classes and properties from dropdown boxes. This work is also being extended by one of the VIVO mini grants as a means for webmasters to identify content of interest in VIVO and formulate the queries necessary to consume VIVO data on other websites. The association search tool dynamically creates a relation graph based on the VIVO data to help user s discover potential semantic relationship s among instances in the data, such as between two researchers or between two organizations. Ontology and outreach team members at Cornell and Florida have worked extensively with the VIVO implementation team at the USDA to review ontology questions and recommend extensions to meet the specific requirements of that organization in adopting VIVO. 3.3 Ontology plans The ontology team will continue to address issues scheduled for the VIVO 1.4 release as well as new issues and requests being raised by implem entation sites within the grant and in the wider VIVO community. These include: Developing a new VIVO ontology module for representing metadata about research data sets, based closely on the work of a consortium of Australian universities funded by the Aus tralian National Data Service 9 Building additional support into the VIVO ontology and application for representing corrections such as the reassignment of authorship attribution when standard name disambiguation techniques have produced spurious results I mplementing the ability for users to link directly from VIVO to externally hosted controlled vocabularies with stable URIs, in collaboration with Stony Brook University through the VIVO mini grant program Continu ing to develop the semantic associa tion search and algorithms to analyze semantic data The ontology team will also participate in a number of collaborative efforts: Continu ing to fine tune the VIVO core ontology based on the feedback from additional institutions adopting VIVO, incl uding institutions other than universities and medical schools. VIVO implementation personnel at the USDA have requested a version of the ontology less focused on academic institutions, for example. Working closely with the eagle i ontology team to extend alignment and data interoperability to deeper levels of the VIVO and eagle i ontolo gies, as well as joint exploration of extensions in clinical and research domains. Continuing to explore models of expertise based on the eagle i an d VIVO ontologies Working with two 2011 CTSA supplemental awards: one focused on representing intellectual property information at the University of Rochester, and a second expanding linkages from VIVO to the CTSA ShareCenter network, based at the Oregon H ealth and Sciences University. Working with Elsevier and Thomson Reuters to evaluate web services of non proprietary bibliographic services. Working with the development team to troubleshoot data harvesting from Harvard Profiles, including resolving any ontology versioning issues or inconsistent data population. Working with the developers of tools including Collexis/Scival Experts and Symplectic El ements to facilitate exporting data conformant to the VIVO ontology.
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 9 Continuation Format Page Working with partners including Symplectic to identify additional online sources of definitive information identifying journals and organizations, preferably in RDF format, to permit link ing to these sources 4 Implementation 4.1 Cornell 4.1.1 D ata Acquisition and Repurposing Ongoing ingest of HR, grants, and courses data Adapted ingest processes to reflect changes to existing data feeds. Changes: type of feed, d epartment identifiers, content mapping Ingested 4 GB of faculty annual report data, May 2011 4.1.2 Data Maintenance In the process of cleaning up deprecated ontologies and data that existed prior to V0.9 Remove deprecated disciplinary portal subset code and data April 2011 4.1.3 App lication Updates and Extensions Upgraded to V1.1 in August 2010 Upgraded to V1.1.1 in October 2010 Upgraded to V1.2 in May 2011 and V1.2.1 in June 2011 4.1.4 Current Tasks VIVO provides researcher profiles to faculty and researchers across the institution for all disciplines at Cornell. The data is being repurposed for websites and centers that cross department and college boundaries. This service provides search and discovery to facilitate collaboration at Cornell and other VIVO or VIVO complia nt systems that are part of the consortium. 4.1.5 Future Considerations Our local Cornell VIVO team is partially supported by the University Provost office and by Albert R. Mann Library. This will continue for another year during which time further uni versity support will be sought. Our hope is to have the VIVO software hosted by Cornell's Information Technology services, but continue to administer VIVO from within the Cornell University Library. We also have submitted three grant propo sals as possible external funding sources. 4.2 University of Florida 4.2.1 Data Acquisition and Repurposing Acquired and ingested data from UF Human Resources (~10,000 UF employees and ~40,000 non UF collaborators), UF Division of Sponsored Programs (~15,900 grants), and PubMed (~8,000 publications) Acquired data from UF Business Services (images) and Registrar (courses) Entered data manually from approximately 1200 CVs across all departments and divisions. Data elements included awards, prev ious positions, research interests, photos, educational training and additional email addresses 4.2.2 Data Maintenance Created new class to separate faculty from courtesy faculty Worked with UF International Ce nter to identify fellowship and other international data Added local geographic data
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 10 Continuation Format Page Refined organization structure at the highest two digit organizational level In the process of adding role data. Roles did not exist prior to version 1.0 4.2.3 Application Upda tes and Extensions Created a SPARQL endpoint for the UF VIVO system Tested release candidates and submitted feedback to Development for version improvements Installed VIVO application 1.0, 1.1, and 1.2 versions (as available) including migration to SDB a nd local branding and Harvester 1.1 version Migrated VIVO to new server administration structure Designed extensions to support the UF International Center its programs and international agreements Installed Harvester Implementation 1.1 Implemented Shibboleth authentication for VIVO 1.0. Turned on self edit for all faculty and staff. 4.2.4 Current Tasks Refreshing DSR grant data Documenting bugs and providing feedback to national development team Integrating VIVO support into the Library service model Dis cussing with CrossRef the use of publication data for VIVO 4.2.5 Future Considerations Transition from implementation to operations Continue to support VIVO system and apply upgrades and patches as available Apply new features as available Create a Technical Adv isory Board Stabilize our ingest refresh cycles Continue to identify data sources Ingest course and image data into VIVO 4.3 Indiana University from the other four VIVO institutions who are involved with local production implementation of VIVO at their respective institutions. 4.3.1 D ata Acquisition and Repurposing Worked with the Indiana CTSI Administration to approve the use of and announce to CTSI researc hers and get CTSIhub participant input to enhance their profile data. This data was then harvested and imported to the production VIVO@IU 10 site for approximately 169 IUPUI faculty and 60 IU Bloomington faculty. Prototype coordination for use of VIVO with t he IU Pervasive Technology Institute: team is working closely with the Drupal CMS managers at IU PTI to determine if VIVO will serve as citation management system for their research center. 4.3.2 App lication Updates and Extensions During the past year, the IU team has installed VIVO versions 0.9, 1.1, 1.1.1, and 1.2 in our test and production installations which we refer to as VIVO@IU Additionally we have installed the VIVO Harvester version 1.1.1 in order to use as an automated broker between our IUIE (Indian a University Information Environment) data warehouse and our production VIVO instance for synchronizing administrative information from trusted sources at IU with the VIVO production instance.
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 11 Continuation Format Page Implementation of VIVO 0.9: implemented VIVO 0.9 and migrated a ll production data to the new version of the software for VIVO@IU. Implementation of VIVO 1.1: implemented VIVO 1.1 and migrated all production data to the new version of the software for VIVO@IU. Implementation of VIVO 1.2: implemented VIVO 1.2 and migrat ed all VIVO@IU data to the latest version of the software including development tie ins for system wide authentication through the IU Shibboleth installation. Implementation of Shibboleth Authentication for VIVO 1.2: implemented shibboleth authentication f or all IU community members in conjunction with our upgrade to VIVO 1.2. VIVO Harvester Implementation 1.1.1: implemented the Harvester 1.1.1 with our IUIE data warehouse in order to provide automatic synchronization between our official administrative dat a sources and VIVO@IU. VIVO Harvester Enhancements 1.2: During the course of our work in implementing Harvester 1.1.1 with our IUIE environment we contributed several bug fixes to the development team at UF for Harvester 1.2. 4.3.3 Current Tasks Our team is also working on 1) extending IU policies for auto populating researcher profile systems for the IU system, 2) enriching data between VIVO@IU and other profile systems in place at IU like the Indiana CTSIhub and the soon to be implemented profile system for the IU School of Medicine, 3) prototyping models for VIVO use by other research centers at IU like the Pervasive Technology Institute and IU NetSci VIVO Instance, 4) working with other peer institutions to provide information about VIVO implementation such as the University of Illinois (I CHASS) and the University of Nebraska, and 5) documenting bugs and other technical issues that arise in production implementation of VIVO and the VIVO Harvester within the Jira tracking environment. Meanwhile, we are working closely with the VIVO Mini Grant recipient at IU who is building a Joomla extension for VIVO data that will be integrated into the HUBzero portal environment. Developing posters for the 2nd annual VIVO Conference: These papers will focus on the data enrich ment tasks between IU CTSIhub and VIVO@IU and our work on Harvester Integration with the IUIE. Implementing 5 Years Worth of Class Teaching Data: This effort aims to bring in up to five years worth of classroom teaching and course data for researcher profi les within VIVO@IU. 4.3.4 Future plans Future plans at IU include: Working closely with the IU Vice President for Research to enable VIVO for all IU campuses. Identifying experts within the office of the IU Vice President for Research at each IU regional campus to work with the IU VIVO Implementation Team on organizational structure implementation and cross mapping between the IUIE (Indiana University Information Environment) for each regional campus. Using VIVO Harvester 1.1.1 to work with PubMed, GoogleScholar, and other open citation sources to enhance citation data wit hin VIVO@IU Working closely with the IU Library Collection Development Division on contracts with either Elsevier or Thomson for one time data dumps to enrich citation data for VIVO@IU. Implemen ting IU regional campuses within the production VIVO environment starting with IUPUI campus. 4.4 Ponce School of Medicine 4.4.1 Data Acquisition and Repurpose Ingest PubMed data in our production instance using the 1.0 release of the harvester. We have populated 41 people records includes all basic research scientists, still lacking clinical researchers and scientists/faculty from public health program
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 12 Continuation Format Page We have loaded all departments in Medical School and Biomedical Sciences PhD Program. We have only modest coverage of faculty publications and very few grants loaded. Publications were ingested from PubMed. Grants have only been manually added. 4.4.2 Data Maintenance Continuing to manually updated data for some profiles. Provide feedback to the national team on our local VI VO issues. 4.4.3 A pplication Update and Extension Test and continuing to update our production VIVO to the latest releases. Continuing to test the various releases of the harvester on the testing server. 4.4.4 Current Tasks PSM will continue to: U pdate VIVO at least o n a monthly basis with the lasted data fetched from our data sources. U pdate VIVO as future releases become available. P rovide support to any institutions that need it and provide any documentation that I have available at the moment or provide remote supp ort as last resort if needed. P rovide support to local users of VIVO. At PSM in year two we kept current with releases of VIVO. 4.4.5 Future Considerations The PSM IS staff will continue to work on the VIVO to keep it current, but that will simply roll into thei r on going workload. Use of VIVO will be important to the development of the PRCTRC consortium (now a U54 will be a CTSA next renewal in 2 years). The consortium members will use Eagle i for resources and will use VIVO for scientific networking. It is exp ected that at time of renewal, each institution will incorporate budget allocation to keep VIVO running and current at each location. 4.5 The Scripps Research Institute 4.5.1 Data Acquisition and Repurpose In July and August 2010, Scripps Library staff entered as complete data as possible for all faculty members of the Department of Chemical Physiology, our "showcase department" for the VIVO National Conference in August 2010. In the months following, we continued to add data to the brief records created for all ot her Scripps faculty, and to create profiles for newly arriving faculty, and delete profiles for departing faculty. We succeeded in exchanging (both importing and exporting) selected categories of data with the Faculty Profile records maintained by the Scri pps IT Services Department on the Scripps home page. This streamlines data entry and data maintenance for both VIVO and ITS. 4.5.2 A pplication Update and Extension Scripps installed the new versions of VIVO as they were released (v.1.1 in September 2010, v.1.1.1 in November 2010, v. 1.2 in March 2011). Following each upgrade, Library staff reviewed existing faculty profiles for errors that resulted from the new releases, made corrections where possible, and reported bugs and issues that we could not resolve local ly to the VIVO JIRA Issue and Project Tracking site for resolution by the national VIVO development team. 4.6 Washington University School of Medicine (WUSM) 4.6.1 Data Acquisition and Repurpose The VIVO instance at WUSM (vivo.wustl.edu) has been populated with faculty (1,920) who are at the medical school at least 50 %, their respective departments (20) and programs and divisions (12). Publications (33,620) and journals (2,881) harvested from PubM ed are also included on the site.
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 13 Continuation Format Page We have continued to collect WU researcher CVs and photos and are in the process of obtaining permission to use the WU grant data. Our team has played an active role in identifying enhancements to the ontology, such as th e need to link grants with researchers and publications, as well as developing and sharing authoritative source for educational institutions. In a testing environment, we have loaded grant data from NIH RePORTER and used e mail as a login option. To have r obust profiles with data that cannot be programmatically harvested from public sources, NIH biosketches or CVs have been collected from all faculty (tenure track and research) and center members for five department/divisions, and the others are being acqui red 4.6.2 Application Update and Extension WUSM has upgraded VIVO from the 1.0 release to 1.2.1. This process from 1.1 to 1.2.1 took a significant amount of time as there were significant changes to the software and heavy testing needed to occur; this resulted i n reporting bugs to the VIVO developers with fixes incorporated in the latest release. The new release necessitated altering aspects of the data ingest process due to changes in the software. 4.6.3 Current and Future Tasks WUSM will C ontinue work on obtaining, updating and ingesting data from current sources (e.g. HR, PubMed, Divisions/Departments) as well as new sources (e.g. Grants and Contracts Office, Web of Science). Automate the ingest process to have at least weekly data renewal. Expan d VIVO to include departments outside of the School of Medicine. Allow researchers to use a single sign on (i.e. WUSTL Key) to log into VIVO and edit certain fields in their profiles. 4.7 Weill Cornell College of Medicine 4.7.1 Data Acquisition and Repurpose Since J une 2010, the Weill Cornell Medical College (WCMC) VIVO Implementation Team accomplished many were able to identify authoritative data sources and est ablish data feeds into VIVO. The integration between which is the ability to automatically ingest update d data for their profiles. 4.7.2 A pplicat ion Update and Extension The WCMC team has also worked closely with the national VIVO team to install each version of VIVO includ ing v1.0, v1.1 and v1.2. With the s branding and have started ingest ing publications from PubMed using the VIVO Harvester. 4.7.3 Current Tasks WCMC is part of a CTSA and we confirmed the part icipation of our partners including the Hospital of Special Surgery, Hunter College and Memorial Sloan Kettering Cancer Center. Each institution will provide data to accurate as we w ould like, as a result the implementation team has crafted a manual data entry plan to help create more robust profiles. We have also formulated a plan for internal WCMC outreach, the goal is to explain to our users the benefits of VIVO and also socialize usage polic ies for the self edit feature and the correction of profiles. 5 Outreach 5.1 Introduction meetings with contributed co ntent has enabled the team to directly engage people outside of the project about VIVO and has encouraged follow up conversations with institutional representatives. VIVO team members have been invited to deliver a number of presentations at national and i nternational conferences a great indicator of the significant interest in the project across a broad range of groups. The o utreach team has
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 14 Continuation Format Page biweekly calls to discuss local issues related to support and adoption issues. These calls will be opened to att endees beyond the 7 funded institutions beginning July 2011. The outreach team has recently focused efforts to provide guidance, outreach ideas, background support, and presentation materials to facilitate outreach efforts at VIVO implementations beyond the original seven. These resources are openly available on the SourceForge wiki 11 and provide a sustainable way to support future adoption activities around the VIVO platform at institutions and organizatio ns. 5.2 VIVO Speakers Bureau/Conference activities The Speakers Bureau team is responsible for identifying appropriate conference venues for VIVO presentations, locating suitable VIVO team speakers and ass isting team members with developing abstracts and meeting deadlines. The Speakers Bureau work was led by Val Davis and Michele Tennant from the University of Florida Since July 2010, VIVO team members have delivered 82 presentations 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 , developed and displayed 33 posters 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 and organized 6 full discussion panels at various conferences and meetings 127 128 129 130 131 Five peer reviewed papers 132 133 134 135 136 have resulted from conference submissions and 5 additional manuscripts 137 138 139 140 141 have been published during this time which directly b enefited from the VIVO funding opportunity. All project publications and presentations are recorded on the SourceForge wiki 142 where presentation materials can be linked for viewers to download and view past presentations. Submissions to future conferences include: World Library and Information Congress: 77th IFLA General Conference and Assembly ; t he 2011 VIVO Conference ; 2011 VIVO Conference ; ScienceOnline London ; Library and Information Technology Association (LITA) National Forum 2011; Internet2 Fall 2011 Member Meeting; the International Federation of Human Genetics Societies/American Society for Human Genetics joint meeting ; AMIA 2011 Annual Symposium ; and the Association of University of Technology Mangers In addition to these activities, the VIVO team has exhibited at 2 conferences 143 144 The exhibit booth offers project members an opportunity to answer questions that conference attendees may have in a relaxed and informal manner. The booth is also a big draw for attendees at c onferences for people who may not have encountered the VIVO project through other national outreach activities. The VIVO team has had an opportunity to develop a number of innovative workshops and tutorials over the course of the last year. These events serve as an opportunity to engage interested parties in a more significant fashion and allow the VIVO team to work side by side with attendees, creating professional relationships and engendering strong support for our open, community based ap proach. At least 32 tutorials have been developed and taught 145 12 Tutorials in 12 Days at NIH series as well as sessions at the 2010 V IVO Conference, the Second Annual Inte rnational Science of Team Science Conference and 24 individual sessions at the 2011 VIVO Implementation Fest. The Indiana Academic Institutions Organizations University of Rochester Weill Cornell CTSC Florida State University USDA x 2 University of Miami CTSA Rare Diseases Work Group University of Albany Agriculture Network Information Center (AgNIC) University of Michigan CTSA Consortium Child Health Oversight Committee University of Cincinnati Northwestern Cell Imaging Portal University of Nebraska x 2 Knowledge Exchange Einstein University USDA VIVO Board Update University of California Davis CTSA Consortium Steering Committee Georgia Institute of Technology Netherlands Bioinformatics Institute, Barend Mons Duke University International Monetary Fund Brown University BioMedCentral King Abdullah University Informatics Key Function Committee University of Melbourne Direct2Experts organizing group UMass Medical School American Psychological Association Georgetown University NIH Howard University CTSA Strategic Goal 3 Committee University of North Texas Lilly.com UMass Lowell Symplectics, Daniel Hook University of California Davis Microsoft Research University of Wisconsin CrossRef Thomson Reuters x 3 Elsevier/Scopus Table 1 Academic and other organizations par ticipating in VIVO webinars July 1, 2010 June 30, 2011
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 15 Continuation Format Page rela ted to the project, including: IU VIVO Ontology Workshop, VIVO & e agle i @ IU Workshop and the NIH Workshop on Value Added Services for VIVO Six additional tutorial sessions have been scheduled for presentation as pa rt of the 2011 VIVO Conference. Tutorials are listed and are in the process of being made available on the SourceForge community wiki 137 Finally, Jon Corson Rikert from the VIVO project and Dr. Melissa Haendel from eagle i attended two STAR METRICS workshops in Washington in January and April in a technical advisory capacity at the request of the STAR METRICS team and the National Institutes of Heal th. 5.3 Adoption and Collaboration There has been a great amount of work in the area of Adoption and Collaboration by the adoption lead, Elly Cramer, and other team members. The adoption and collaboration team has provided 49 webinars to academic institutions and organizations across the country (see Table 1 ). Requests for information from the website contact form and other referrals are initially handled by the adoption team lead and routed to the proper person as needed (administrative, develop ment, ontology, etc). We have a team of project members representing different aspects of VIVO that can be recruited to present at the webinars. 5.4 VIVO Publishers and Aggregators Our activities in this area focus upon developing relationships with publisher s and aggregators for the purpose of data ingest and availability in VIVO. We have endeavored to work with these groups in a straightforward fashion with specific pri nciples as our guide, 1) We request basic, non copyrightable data elements ; 2) We request that data must be available in perpetuity and 3) W e emphasize that instances must be able to store and use the data in a manner consistent with linked open data We have a number of exciting developments that will make it poss ible for institutions to take advantage of an institutional subscription to a data provider or that will allow an institution to purchase bulk data in batch form from the data provider. We continue to actively pursue other data source options for instituti ons and organizations with a VIVO instance. We have been encouraged by the willingness of content providers to work with us to achieve agreements that allow data to be stored in a manner consistent with linked open data (allowing for unlimited use and reuse of the data as it becomes part of the linked open data cloud) and also the willingness o f data providers to allow institutions to have access to data elements in perpetuity both reflect a new understanding and recognition of the growing role that the semantic web plays in research and scholarship. Additional content providers are welcome to participate, and we maintain an open spirit of collaboration. 5.4.1 Web of Science Cornell University, Washington University and the University of Florida will participate in a p ilot to begin on July 1 and run through September 30, 2011. The results of this p ilot will serve as a guide to future institutions to use Web of Science data to populate the VIVO profiles of their researchers. P ilot institutions are entitled to use the Web of Science web services API to access data. The web service will provide the fol lowing data for source records from the Web of Science: author, title, source, author keywords, UT (WoS identifier), ISSN, ISBN, DOI, and IDS (WoS identifier for document delivery). Web of Science records may be included in the VIVO system and available as open linked records. Each of the three institutions can use the web service to populate their implementation of VIVO using WoS data authored by their faculty, students or affiliated researchers. Each record from the Web of Science must contain a link back to the WoS record by relying on the UT data element. The participating pilot institutions will also have access to the Article Match Retrieval (AMR) service to access current times cited counts for each article. The times cited count can: be di splayed in the VIVO system with the article information and must link back to the Web of Science citing articles results. The times cited content cannot be made available as open linked data, but can be displayed on the specific article page within an ins 5.4.2 BioMed Central P reliminary work has been done related to the use of an open source protocol called SWORD to facilitate transfer of automatic article feeds to its member institutions of articles BMC publish es that have member institutional affiliation This work is ongoing.
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 16 Continuation Format Page 5.4.3 Scopus Scopus subscribing institutions may extract and index Affiliation Data (as defined below) from the SciVerse Scopus online service respecting published journal articles, abstracts, co nference proceedings, technical reports, presentations/lectures, and other research and intellectual output as published for the Subscriber by its affiliated authors, to load in, make publicly accessible from at no charge, and store in perpetuity in, the S of any Affiliation Data shall at and incorporate links in Affiliation Data to the relevant landing page in SciVerse Scopus from which such Affiliation Data was extracted. be limi ted to the following bibliographic metadata : author name, author profile number, author country of residence, author affiliation, document title, document publication year, source title, volume, issue, pages, source and document type, publisher, ISSN, DO I, subject category (ASJC). CAS registration numbers, author contact information, author profiles, non English language tags, chemical names and controlled vocabulary are excluded. 5.4.4 Mendeley Team members have recently begun conversations with Mendeley to le verage their rich bibliographic metadata to populate author profiles using the Mendeley API Mendeley currently boasts over 31 million papers in their database. The discussions with Mendeley are ongoing and woul d provide another avenue for a local VIVO ins tance to acquire bibliographic data for VIVO profile s. 5.4.5 CrossRef We have had discussions with representatives from CrossRef about data acquisition options for VIVO. Data from CrossRef are open and can be consumed and repurposed. CrossRef offers a library affiliate program which allows users to query through 1) a web interface (login and use XML query for batch) 2) an openURL end user interface (single search) or they can deliver data through a bulk load (which they call CMS services). CrossRef can offer m any of the same bibliographic metadata fields that are available through other data aggregators (such as Scopus or Web of Science), however they do not provide affiliation information. This work is ongoing. 5.5 Other Outreach The VIVO project has been highlig hted at least 23 times in a variety of local, national, and international media coverage 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 The VIVO project has been the subject of hundreds of blog posts, Friend Feed posts, Tweets, and other social networking communication vehicles The VIVO project continues to maintain an aggressive social media marketing strategy to highlight various efforts of the project through a variety of information stre ams. VIVO has a page on Facebook 169 a group on LinkedIn 170 and maint ains an active presence of Twitter 171 to help engage the public, promote the project and direct people to the project website 172 and SourceForge community site 7 5.6 Outreach Activities at VIVO Institutions VIVO team members are engaged in outreach efforts at v arying levels at the partner institutions. Most institutions support outreach efforts through a library based model of support and dissemination. This model a trusted entity on campus with a strong tradition of service and support to their user communities via liaison relationships of librarians to their local academic community. 5.6.1 Cornell University Cornell University outreach efforts have focused on (1) buil ding university level support to incorporate VIVO into the fabric of the Cornell information technology infrastructure, (2) staying current with changing formats and access restrictions of authoritative data sources (e.g. Office of Human Resour ces, Office of Sponsored Programs, Registrar, and faculty reporting information), and (3) understanding the research and profile needs of faculty and researchers through the eyes of the library. We have monthly meetings with Dr. B arbara Knuth in the Provost Office who provide funds of the Provost to review priorities and progress in our Provost funded VIVO implementation project Dean Krafft and Jon
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 17 Continuation Format Page Corson Rikert met with the new CIO for Cornell University to make him aware of VIVO and will continue to bring ongoing developments to his attention academic and research missions Several librarians in different knowledge domains participate actively as VIVO curators and are helpful in connecting with academic departments and graduate programs L ibrary connection s also provide opportunities for round table discuss ions, council meetings, orientation booths, and interactions with specialized centers (e.g Sus tainability, Entrepreneurship). We provide regular training sessions for college and department level administrat ors to learn how to edit in VIVO to take advantage of their familiarity with their organizational area and provide a clearer picture of the university structure. Cornell University and University of Florida staff provide consultation support to the National Agriculture Library to assist with their USDA implementation of VIVO and meet regularly with the USDA/VIVO advisory board as part of this collaboration. 5.6.2 Indiana University meetings with leaders have yielded great support from the research administration area, while presentations at brown bags and individual training sessions with departmental staff have spread the word about VIVO and stoked interest at a grass roots level. One of the most notable efforts focused upon work with the with the Indiana CTSI Administration to enhance CTSI researcher profile data. This data was then harvested and imported to the production VIVO@IU 173 site for approximately 169 IUPUI faculty and 60 IU Bloomington faculty. The Indiana team has taken opportunities to promote VIVO on a national scale, most notably by coordinating the VIVO Boot Camp that was a pre conference addition to the 2011 Code4Lib Conference, held on the campus of Indiana University in Bloomington, IN. This brought together colleagues from Cornell University, Indiana University and Cornell Weill Medical Center to offer a comprehensive session on VIVO adoption for the Code4Lib community. 5.6.3 Ponce School of Medicine The team at Ponce Scho ol of Medicine provides feedback to the national team on our local VIVO issues and offers support to other institutions to install VIVO on a Windows environment and provide guidance to get support from the national team or act as an intermediary. We have a ssisted the following organizations with implementation: Centro Agronmico Tropical de Investigacin y Enseanza (CATIE) Costa Rica Universidad Central del Caribe (Joel Nieves attended implementation fest with partial sponsorship from Ponce) University o f Puerto Rico We have presented VIVO to several other schools that are part of a consortium/network to which PSM belongs: March 16, 2011: Puerto Rico Clinical and Translational Research Consortium (PRCTRC U54RR026139), short presentation made about VIVO t o University of Puerto Rico and Universidad Central del Caribbe, both institutions are implementing VIVO (UPR contact Jose Conde & Humberto Ortiz; UCC contact Robert Hunter & Joel Nieves). April 11 12, 2011: Research Centers in Minority Institutions (RCMI) Program Directors meeting. Discussed VIVO without a formal presentation follow up with Tuskeegee University/Cesar Fermin, Charles Drew University/Keith Norris, Jackson State University/James Perkins, Florida A&M/Karam Soliman follow up has not yet led to implementation decision by these institutions.
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 18 Continuation Format Page 5.6.4 The Scripps Research Institute Scripps has postponed launching its major Outreach effort to on campus users pending the following conditions, on site: the PubMed article Harvester is functional, the inter institutional search feature is functional, and the ability for users to update their own profiles is easy and intuitive The Library Director made an informal presentation on VIVO to the Library Director at California Institute of Technology, Pasadena, Cal ifornia in November 2010. At the invitation of a UF Librarian, Scripps Librarians contributed to abstracts and text for two presentations at the NCNMLG/MLGSCA Conference in February 2011: a paper, "Sustaining Networks of Researchers: Experiences with the V IVO Collaboration at University of Florida and The Scripps Research Institute," and a poster, "Sustaining our Future through Innovation VIVO: Library Based Support for Researcher Networking." Throughout Year 2, Library staff continued to provide feedback to, and learn from conference calls with the national Outreach team. 5.6.5 University of Florida The University of Florida (UF) VIVO Outreach team has presented to at least 44 Departments and Organizations at UF since July 2010. The team has presented VIVO posters at four campus research days since July 2010 and the UF VIVO Outreach Training team has conducted 7 training sessions for library employees informing them about VIVO. VIVO has been presented to important UF organizations, including: College of Dentistry Curri culum Committee (April 2011). UF migrated content from Confluence to the SourceForge wiki and improved categorization of content. UF a ssisted in national ontology development and identified and implemented local ontology extensions for UF International Ce nter data, internal/external organizations, and courtesy faculty. Results of these efforts were posted to SourceForge, serving as examples for others. The UF VIVO Outreach team has presented 10 posters off campus at conferences and meetings since July 201 0 and they have given approximately 16 presentations at national meetings/events. The UF Outreach team has made significant contributions to other project efforts led the planning and migration of materials from Confluence to SF wiki (ongoing). The UF Outr each team led the planning and coordination of the 2011 VIVO Hackathon in May and the UF Outreach team has received IRB approval to conduct usability testing on the VIVO interface (ongoing). The UF VIVO Outreach has had articles published in Library News a nd The Post, has been advertised on the my UF L s plash p age 174 and through posters, postcards, handouts, table tents and other means 5.6.6 Washington University Washington University outreach activities have consisted of a variety of efforts, including presentatio ns, one on one conversations, and local press. Over 40 presentations have been given to various stakeholders at Washington University, including: IT directors from WU and our partner institutions, various divisions and departments, high level stakeholders such as the Associate Dean for Research, the Associate Vice Chancellor for Research, the Assistant Vice Chancellor and Executive Director of Corporate and Foundation Relations, the Dean of the School of Medicine, and the Research Affairs Committee (a group comprised of department and division chairs at the School of Medicine). VIVO has been introduced in new graduate studen t orientation activities, in stand alone lectures during the Office of Faculty Affairs lecture series in March and also as part of a gen eral lecture on data in the Introduction to Genomic Medicine seminar series. Various one on one conversations and email exchanges with faculty members have taken place during this time and the WU VIVO has been featured in the Institute of Clinical and Tran slational Sciences (ICTS) newsletter 175 and also in the WU Record 176 We have also reached out about VIVO to ICTS institutional partners including: BJC HealthCare, Saint Louis University, and St. Louis College of Pharmacy. Future efforts include working on adoption related institutions and organizations that regularly collaborate with Washington University investigators. L ocal outreach activities will continue at Washington University School of Medicine.
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 19 Continuation Format Page In addition, t he WUSM Implementation team aggregated all the educational institutions with a 4 year degree or higher, manually curated them for accuracy, and shared them on SourceForge for others to use. We felt this was necessary as there were multiple representations of the same institution (e g. Texas A&M vs. Texas A & M) that prevented an accurate assessment of within and across institutions. 5.6.7 Weill Cornell Medical Colle ge During the time period between July 1, 2010 and June 30, 2011, Weill Cornell's VIVO outreach efforts have focused on our CTSC partners as well as other Weill Cornell affiliates. We have also presented at two national meetings whose focus is on informati on technology and libraries. We have met with the following organizations and presented an overview of VIVO to each: Hospital for Special Surgery (HSS; November, 2010). We are working with HSS now to help them import data into the Weill Cornell instance of VIVO. Hunter College of the City University of New York (November, 2010). Hunter College has decided to install their own instance of VIVO, so we had follow up discussions with them to provide an overview of this process and to give them some examples of how custom reports that were important to their senior leadership could be created via SPARQL queries. Memorial Sloan Kettering Cancer Center (MSKCC). We continue out reach efforts with MSKCC and are working toward an import of their data into the Weill Co rnell instance of VIVO beginning Q1 of 2012. The Methodist Hospital (Houston) National level VIVO Outreach has been accomplished by Paul Albert of the Weill Cornell Library in his presentations at the Computers in Libraries conference in March 2011 and at Code4Lib in February, 2011. 6 Sustainability The sustainability of VIVO as a community, as a development and as a support effort has many elements. We have developed partnerships with vendors regarding support, promotion and access to data. Additional research partnerships afford opportunities for future grant funding and institutional support. Community members are joining our implementation, development and outreach calls. Our events provide an opportunity to spread the word of VIVO activities, as we ll as capital ize on the vitality and creativity of the VIVO community. 6.1 VIVO Open Source Community The centerpiece of the VIVO community is the VIVO open source community site 7 Code, wiki, sup port, and more are available there. The site was launched this year and has seen explosive growth with over 280 pages of content. The project continues to move into the open, generating additional collaborators. 6.2 VIVO Events The VIVO project has established four events that should b e sustainable using a mixture of institutional, sponsor and registrant support. 1) The VIVO conference is designed to be an annual large scale gathering of all those interested in all aspects of VIVO. 2) The VIVO Hackathon is an opportunity to bring toge ther the best and brightest semantic web developers from around the world to brainstorm and create new opportunities for VIVO and the semantic web related to scholarly discourse and discovery; 3) the VIVO workshop provides an opportunity for senior level b rainstorming regarding the needs of VIVO constituents and approaches to meeting those needs; and 4) the VIVO Implementation Fest provides training and hands on support to jump start VIVO implementations. 6.2.1 VIVO Conference 2010 The first annual VIVO conferenc e 177 was held at the New York Hal l of Science, August 12 13, 2010 The conference drew 207 registrants. Keynote speakers were Noshir Contractor of Northwestern University and James Hendler of the Tethered World Institute a t Rensse laer Polytechnic Institute Pre conference workshops were held on visualization, ontology and implementation. Reviews from the conference were very positive and the conference received significant corporate and institutional sponsorship, obviating the need for the use of
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 20 Continuation Format Page grant su pport. Attendees came from seven countries. Discipline representation was eclectic with strong participation from library science, university administration, biomedical science, social network analysis, informatics and agriculture. A second conference w ill be held August 24 26 2011 at the Gaylord Hotel in Washington DC. Registration, sponsorship and paper submissions are all significantly up from last year. 6.2.2 VIVO Hackathon The 2011 VIVO Hackathon was held May 4th 7th, 2011 at the Health Science Center Library, University of Florida, in Gainesville, Florida. There were 15 attendees, ten from institutions outside of the VIVO team, and five prominent ideas that emerged: SameAs: Using the publication corpus of two schools (work was demonstrated using the publication RDF from Harvard and UF) identify common publications through PubMedID. Create sameAs assertions and register these assertions at sameas.org. Use the assertions to inform schools of authors known at one school, but unknown at another. Assert the sameas of these common authors and register these assertions at sameas.org. Using this approach, Harvard can learn of authors of its joint papers with Florida who are located at Florida. Inversely, Florida can learn of Harvard authors and their profile URIs that are fou nd in the Florida publication corpus. This approach has significant merit for creating the web of data deeply interlinking research networking systems. Sabaku: A game platform for connecting people presentations and events. Sabaku apps running on smart compete to locate and create semantic data. Exposing visual ization data in VIVO as a Data C ube 178 an RDF format for statistical purposes The URI of the data cube result ing from a VIVO visualization can then be used as input to statistical analysis software accepting data cube vocabulary. Creating standardized concept representations for expanding semantic search Using the ConceptWiki and DB p edia, map keywords expressed by faculty using open terminology into structured concept maps resulting in the ability to expand concept terms for use in search. Drupal Views: Views can query SPARQL endpoints such as VIVO Drupal Views can then be used to present VIVO information within Drupal web sites. RDFa: Add RDF a to the HTML of VIVO display pages, providing semantic content in the HTML, which is useful for search engines. 6.2.3 NIH Workshop on Value Added Services for VIVO The second annual VIVO workshop was held on the campus of Indiana University March 25 26, 2011 179 Twenty three thought leaders from research networking, federal agencies, the semantic web community and the sciences discussed potential applications that would rely on the information infrastructure being created b y VIVO. What do practitioners need and want? What is practical to deliver now and in the future? What work is needed to get from where we are today to where we need to be to support research and scholarship in the future? 6.2.4 Implementation Fest The Implementation Fest was held June 23 24, 2011 on the Washington University School of Medicine campus. The Fest was developed as a way for the VIVO project to help facilitate committed and ongoing implementations outside of the NIH funded project in a s mall group environment. Two tracks were offered at the Fest (technical and p o licy/adoption) to address the diverse challenges that may be associated with implementation and adoption of VIVO. Nearly all of the groups that attended have VIVO installed and ha ve already ingested data into their VIVO instance s. Institutions represented were: USDA, U of Nebraska, CU Boulder, Duke, SUNY Stony Brook, U of North Texas, Hunter College, American Psychological Association, Symplectic, Inter American Institute for Coope ration on Agriculture (IICA), Universidad Central del Caribe, and Georgia Tech.
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 21 Continuation Format Page 6.3 Transition to Operations at each institution 6.3.1 Cornell University Cornell has been operating VIVO in production since 2003 and will continue to do so from the Mann Agricultural L ibrary with institutional support. 6.3.2 University of Florida The UF Libraries, in collaboration with the Clinical and Translational Science Institute, will be sustaining VIVO in the future. On September 1st, 2011 VIVO transitions from implementation to operati ons. UF has approached operations work by separating into four areas: Management/Governance, Data Stewardship, System Administration, and Outreach. The library will manage all areas: Management/governance will include a Library Management Team supported by a Technical Advisory Board; UF will hire a Data Curator who will manage all aspects of VIVO data; system administration is being fully transferred over from the grant project team to the Library Systems department; and outreach will be integrated into exi sting support services within the Library. 6.3.3 The Scripps Research Institute TRSI expects to maintain its VIVO instances following the end of the grant, particularly if the inter institutional search feature is functional and if the automatic ingest of publi cations data from PubMed is functional. The robust search features of VIVO, enabled by the triples, make VIVO the superior choice for identifying individual scientists on the Scripps faculty who are performing specific types of research. As such, we antici pate VIVO will serve as an important research tool for faculty, postdocs, and graduate students, as well as outside searchers, who are seeking to identify potential collaborators at Scripps. We are considering expanding the Scripps VIVO d atabase to include profiles of p ostdocs an d graduate s tudents. Further, the Scripps Translational Science Institute (funded by a CTSA grant) has expressed interest in having profiles of their researchers entered into the Scripps VIVO instance in the future. If the inter ins titutional search feature is functional, we will encourage other local biotech organizations, such as The Salk Institute and the Sanford Burnham Medical Research Institute, to implement their own VIVO instances, further strengthening opportunities for coll aborations between our various faculties. Scripps Library and ITS staffs, who have now developed some expertise in implementing VIVO, could serve as a local resource that other local implementing sites could call upon for advice. Work on the Scripps VIVO instances will continue to be performed by Library and ITS staff members, now as part of their regular assigned duties, without need f or additional external funding. 6.3.4 Ponce School of Medicine The Ponce VIVO implementation will be maintained using institutio nal funds. Ponce has a strong interest in developing VIVO across its natural partners and has supported VIVO work at multiple partner institutions. 6.3.5 Washington University School of Medicine The support of VIVO was extensively written into the WUSM CTSA rene wal. If funded, the WUSM VIVO team will contribute to VIVO Consortium activities with development of features that are of use in the academic research environment, specifically in the areas of profile editing and curation, and we will also pursue co funded projects with other VIVO Consortium members. In the next funding period, we will continue to work with VIVO consortium members as well as other adopters of VIVO and contributors to VIVO code to extend its functionality and facilitate integration with othe r systems such as our local resources (core facilities) application and department center and institute specific web sites. 6.3.6 Weill Cornell College of Medicine Immediately after August 2011, VIVO will supplement the current WCMC profile systems. We will determine if VIVO will replace them and become the sole enterprise wide profiling system for all WCMC faculty. We hope to auto ingestion of profile data and publications and the semantic search capabilities within the national VIVO network.
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 22 Continuation Format Page VIVO is a long term commitment for WCMC. When the grant and carryover funding are exhausted, the project will be sponsored by the CTSC with operational support fr echnology Services (ITS) group. 6.4 Governance VIVO governance consists of a team lead group with weekly calls, a principal investigator group that meets as needed, and a technical advisory board which meets regularly via conference call to provide input into technical directions, assure alignment with other efforts world wide and apprise the VIVO team of opportunities for further development of both the software and the community. A scientific advisory board is being formed to provide additional input on the needs of researchers and scholars. These efforts will be transitioned in the coming year to open community processes. Using the conference as a gathering point and annual check point, the governance grou ps will eventually set a course for further VIVO development. 6.5 Additional VIVO Activities VIVO team members have been active in seeking new partnerships and support. Over fifty institutions have VIVO pilot projects or VIVO implementation projects underway, including the USDA, the American Psychological Association, and the National Institutes of Health. The VIVO software has been downloaded over 8,000 times. VIVO support continues to grow in the international agricultural science community, the biomedical sciences in collaboration with CTSAs beyond the five in the original VIVO consortium, and in the semantic web community. 7 Evaluation Evaluation has become a robust process, and at least three primary domains have been determined to be significant in the ass essment and understanding of this multi institutional project: 1) the nature and needs of collaborating across multi institutions; 2) needs for implementing VIVO across institutions; and, 3) the development and assessment of the application itself. Only th e third item had a focus within the grant. 7.1 T he nature and needs of collaborati on across multi institutions The first domain deals with the nature of both the personnel and technical needs when forming a working relationship across many sites. The VIVO team has three broad groups development, implementation, and outreach each with different functions and communication styles. While face to face time has proved invaluable for all, the manner in which that time is used and valued varies across the groups. Significant improvement in development has occurred over the past year when the developers have spent face to face time working with one another. Over the past year, this took place through two developers at Indiana working at Cornell for five developers from Cornell and two from IU went to UF for three days to work. 7.2 N eeds for implementing VIVO across institutions The second domain pertains to assessi ng the implementation needs of each site in installing and populating VIVO. A s articulated in Sections 4 and 6 implemented VIVO to at least version 1.2 and have aggregated considerabl e data. For more complex institutions (e.g. IU and WUSM) it has typically taken to acquire access and get permission to make the data publicly available. From site visits and other input to the evaluator, gaining access to, manip ulating, verifying, programmatically ingested people, educational background, and photos; publications and grant data have proven to be difficult to ingest. 7.3 T he development and assessment of the application itself The VIVO User Interface team has performed three types of usability testing during the course of the grant: heuristic analyses; informal, usability interviews; formal, task based usability testing; and, research evaluation.
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 23 Continuation Format Page The heuristic analyses involv ed having people with usability design or HCI backgrounds review the application (or large functional areas within the application) and provide feedback on design inconsistencies and possible user interaction issues. For the interviews, we int erviewed potential end users and reviewed parts of the application with them, eliciting feedback on what they perceived were the strengths and weakness of VIVO. The task based tests involved giving participants a series of specific tasks to perform using t he application. Both the interviews and the task based tests were recorded on video using the Morae software package. All three types of testing revealed flaws in the design and user experience of the VIVO application. These flaws ranged from the very simp le, such as inconsistent capitalization on submit buttons, to more complex issues involving navigation and form completion. Whenever these patterns were identified, we created issues using the Jira bug and issue tracking software for them. We then ana lyzed each Jira issue and made the appropriate user interface design change within the application. The research evaluations have occurred to understand how and why VIVO would be used. These evaluations are still underway, but preliminary results indicate that there are many more uses for VIVO than identified in the grant. Some of these include biosketch generation a nd assessing researcher impact. The evaluation effort has moni tored growth in the use of VIVO on line resources during the year. The change in accessing the VIVO sites VIVOweb .org and VIVO instances at the seven institutions has increased 130% since the sa me time last year with over 625,000 visits and 1.2 m illion page views. While the number of new visitors has remained about the same, people are spending slightly longer times on the site and looking at more pages on average. Over the past year there have been views to at least one of the VIVO sites from peo ple in 209 countries and territories other than the United States, where about 81% of the internet users log onto a VIVO site. While the greatest number of visitors outside the US comes from China there has been an almost 300% increase in visitors from many countries inc l uding Russia and Costa Rica as compared to last year. Additionally, there were approximately 1,400 downloads of VIVO insta llation documents. 8 Summary The VIVO project has made significant progress over its second year. Implementations at the original seven schools have been or are now planned to transition to sustainable institutional operations. Development has produced a major release and two maintenance releases to the core software along with four releases to the Harvester software. The ontology has matured and we have demonstrated interoperability with significant related ontologies. Outreach has been strong, generating interest and mind share across many disciplines with significant strength in library science, agriculture and biomedical science. Future efforts will further extend interest in to new discipline areas, as well as new geographical areas. VIVO has established a growing open source community, physically instantiated on line at vivo.sourceforge.net, but more importantly, consisting of dozens of partners, implementers and contributors meeting and discussing and working on VIVO This communit y forms the basis for the sustainability of development, the creation of support materials and opportunities and further sharing of ideas. Significant effort remains to establish open community governance and insure an open future for VIVO. Figure 5 Google Analytics for VIVO project sites
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 24 Continuation Format Page Challenges remain in simplifying data ingest, providin g additional sources of ingest and simplifying the internals of the VIVO system for open source development. The community has been clear in its needs for better instructional materials, lowering barriers to entry created by the fundamentally new approaches VIVO takes to representing data and providing data via the semantic web. Additional simplification of inge st, the creation of data ingest wizards, as well as materials describing simple process es for ingest are all needed. Many schools desire a turn key solution one that requires very little effort to set up and implement. We will continue to partner with others we strive to lower the effort needed to implement VIVO. Further developm ent will simplify VIVO internal code structure allowing greater open source participation. Provenance and access control need to be further improved. Despite these c hallenges, VIVO faces a bright future. Schools continue to adopt. Implementations continue to grow. Participation in development, implementation, support, interest in the conference, attendees on calls are all up significantly. Interoperability with ot her linked open data systems has been demonstrated. In the years ahead, VIVO will participate in the emergence of a web of data, linking VIVO information to information in other systems creating opportunities for research and scholarship discovery and co llaboration around the world. 9 References 1 Open Archives Initiative Home Page. http://www.openarchives.org/ Accessed June 30, 2011. 2 National Researcher Networking Visualization site. http :// nrn cns iu edu / Accessed June 29, 2011. 3 Apache Solr for Drupal. http://drupal.org/ project/apachesolr Accessed June 30, 2011. 4 VIVO Development Road Map (poster). http :// www vivoweb org / files / VIVO 2010_ DevelopmentRoadmap Poster pdf Accessed June 29, 2011. 5 Gephi home page http :// gephi org Accessed June 29, 2011. 6 Identity in Research Infrastructure and Scientific Communication (IRISC) 2011 Workshop. http:// irisc workshop.org/irisc2011 helsinki/ Accessed June 29, 2011. 7 VIVO Open Source Community home page http://vivo.sourceforge.net Accessed June 30, 2011. 8 eagle i site. http :// www eagle i org Accessed June 29, 2011. 9 Wolski, M., Richardson, S., and Rebollo, R. (2011). Building an Institutional Discovery Layer for Virtual Resea rch Collections. D Lib Magazine, May June 2011, Volume 17, Number 5/6. 10 Indiana University VIVO Home Page. http://vivo.iu.edu Accessed June 30, 2011. 11 VIVO SourceForge Adoption and Outreach page. https://sourceforge.net/apps/mediawiki/vivo/index.php?title=Adoption_and_Outreach Accessed June 30, 2011. 12 Envisioning (Biomedical) Science. K. Brner. Office of Res earch Information Systems, NIH, Bethesda, MD, MD. July 22, 2010. 13 VIVO: Enabling National Networking of Scientists. KL Holmes. Invited presentation. 50th Anniversary of the Department of B iochemistry, Biophysics, and Molecular Biology, Iowa State Univers ity, Ames, IA, July 2010. 14 VIVO: Opening Plenary Session. M Conlon, K Holmes. First Annual VIVO National Conference, August 12, 2010. 15 VIVO: users, interface, design, and evaluation. E Cramer, L McIntosh, N Cappadona, M Bevia. First Annual VIVO Nationa l Conference, August 12, 2010. 16 VIVO Data Analysis and Visualization: How to Program, Extend and Utilize. M. Linnemeier, C. Tank & K. Brner. First Annual VIVO National Conference, New Yor k, NY. August 12, 2010. Figure 6 VIVO sites across North America and beyond
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 25 Continuation Format Page 17 Implementing VIVO at your institution. C Case, V Davis, A Rockwell, S Russell Gonzalez. First Annual VIVO National Conference, August 12, 2010. 18 Semantic modeling for scientists. Y Ding. First Annual VIVO National Conference, August 12, 2010. 19 Deriving physician's expertise profiles based on ICD9 Coded encounter note logs. V Brodsky, T Tran, S Kessler II, C Cole. First Annual VIVO National Conference, August 12, 2010. 20 Finding specialists using interface terminology and concept based hierar chical reference terminology. R Charlot, C Cole, A Cheriff, A Kanter, F Masarie, A Wang, A Oganesova, F Naeymi Rad. First Annual VIVO National Conference, August 12, 2010. 21 Next steps for research networking in science. K Borner, S Leicht, T Schleyer, G Weber, J Austin, M Conlon. First Annual VIVO National Conference, August 13, 2010. 22 Mapping scientific networks. K Borner. First Annual VIVO National Conference, August 13, 2010. 23 VIVO development overview. J Corson Rikert, C Barnes, M Linnemeier, S Williams, N Raum. First Annual VIVO National Conference, August 13, 2010. 24 Design and development of a modular harvester framework for data ingest. S Williams, C Haines, D Scheppler, N Skaggs, C Barnes, N Raum, Y Li. First Annual VIVO Nat ional Conference, August 13, 2010. 25 Standardizing VIVO URLs: how standard is standard? M Conlon. First Annual VIVO National Conference, August 13, 2010. 26 Configuring and leveraging a SPARQL end poi nt for VIVO. C Barnes, N Raum, C Haines, S Williams, N Skaggs, D Scheppler, Y Li. First Annual VIVO National Conference, August 13, 2010. 27 Drawing organizational charts using VIVO. A Rockwell. First Annual VIVO National Conference, August 13, 2010. 28 Pu blications research and automated author disambiguation: collaboration between University of Florida & Cornell University. C Westling, N Skaggs. First Annual VIVO National Conference, August 13, 2010. 29 VIVO: Closing Plenary Session. M Conlon, J Corson R ikert, E Cramer, V Davis, K Holmes, D Krafft, L McIntosh. First Annual VIVO National Conference, August 13, 2010. 30 Designing Insightful (Network) Visualizations of Scholarly Activity. K. Brner. Networks and Network Analysis for Humanities: An NEH Instit ute for Advanced Topics in Digital Humanities, IPAM, UC Los Angeles, CA. August 16, 2010. 31 Semantic web portal: a platform for better browsing and visualizing semantic data. Y Ding, Y Sun, B Chen, K Brner, L Ding, D Wild, M Wu, D DiFranzo, AG Fuenzalida D Li, S Milojevic, S Chen, M Sankaranarayanan. Procee edings of the 2010 International Conference on Active Media Technology, Toronto, Canada, August 28 30 32 VIVO: Enabling National Networking of Scientists. M. Conlon. Federal Demonstration Project, Wash ington DC. August 30, 2010. 33 VIVO and VIVO@IU. K. Brner. University Information Technology Services Presentation, Indiana University, Bloomington, IN. September 17, 2010. 34 The Changing Role of Libraries in Discovery. EJ Cramer [panelist], VIVO Collabo ration. Invited Panel, Ithaka Sustainable Scholarship C onference 2010, New York, New York, September 28th, 2010. 35 VIVO: Semantic modeling for scientists. Ying Ding. School of Informatics and Computing, October 11, 2010, Bloomington, IN, USA 36 Semantic W eb. Ying Ding., Invited talk at Monroe County Public Library, October 13, 2010, Bloomington, IN, USA 37 Going the distance: VIVO: Reaching out to faculty in support of a national network of researchers. L Butson. Mid Atlantic Chapter of the Medical Library Association. Chapel Hill, NC, Oct. 15 19 2010. 38 Towards a Macroscope for Science Policy Decision Making. K. Brner, K. W. Boyack. NSF SciSIP Grantees Workshop: Toward a Community of Practice, Washington DC. October 19, 2010. 39 Networking for Cores: New Options for Synergism. SD Crosby, G Grills, M Detwiler, G Farber, KL Holmes. VIVO. Invited Panel, Midwest Association of Core Directors annual meeting, Chicago, IL, October 23, 2010. 40 An Overview of VIVO at IU. K. Brner, Y. Di ng, R. H. McDonald, W. Barnett. Office of the Vice Provost for Research, Blooming ton, IN. October 27, 2010. 41 VIVO, the Library, and the User Experience. EJ Cramer [presenter], VIVO Collaboration. Submitted paper, Annual Charleston Conference 2010, Charle ston, SC, November 3 6, 2010. 42 NSF Workshop: Changing the Conduct of Science in the Information Age Workshop. M Conlon. Washington DC. November 12, 2010.
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 26 Continuation Format Page 43 VIVO: Building a Social Network of Scientists. R McDonald [Co Presenter], Part of the Data to Ins ight Center Tutorial Session at SC10 (Supercomputing 2010), New Orleans, LA, USA, November 14, 2010. 44 VIVO: Building a Social Network of Scientists. R McDonald [Co Presenter], Part of the Indiana University New and Emerging Technologies Tutorial at SC10 (Supercomputing 2010), New Orleans, LA, USA, November 15, 2010. 45 VIVO: A Library based Tool for Renewing and Enhancing Collaboration and Networking among Researchers. Norton, Hannah, Tennant, Michele R., Butson, Linda, Edwards, Mary, Schaefer, Nancy, Fer ree, 'Nita, Jesano, Rae, Auten, Beth, Henning, Sara, Conlon, Mike. Southern Chapt er of the Medical Library Association, Southern Chapter of the Medical Library Association 2010 Annual Meeting, St. Petersburg FL November 15, 2010. 46 Plug and Play Macrosco pes: Custom Tools for Data Analysis, Modeling, and Visualization. K. Brner. The Challenges of Visualising Biological Data, Swindon, Wiltshire. November 16, 2010. 47 Linked Open Data: The Promises and the Pitfalls...Where Are We and Why Isn't There Broader Adoption? Dean B. Krafft [panelist]. Coalition for Networked Information Fall Fo rum, Arlington, VA, December 13, 2010. 48 What's keeping us from Open Science? Is it the powers the be, or is it... us? D Dobbs, M Dye, J Reichelt, K Holmes, J Timmer, S Wood. ScienceOnline 2011, panel discussion, Durham, NC, January 15, 2011. 49 Science Online Project Showcase. K James, S Collins, K Holmes, A Ebsary, H Menninger. ScienceOnline 2011, panel discussion, Durham, NC, January 16, 2011. 50 VIVO Core Ontology. Ying Di ng. Code4Lib 2011 Conference, Bloomington, IN. February 7 10, 2011 51 Semantically Modeling of Scientist. Ying Ding. School of Medicine, CTSA, Case Western Reserve University, February 14, 2011, Cleveland, Ohio, USA 52 Plug and Play Macroscopes That Empower Science. K. Brner. Center for Bioinformatics and Computational Biology, Nation al Institute of General Medical Sciences, NIH, Washington, DC. February 17, 2011. 53 Sustaining Networks of Researchers: Experiences of t he VIVO Collaboration at the University of and Florida and The Scripps Research Institute. Beth Auten [presenter], Paul a King, Linda Butson, Hannah Norton, Michele Tennant, Mike Conlon, VIVO collaboration NCNMLG/MLGSCA Joint Meeting, San Francisco, CA. Feb ruary 23 26, 2011 54 Researcher Networking: Supporting collaboration and discovery. K Holmes. Invited lecture, Leadership in Interdisciplinarity, Networking & Collaboration (LINC) Conference, St. Louis, MO, February 24, 2011. 55 VIVO at IU IU Digital Library Program Brownbag Session, March 2, 2011, Bloomington, IN, USA. 56 Opening comments. M Conlon. VIVO 18 month team meeting. March 3, 2011. 57 Development plans. C Barnes. VIVO 18 month team meeting. March 3, 2011. 58 Implementation Fest. V Davis. VIVO 18 month team meeting. March 3, 2011. 59 Outreach & Adoption. KL Holmes VIVO 18 month team meeting. March 3, 2011. 60 Ontology. S Mitchell. VIVO 18 month team meeting. March 3, 2011. 61 VIVO Social Network Visualizations. K. Brner. VIVO 18 month review, Bloomington, IN. March 3, 2011. 62 Breakout Session: Planning for the fi nal report of the project. L McIntosh [session facilitator]. VIVO 18 month team meeting. March 3, 2011. 63 Breakout Session: Sustainability and VIVO effort following end of year 2. R McDonald [session facilitator]. VIVO 18 month team meeting. March 3, 2011 64 Breakout Session: Work to be accomplished during the next six months. K Lee [session facilitator]. VIVO 18 month team meeting. March 3, 2011. 65 Closing comments. M Conlon. VIVO 18 month team meeting. March 3, 2011. 66 Interactive Maps of Science and Technology. K. Brner. The Third International Workshop on Network Theory: "Web Science meets Network Science", Evanston, IL. March 4, 2011. 67 VIVO: Enabling National Networking of Scientists. KL Holmes, C Barnes, Y Ding, V Davis, M Conlon. Contributed pa nel, AMIA Joint Summits, San Francisco, CA, March 9, 2011. 68 Opening comments. M Conlon. Value Added Services for VIVO. Workshop in Bloomington, Indiana. March 25, 2011. 69 Closing comments. M Conlon. Value Added Services for VIVO. Workshop in Bloomington Indiana. March 25, 2011. 70 VIVO, a semantic data infrastructure for research discovery across disciplines. M Conlon [comments]. Science on FIRE: Facilitating Interd isciplinary Research and Education Symposium, Boulder, CO, March 29, 2011. 71 VIVO Resear cher Networking Update. L McIntosh, EJ Cramer, J Corson Rikert. Contributed presentation. Coalition for Networked Information Spring 2011 Membership Meeting, San Diego CA, April 5, 2011.
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 27 Continuation Format Page 72 Atlas of Science: Envisioning Scholarly Data. K. Brner. HUBbub 2 011!, Indianapolis, IN. April 6, 2011. 73 Cyberinfrastructure and Datasets for Science of Team Science Research. K. Brner. Second Annual International Science of Team Science Conference, Chicago, IL. April 13, 2011. 74 Knowledge Management for Collaborative Research: Research Networking Tools Workshop. VIVO. KL Holmes. Second Annual International Science of Team Science Conference, Chicago, IL. April 14, 2011. 75 Semantically Modeling of Scientist: the VIVO ontology. Yi ng Ding. City University of London, London, UK, May 2, 2011 76 Opening Comments. M Conlon. VIVO Hackathon, Gainesville FL. May 4, 2011. 77 Closing comments. M Conlon. VIVO Hackathon, Gainesville FL. May 7 2011. 78 VIVO: Click...search...discover...collaborate! HF Norton. Contributed presentation. Medical Library Association Meeting, Minneapolis, MN, May 15, 2011. 79 Clinical and Translational Science Awards Renewal Activities: A Vital Role for Libraries. KL Holmes and CC Sarli. Contributed presentation. Medical Library Association Meeting, Minneapolis, MN, May 16, 2011. 80 Library based Support for Translational Science: Supporting Clinical Research. JL Lyon. Keynote panel, American Association for the Adv ancement o f Science, Medical Library Association Meeting, Minneapolis, MN, May 16, 2011. 81 Library based Support for Translational Science: [Bioinformatics Instruction & Consultation, Collaboration, and Evaluation]. KL Holmes. Keynote panel, American Asso ciation fo r the Advancement of Science, Medical Library Association Meeting, Minneapolis, MN, May 16, 2011. 82 VIVO: Enabling National Networking of Scientists. VI Davis. USAIN Board Meeting, Beltsville, MD, May 17, 2011. 83 VIVO: Enabling National Networking of Sci entists. VI Davis. AgNIC 2011 Annual Meeting, Beltsville, MD, May 18, 2011. 84 Open Access to Research Discovery: The VIVO Project. M Conlon. Open Access Symposium, University of North Texas, Denton Texas. May 20, 2011. 85 Role of Librarians in the Develop ment of Computer Mediated Social Networks: Challenges and Lessons Learned From VIVO Implementation and Outreach. R Garcia Milian*, HF Norton*, B Auten, A Buhler, V Davis, N Ferree, KL Holmes, M Johnson, S Russell Gonzalez, N Schaefer, MR Tennant, M Conlon, and VIVO Collaboration. Contributed paper, Biomedical and Life Sciences Division contributed papers session, Special Libraries Association Annual Conference, Philadelphia, PA. June 2011. 86 Research Discovery and Collaboration. KL Holmes. Invited Presentation, Spotlight Session, Collaborations Across Disciplines. SLA 2011 Annual Conference, Philadelphia, PA. June 13, 2011. 87 Visualizing Science. KL Holmes. Invited Presentation, Spotlight Se ssion, Visualizing Science. SLA 2011 Annual Conference, Philadelphia, PA. June 13, 2011. 88 VIVO, A Semantic Web Application for Research Discovery and Scholarship. M Conlon [presenter]. Biomedical Informatics Beyond Borders. London. June 14, 2011. 89 Sema ntically Modeling of Scientist: the VIVO ontology. Ying Ding. Chinese Science and Technology Information Center, Beijing, China, June 15, 2011 90 Semantically Modeling of Scientist: the VIVO ontology. Ying Ding. Peking University, Tsinghua University, Beij ing Normal University, Beijing, China, June 16, 2011 91 Semantically Modeling of Scientist: the VIVO ontology. Ying Ding. Remin University, Beijing, China, June 20, 2011 92 Semantically Modeling of Scientist: the VIVO ontology. Ying Ding. Dalian Technologi cal University, Dalian, China, June 24, 2011 93 Semantically Modeling of Scientist: the VIVO ontology. Ying Ding. Library of the Chinese Academy of Sciences, Beijing, China, June 27, 2011 94 VIVO Implementation at Indiana University. Brian Keese, Jon W. Du nn, and Robert H. McDonald. Contributed Poster, 2010 VIV O Conference, Queens, NY, August 12, 2010. 95 Implementation and Adoption of VIVO at Washington University School of Medicine. Kristi L. Holmes, Sunita B. Koul, Leslie D. McIntosh,Caerie Houchins, Geo rge Joseph, and Rakesh Nagarajan. Contributed Poster, 20 10 VIVO Conference, Queens, NY, August 12, 2010. 96 Places and Spaces: Mapping Science. Katy Brner and Elisha F. Hardy. Contributed Poster, 2010 VIVO Conference, Queens, NY, August 12, 2010. 97 Using the R Programming Language for VIVO Application Programming. Mike Conlon. Contributed Poster, 2010 VIVO Conference, Queens, NY, August 12, 2010.
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 28 Continuation Format Page 98 Assessment of Research Impact: A Role for VIVO. Kristi L. Holmes and Cathy C. Sarli. Contributed Poster, 20 10 VIVO Conference, Queens, NY, August 12, 2010. 99 "It Takes a Village": Implementation of VIVO at the University of Florida. Amy G. Buhler, Valrie I. Davis, Sara Russell Gonzalez, Margeaux Johnson, Hannah Norton, Mike Conlon, and VIVO C o llaboration. Cont ributed Poster, 2010 VIVO Conference, Queens, NY, August 12, 2010. 100 Repurposing VIVO Content with Drupal. Miles Worthington. Contributed Poster, 2010 VIVO Conference, Queens, NY, August 12, 2010. 101 Implementation of VIVO at Ponce School of Medicine th e Challenges of a Small School Setting. Ricardo Espada, Damaris Torres, Michael Vega and Richard Noel. Contributed Poster, 2010 VIVO Conference, Queens, NY, August 12, 2010. 102 VIVO Cornell: The Life Cycle of Information. Ellen J. Cramer and Elizabeth (Tob i) Hines. Contributed Poster, 2010 VIVO Conference, Quee ns, NY, August 12, 2010. 103 VIVO Users, Interface Design, and Evaluation: Lessons Learned. Leslie McIntosh, Nick Cappadona, Manolo Bevia, and Ellen J. Cramer. Contributed Poster, 2010 VIVO Conference, Queens, NY, August 12, 2010. 104 Virtual Appliance: Releasing Without an Executable. Christopher Barnes, Christopher Haines, Yang Li, Narayan Raum, Dale Scheppler, Nicholas Skaggs, and Stephen V. Williams. Contributed Poster, 2010 VIVO Conference, Queens, NY, August 12, 2010. 105 Drawing Organizational Charts Using VIVO. Alex Rockwell. Contributed Poster, 2010 VIVO Conference, Queens, NY, August 12, 2010. 106 VIVO Development Road Map Poster. Jon Corson Rikert, Christopher P. Barnes, Micah Linnemeier, Stephen Williams, Narayan Raum, Nick Cappadona, Brian Caruso, B rian Lowe. Contributed Poster, 2010 VIVO Conference, Queens, NY, August 12, 2010. 107 Weill Cornell Medical College VIVO Implementation. Kenneth Lee, Dan Dickinson and Curtis Cole. Contributed Poster, 2010 VIVO Conference, Queens, NY, August 12, 2010. 108 VIVO: Enabling National Networking of Scientists. KL Holmes, VIVO Collaboration. Contributed poster, Midwest Association of Core Directors annual meeting, Chicago, IL, October 21 23, 2010. 109 VIVO: Researcher Networking and Discovery Across Disciplines. Norton, Hannah F., Garcia Milian, Rolando, Tennant, Michele R., Henning, Sara, Conlon, Mike. University of Florida Genetics Institute ( Florida Genetics 2010: The Sixth Annual Symposium of the UF Genetics Institute, Gainesville, FL, October 27, 2010 110 Training and Support for VIVO, a National Network of Scientists. M Edwards, S Henning, E Brooks, MR Tennant, L Butson, H Norton, N Schaefer, R Jesano, B Auten, M Conlon, VIVO Collaboration. Southe rn Chapter of the Medical Library Association Annual Meeting, contr ibuted poster, St. Petersburg, FL, November 2010. 111 Enhancing Multi Disciplinary Collaboration with VIVO. Norton, Hannah F., Garcia Milian, Rolando, Lyon, Jennifer A., Schaefer, Nancy, Ten nant, Michele R., Blackburn, Kaitlin, Conlon, Mike, University of F lorida Emerging Pathogens Institute, Emerging Pathogens Institute Research Day, Gainesville, FL, February 10, 2011. 112 VIVO: Enabling National Networking of Scientists. KL Holmes, EJ Cramer K Chiang, V Davis, Sara Henning, M Conlon, and VIVO Collaboration Contributed poster, American Association for the Advancement of Science Annual Meeting, Washington, DC, February 20, 2011. 113 Sustaining our Future through Innovation -VIVO: Library Based Support for Researcher Networking. Beth Auten, Paula King, Linda B utson, Hannah Norton, Michele Tennant, Kaitlin Blackburn, VIVO Collaboration. NCNMLG/MLGSCA Joint Meeting, San Francisco, CA. February 23 26, 2011 114 VIVO: Support for Translational Researc h. MR Tennant, KL Holmes, C Barnes, Y Ding, V Davis, SR Gonzales, S Mitchell, M Conlon. Contributed poster, AMIA Joint Summits, San Francisco, CA, March 7, 2011. 115 Disambiguation of Data for the Semantic Web. N Skaggs, C Westling, SV Williams, CA Haines. Contributed poster, AMIA Joint Summits, San Francisco, CA, March 10 2011. 116 Lessons Learned in Evaluating VIVO. L McIntosh, EJ Cramer. Contributed poster, AMIA Joint Summits, San Francisco, CA, March 10, 2011. 117 VIVO Harvester: Aggregation of Scholarly Data into a Semantic Data Store for use in a National Network of Scientists SV Williams, C Barnes, N Skaggs, N Raum. Contributed poster, AMIA Joint Summits, San Francisco, CA, March 10, 2011. 118 VIVO: Creating Connections. Conlon, Mike, Blackburn, Kaitli n, Norton, Hannah F., Garcia Milian, Rolando, Tennant, Michele R. U niversity of Florida College of Medicine Research Day, March 14, 2011
Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 29 Continuation Format Page 119 VIVO: Are You Connected? Blackburn, Kaitlin, Edwards, Mary, Feree, Nita, Garcia Milian, Rolando, Norton, Hannah, Sch aefer, Nancy, Conlon, Mike. College of Public Health and Health Pro fessions Research Day 2011. March 23, 2011 120 Building an Interdisciplinary Collaboration Community with VIVO. A Buhler, M Johnson, S Russell Gonzalez, K Blackburn, M Conlon, VIVO Collabora tion. Contributed poster. Association of College & Research Librari es National Meeting, Philadelphia, PA, March 31, 2011 121 VIVO: Enabling National Networking of Scientists. KL Holmes [co presenter], MR Tennant [co presenter], K Brner, M Conlon, and VIVO Collaboration. Contributed Poster. Second Annual International Scie nce of Team Science Conference, Chicago, IL. 12 April 2011. 122 The Role of a National Conference in Engendering Support and Adoption: VIVO 2010. HF Norton, MR Tennant, KL Holmes, K Borner, JRS Coffey, A Turner, N Ferree, K Blackburn, M Conlon, and VIVO Col laboration. Contributed poster. Medical Library Association Meeting, Minneapolis, MN, May 17, 2011. 123 VIVO: A Tool for Collaboration in Public Health. NM Schaefer [presenter], KL Holmes, K Blackburn, M Conlon, VIVO Collaboration. Contributed Poster. PHI20 11, Orlando, FL, 25 May 2011. 124 VIVO: Researcher Networking and Discovery Across Disciplines. M Conlon, MR Tennant, KL Holmes. GIR AAMC. Miami, FL, June 7, 2011. 125 VIVO. M Conlon. CTSI Re search Day. Gainesville, FL, June 10, 2011. 126 A Detailed Comparison of Four Research Networks: VIVO, Epernicus, ResearchGate, and Mendeley. R Garcia Milian, HF Norton, VI Davis, KL Holmes, S Russell Gonzalez, MR Tennant, M Conlon, and VIVO Collaboration. Contributed poster. Special Libraries Association Annual Conferenc e, Philadelphia, PA. June 2011. 127 Implementation of VIVO: experiences from two VIVO installation sites. V Davis [facilitator], C Houchins, S Koul, L McIntosh, S Russell Gonzalez, A Rockwel l. panel presentation. First Annual VIVO National Conference, Augus t 13, 2010. 128 VIVO outreach and adoption: experiences on the local and national level. K Holmes [facilitator and presenter], EJ Cramer, V Davis, S Henning, MR Tennant. panel presentation. First Annual VIVO National Conference, August 13, 2010. 129 VIVO Bootcamp. R Cobine, P Albert, Y Ding, B Keese, M Linnemeier, N Cappadona. Code4Lib 2011, pre conference presentation, Bloomington, IN, February 7, 2011. 130 VIVO: Enabling National Networking of Scientists. KL Holmes, C Barnes, Y Ding, V Davis, M Conlon. Contributed panel, AMIA Joint Summits, San Francisco, CA, March 9, 2011. 131 Library based Support for Clinical and Translational Research: The Informationist MR Tennant, KL Holmes, L Johnson, JA Lyon. Contributed panel, AMIA Joint Summits, San Francisco, CA, M arch 10, 2011. 132 Designing Insightful (Network) Visualizations of Scholarly Activity. Presented to the Network and Network Analysis for the Humanities Workshop, Institute for Pure and Applied Mathematics, University of California, Los Angeles, August 16, 2010. Retrieved from http://ivl.slis.indiana.edu/km/pres/2010 borner i nsightful viz neh.pdf 133 Semantic web portal: a platform for better browsing and visualizing semantic data. Y Ding, Y Sun, B Chen, K Brner, L Ding, D Wild, M Wu, D DiFranzo, AG Fuenzalida, D Li, S Milojevic, S Chen, M Sankaranarayanan. Proceedings of the 2010 International Confe rence on Active Media Technology, Toronto, Canada, August 28 30 Retrieved from http://ivl.slis.indiana.edu/km/pub/2010 ding et al swp.pdf 134 VIVO, a semantic data infrastructure for research discovery across disciplines. M Conlon. Contributed abstract. Science on FIRE: Facilitating Interdisciplinary Research and Education Symposium, Boulder, CO, March 28 29, 2011. Retrieved from http://firesymposium.colorado.edu/FIRE/assets/fire abstracts final 135 Role of Librarians in the Development of Computer Mediated Social Networks: Challenges and Lessons Learned From VIVO Implementation and Outreach. R Garcia Mili an*, HF Norton*, B Auten, A Buhler, V Davis, N Ferree, KL Holmes, M Johnson, S Russell Gonzalez, N Schaefer, MR Tennant, M Conlon, and VIVO Collaboration. Contributed paper, Biomedical and Life Sciences Division contributed papers session, Special Librarie s Association Annual Conference, Philadelphia, PA. June 2011. Retrieved from http://units.sla.org/division/dbio/events/conf_current/contr_papers.html 136 Mitchell, S., Torniai, C., Lowe, B., Corson Rikert, J., Wilson, M., Ahmed, M., Chen, S., Ding, Y., Rejack, N., & Haendel, M. (2011).Aligning Research Resource and Researcher Representation: The eagle i and VIVO Use Case (poster). International Conference on Biomedical O ntology (ICBO), July 28 30, 2011, Buffalo, NY, USA. 137 Semantic web portal: a platform for better browsing and visualizing semantic data. Y Ding, Y Sun, B Chen, K Brner, L Ding, D Wild, M Wu, D DiFranzo, AG Fuenzalida, D Li, S Milojevic, S Chen, M Sankara narayanan. Lecture Notes in Computer Science. Vol. 6335, 448 460.
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Program Director/Principal Investigator (Last, First, Middle ): Conlon, Michael PHS 398/2590 (Rev. 06/09 ) Page 31 Continuation Format Page 172 VIVO project page. http://vivoweb.org/ Accessed June 29, 2011. 173 Indiana University VIVO. http :// vivo iu edu Accessed June 29, 2011. 174 myUFL splash page. http://my.ufl.edu Accessed June 29, 2011. 175 Washington University ICTS December 2010 Newsletter. http://icts.wustl.edu/about/Dec2010ICTSNews.pdf Accessed June 29, 2011. 176 Washington University Record. http://news.wustl.edu/news/Pages/21344.aspx Accessed June 29, 2011. 177 VIVO 2010 Conference. http://vivoweb.org/conference2010 Accessed June 29, 2011. 178 The RDF DataCube Vocabulary. http://publishing statistical data.googlecode.com/svn/trunk/specs/src/main/html/cube.html Accessed June 29, 2011. 179 Value Added Services for VIVO. http://scimaps.org/flat/meeting/110325/ Accessed June 29, 2011.