VIVO updates July 21, 2018 -- grants, jenatools, your content here

Grant opportunities  The VIVO Project is always looking for ways to improve the software, the community, and the ontology.  One way to improve things, or try new things is through grant funding.  Funding agencies often have programs related to metadata, data sharing, tooling, and other topics related to VIVO.  The VIVO Resources Action Planning group is looking to identify grant opportunities that might be appropriate for VIVO.  

The group has developed a document describing various initiatives that may be fundable by a grant.  See Grant Opportunities.  Interested?  Have ideas about grants?  Want to help?  Please contact Terrie Wheeler at Weill Cornell Medicine.

jenatools  New with VIVO 1.10 are command line tools jena2tools and jena3tools.  Jen2tools works with Jena 2 VIVO systems (version 1.9.3 and prior).  Jena3tools works with Jena 3 VIVO systems (version 1.10 and whatever comes afterwards).  These tools import and export the configuration and content triple stores of your VIVO system.  Using Jena2tools, you can export your VIVO 1.9.3 or earlier triple stores to "TRiG" format.  Then using Jena3tools, the TriG format can be reloaded into an newly created VIVO 1.10 to upgrade to Jena 3.  TriG format preserves the information regarding the graph the triple came from.  In this way, the graph structure of the upgraded triple store is identical to the previous triple store.

But the jenatools can export to any of the popular RDF serialization formats – RDF/XML, JSON-LD (only supported for Jena 3 export), N-Triples, and Turtle.  Using Jenatools, you can create a complete export of your VIVO, capturing the data for use in any other software, or for posting or sharing with others.

VIVO has always been about sharing data.  With jenatools, your entire triple store can be exported and shared as a single file. 

About VIVO Updates  VIVO Updates is an almost weekly newsletter of happenings in the VIVO Community. VIVO Updates is published to our wiki here:  VIVO Updates  where it is searchable using the wiki search.  VIVO Updates is also available on the VIVO Web site here:  VIVO Blog.  The Updates are sent each week to the VIVO Email Lists and tweeted.  Links to VIVO Updates appear in various Duraspace communications including the Member newsletter and Duraspace Digest with several thousand readers.   If you have an idea for VIVO Updates, please drop me a note.  Material received by Saturday can appear on Sunday.



Mike Conlon VIVO Project Director

VIVO Updates July 15 -- Leadership Group, Internationalization, Version 1.10, Fall Camp, Decentralization

Welcome New LG members!  Please help me welcome Christian HauschkeVioleta Ilik and Alex Viggio as new community members of the Leadership Group.  Each has been actively shaping the VIVO project.  They are all wonderful to work with. 

Leadership Group elections are now complete for the year.  The Leadership Group meets monthly to review progress and set direction for the project.  The Leadership Group will soon name a Steering Group to help it with its work.

I18n meeting  Interested in helping VIVO improve its multi-lingual capabilities?  The Internationalization Task Force is back in business after a hiatus.  The group will be setting goals wand working toward making VIVO a truly international application.  The first meeting of the task force will be held this week.

VIVO 1.10  VIVO 1.10 was released this week.  Special thanks to Ralph O'Flinn of the University of Alabama, Birmingham, who served as the release manager!  Here are the links:

VIVO 1.10 was led by the VIVO Committers and Developers with major support from Andrew Woods .

The following individuals provided code, documentation and/or testing for the release:  

Qazi Azim Ijaz Ahmad, Sabih Ali, Martin Barber, Jim Blake, Mike Conlon, Don Elsborg, Kitio Fofack, Ken Geis, Benjamin Gross, Huda Khan, Ted Lawless, Jacob Levernier, Brian Lowe, Jose Luis Martin, Christian Hauschke, Violeta Ilik, Steve McKay, Javed Muhammed, Simon Porter, Ralph O'Flinn, Graham Triggs, Tatiana Walther, Marijane White, Stefan Wolff, Andrew Woods, and Rebecca Younes

Thank you all!

New York, New York!  VIVO Camp is coming to the Big Apple, October 18-20, 2018 at Columbia University!  Join instructors Violeta IlikHuda KhanBenjamin Gross, and Mike Conlon for 2.5 days of VIVO, including implementation, data sources, ontology, Karma, and new features in 1.10! Stay tuned for news about registration!

The Delicate Dance of Decentralization  Professor Ruben Verborgh, a 2016 VIVO Conference invited speaker, presents paradigm shifts related to the decentralization of data via linked open data.

Verbogh, R "The delicate dance of decentralization and aggregation," Presented at the International Conference of the European Library Automation Group, 5 June 2018.

VIVO 1.10 introduces three new features for making data available for decentralized, distributed access, and for aggregation:

VIVO shares its data naturally.  These new capabilities open new possibilities for building distributed applications using VIVO.  Let us know when you've upgraded to 1.10.  We'd like to build distributed applications.



Mike Conlon VIVO Project Director



VIVO 1.10 available for download

July 10, 2018

From Mike Conlon, VIVO Project Director, on behalf of the VIVO Committers

VIVO 1.10 is now available!

VIVO 1.10 contains new features, performance improvements, and bug fixes.  Some highlights:

  • Support for RDF 1.1
  • A new Triple Pattern Fragments API
  • Support for the Data Distribution API
  • Support for Direct2Experts
  • Support for ORCiD API 2.0
  • Use of Argon2i password hashing
  • More than 40 improvements in code, and code used by VIVO
  • 15 bug fixes
  • Search results render faster if they contain Person results

  • Indexing time has been improved

  • Full handling of TDB type conversions, preventing isomorphic test failures that result in reloading filegraph on restart

  • Graph URIs are now cached for triple stores using a Jena implementation - this is a significant difference for TDB triple stores

  • Updating data via the UI is faster

For a complete list of improvements, see the VIVO 1.10 Release Notes

VIVO 1.10 can be downloaded now from

Upgrading to VIVO 1.10 requires a triple store unload, use of provided utilities to upgrade, and a reload.  See Upgrading VIVO

VIVO 1.10 was led by the VIVO Committers and Developers with major support from Andrew Woods.

The following individuals provided code, documentation and/or testing for the release:  

Qazi Azim Ijaz Ahmad, Sabih Ali, Martin Barber, Jim Blake, Mike Conlon, Don Elsborg, Kitio Fofack, Ken Geis, Benjamin Gross, Huda Khan, Ted Lawless, Jacob Levernier, Brian Lowe, Jose Luis Martin, Christian Hauschke, Violeta Ilik, Steve McKay, Javed Muhammed, Simon Porter, Ralph O'Flinn, Graham Triggs, Tatiana Walther, Marijane White, Stefan Wolff, Andrew Woods, and Rebecca Younes

A detailed listing of all known people/institutions who contributed to VIVO 1.10 is available in the Release Notes. If you contributed and were not listed, please let us know so that we can correct it!

As always, we are happy to hear back from the community about VIVO. Please let us know what you think of 1.10!

VIVO Updates July 8, 2018 -- Registry, China, Books

VIVO Site Registry  The VIVO Site registry is a list of all the known VIVO sites in the world.  I get asked all the time "Is there a list of VIVO sites?"  Well, yes, there is.  You can find the site registry here:
Is your site in the registry?  Hint:  you don't need to be in production, we think it's really cool to hear you have a site in development.  To add your site to the registry, click here:
Association of Data, Information and Society, Nanjing China  I had the recent honor to be invited to give a talk on VIVO at the inaugural conference of the Association of Data, Information, and Society at Nanjing University in Nanjng, China.  You can find my slides here: 
The association has a goal of increasing contact between information and data scholars in China with those in the rest of the world.  The conference had over 200 attendees and included talks by Gary Marchionini of the University of North Carolina, Ying Ding of Indiana University, Mark Musen of Stanford University, Jim Hendler of RPI, Dean Allemang of Working Ontologist (see below), Stefan Decker of RWTH Aachen University, Ahmed Abbis of the University of Virginia, and Barend Mons of Leiden University in the Netherlands. 
Next year's conference is expected to be held in Wuhan China, and will be chaired by Mark Musen of Stanford University.
VIVO Books  From time to time, I'll pass along books I have found to be useful in thinking about VIVO and learning more about its information underpinnings.  If you work with VIVO and want to understand more about its information system and its representation of scholarship as linked open data, you won't do better than "The Semantic Web for the Working Ontologist" by Jim Hendler (two-time VIVO conference keynote speaker) and Dean Allemang, whose consulting company is called "Working Ontologist".  Jim and Dean clearly describe the semantic web, linked data, and ontology.  For anyone with a background in data representation, and  particularly for anyone who has wondered if relational tables are the only way, this book shows how connected graphs of data work, why they are important, and how, through ontology, they provide the best mechanisms yet found for sharing data.  Unlike other information representation systems, linked data includes its semantics, allowing deep processing by machines, and simplified processing and sharing for humans and machines.  If the semantic web or ontology seems complex, this book will help.  And once you've read it, you may find it difficult to understand how other information representation systems scale.  Extremely well-written and entertaining, with extensive examples and clear thinking, its hard to imagine a better introduction to the way the semantic web represents information.  I can't recommend this book highly enough.  Should be required reading for all of us creating open data for scholarship, and all of us working on VIVO. 

Allemang, Dean, and Hendler, James Semantic Web for the Working Ontologist, Second Edition: Effective Modeling in RDFS and OWL 2nd Edition, Morgan-Kaufmann, 384 pages.  ISBN 978-0123859655



Mike Conlon VIVO Project Director


VIVO Updates July 1, 2018 -- Membership Task Force, Action Planning, Leadership Group Elections

Membership Task Force  A membership task force for VIVO is forming. See 2018 Membership Task Force. Participants include Terrie Wheeler, Weill Cornell Medicine, Virginia (Ginny) Pannabecker, Virginia Tech, Dong Joon (DJ) Lee, Texas A&M University, and Ann Beynon of Clarivate. If you would like to participate, please contact Mike Conlon. The group is tasked with working with Duraspace and the community to build relationships with those who may be interested in financially supporting the VIVO project as members. Membership is the key means by which VIVO grows. If you have ideas about growing membership or know of those who might consider becoming members, please contact one of the task force members.

Action Planning The Action Planning Process, which began March 1 and will run through Feb 28, 2019, is making progress in five areas — product evolution, resources and membership, community development, vision, and governance and structure. See updates here (new material is on the bottom of the document)

Leadership Group Elections The VIVO Leadership Group is looking to add three new members, elected by the member community liaisons. The Leadership Group is the top-level governance group for the VIVO project. Chaired by Julia Trimmer of Duke, the Leadership Group sets fundamental directional for all aspects of the project. Nominations have been received, and voting will occur through July 11. Look for an announcement here in two weeks of new Leadership Group Members. We appreciate the interest of the nominees and look forward to having new members of Leadership soon.

Are you interested in having your institution participate in the direction of the project? Become a member, financially supporting VIVO. Becoming a member is the best way to help VIVO succeed. See



Mike Conlon VIVO Project Director



VIVO Updates June 17, 2018 -- Nominations for Leadership Group, EuroCRIS, Membership Drive

Nominations for Leadership Group open Each year, VIVO elects three community members to serve on the VIVO Leadership Group. Any person at a VIVO member institution can nominate up to three people to serve. To make a nomination, you must be at a VIVO member institution. Not at a member institution? That’s easy to fix, become a member. To become a member, see Become a Member Now that you are at member institution, send the names of the people you would like to nominate to Kristi Searle at Duraspace. You can nominate anyone you like, including people who have served as community members previously. Kristi will check with each person nominated to make sure they are willing to serve. If they are, they will be asked to provide a short bio to use in the election. Nominations are due June 25, 2018. We look forward to hearing from you!

EuroCRIS I had the pleasure of attending the 2018 EuroCRIS meeting in Umeå Sweden this past week. EuroCRIS meets every other year, and gathers people interested in “CRIS” systems — current research information systems — these are systems that record the research outputs of a research organization. Some people refer to VIVO as a CRIS system. CRIS systems focus on research outputs, not people, and often are directly associated with repositories where the research outputs are stored. In Europe, due to open access and other compliance and reporting requirements, it is increasingly common for a university to *require* that all research outputs be stored in the university’s repository. A very popular choice for such work is DSpace, another Duraspace project. DSpace-CRIS is a modification of DSpace that supports the production of simple profiles of researchers with content in the repository. Much of the conference health with issues of CRIS systems, DSpace-CRIS, and the compliance requirements.

I had the chance to meet and discuss these ides with colleagues from the VIVO community, DSpace community, and Duraspace including Michele Minielli (Duraspace), David Baker (CASRAI), Brian Lowe (Ontocale), Tatiana Walter (TIB Hannover), Anna Guillaumet (SIGMA, and VIVO Leadership Group), Jordi Cuni (SIGMA), Andrea Bollini (4Science), Caroline Birkle (Managing Director Converis), Ed Simons (President, EuroCRIS), Anna Clements (University of Glasgow), Susana Moriati (4Science), Pablo de Castro (EuroCRIS board), Jan Dvorack (Infoscience, Czech Republic), and Miguel-Angel Sicilia (University of Alcalá, Spain) .

Tatiana Walter gave an excellent talk on the effort to map KDSF in Germany to VIVO. Basic concepts of mapping were covered as well as difficulties that were resolved in the mapping of KDSF. Her talk will be available on the conference web site.

EuroCRIS has a CRIS system output format, CERIF-XML. Many CRIS systems are able to produce CERIF-XML. A mapping of CERIF-XML to VIVO was completed several years ago. It needs to be updated. With a new mapping, an XSLT could be constructed to export VIVO RDF triples from CERIF-compatible CRIS systems. We hope to hear more about the updated mapping and XSLT transform work in the months to come.

The meeting was an excellent chance to discuss CRIS concepts with European colleagues, and to keep up to date on CRIS thinking and activities in Europe.

Membership Drive Interested in helping VIVO grow its membership? Please contact Julia Trimmer VIVO is looking for a person to join the membership drive.

Go VIVO!MikeMike Conlon VIVO Project Director



VIVO Updates — survey, conference, leadership, travel, Dean Krafft

What do you value about VIVO?  VIVO is conducting a short survey.  Three simple questions.  We started the survey at the conference and have received many thoughtful replies. Not able to attend the conference?  Please respond here: VIVO Value Survey.  Please share with your colleagues and encourage that they share.  We'd like to hear from everyone about VIVO. 

A Wonderful Conference  The Ninth Annual VIVO Conference was held this past week at the beautiful JB Duke Hotel on the campus of beautiful Duke University.  The conference provided a perfect setting for seeing the work of others, sharing and discussing current ideas, and learning more about VIVO, ontology, linked data, research information, faculty profiles, and much more.  This year the organizers welcomed people working on other systems that collect and provide information about research activities and outputs. 

A special thanks to Paul Albert who served as conference chair.  Paul did an outstanding job.  Eric Meeks served as program chair, organizing posters, presentations, invited talks, workshops, and introducing "unconference" sessions organized during the conference.  Julia Trimmer served as local host, working with the hotel and university to insure everyone had everything they needed.  They were supported by a conference team.  Together they put on quite an event!

Did you present at the conference?  As we have done in years past, we are making conference materials available through OpenVIVO.  You can post your materials to Figshare ( Be sure to identify yourself and your collaborators using ORCiD, and tag your work #vivo18.  The VIVO Project has automated scripts that pull in metadata from Figshare and populate OpenVIVO.  We wish all conferences worked this way.

Leadership Group  The Leadership Group is on the move.  Lots of news:

  • Julia Trimmer of Duke University has been elected acting chair of the Leadership Group and the Steering Group.
  • Ginny Pannabecker of Virginia Tech has joined the group replacing Julie Griffin
  • Doug Hahn of Texas A&M has joined the group replacing Michael Bolton
  • Muhammad Javed of Cornell has joined the group replacing Dean Krafft
  • An election for the bronze members representative is being concluded
  • An election for three community representatives will begin shortly.  Each will be elected to one year terms.
  • The group will be meeting every four weeks and has adopted some new processes for conducting its business.  The group will name the VIVO Steering Group in the weeks ahead.  The Steering Group will assist Leadership by raising and discussing issues facing the project, and drafting documents for Leadership approval.

Upcoming Travel  I will be on the road a bit over the next four weeks.  Next week, I'll be in Umeå, Sweden for the EuroCRIS 2018 meeting.  See  The meeting brings together people interested in Current Research Information Systems (CRIS).  The following week I will be in Montreal for a CASRAI workshop, then in Philadelphia for a family gathering.  After a few days home, I will be heading to Nanjing, China for the inaugural meeting of the Association for Data, Information, and Society.  I'll be back home July 9.  Should be great travels.  My email may be a bit slow during some of these trips.  I appreciate your patience.

Dean Krafft  As we heard above, Dean Krafft, Chief Technologist of the Cornell University Libraries is stepping down from the VIVO Leadership Group, and from the VIVO Steering Group chair position, which he has held since VIVO joined Duraspace in 2013.  I met Dean in 2009 in the writing of the VIVO grant proposal to the National Institutes of Health.  We have worked closely together over the last nine years. It would be hard to imagine a better colleague, nor a person who has been more steadfast, supportive, creative, insightful, and professional in all he has done for VIVO over all these years.  The community owes Dean an immeasurable debt of gratitude.  Dean, you will truly be missed. 


Mike Conlon VIVO Project Director



VIVO 1.10.0-RC-1 available for testing

June 1, 2018

The VIVO 1.10.0 release candidate is available for testing. Pending any issues discovered in the testing of the release candidate, the 1.10.0 release is planned for June 29, 2018.

The primary features/updates found in this release include:

  • Support for RDF 1.1 via Jena 3

  • Documentation for integrating the Data Distribution API

  • TPF Endpoint

  • Direct2Experts Endpoint

  • Improvements in Internationalization

  • Upgrade of password encryption to Argon2i

  • Jenatool for import and export of entire triple stores

  • vivo.owl consolidated ontology assertions

  • Many internal improvements in support of theming

  • Many internal improvements to upgrade dependencies

  • Many bug fixes

A full list of JIRA tickets addresses by this release can be found here:

To test the release candidate download and build from the source code to deploy into a servlet container


Download a no source vagrant

See the VIVO 1.10 Technical Documentation wiki for instructions:

Community testing of this release candidate is critical. Please provide your feedback on the release testing page

Mike Conlon

VIVO Project Director

VIVO Updates May 27 -- Conference, new LG members, Welcome Erin, Meetings this week

One week to the VIVO Conference  It's not too late to register and attend the VIVO Conference.  It's not too late to submit a poster.  Hop on to learn more.  

Welcome new members of the VIVO Leadership Group  This week we welcome two new members to the VIVO Leadership Group:

  • Anna Guillaumet, SIGMA (Spain).  SIGMA is a non-profit company supported by ten leading Spanish universities.  SIGMA develops and hosts software supporting students and researchers in Spain.
  • Frederico Ferrario, Cineca (Italy).  Cineca is a consortium of 62 research universities in Italy.  Cineca develops and provides information technology solutions supporting research.

We appreciate their willingness to serve and look forward to their insight regarding VIVO.

The VIVO Leadership Group meets monthly, and provides strategic direction for VIVO.  Representation on the Leadership Group is determined by membership, and by community elections.  See the VIVO Project Charter for a description of the group and its responsibilities.

You may wish to become a member of VIVO and participate in project governance.  See Become a Member for more information.

Welcome Erin Tripp!  Erin Tripp assumes the role of interim CEO of Duraspace June 1.  Previously Erin served as Duraspace Business Development Manager.  In that role she has worked to improve the service provider program, and has led the Research Graph VIVO Cloud Pilot project, gaining significant experience with VIVO.  I have worked with Erin throughout her time at Duraspace.  She will do an outstanding job in her new role.  Please join me in welcoming Erin!

Meetings this week  We don't have an interest group meeting on Thursday this week (fifth Thursday of the month), but we have three others (lots going on in VIVO Land).



Mike Conlon VIVO Project Director

VIVO Updates May 13, 2018 -- Conference, Apps and Tools, Sprint 2, Spring cleaning, Debra Hanken Kurtz

Two weeks to the JB Duke Hotel and the Ninth Annual VIVO Conference.  The VIVO Conference is coming up, June 6-8 at the JB Duke Hotel on the campus of Duke University in Durham, North Carolina, served by the Raleigh-Durham airport,  and includes a great line-up of keynote speakers, community presentations, posters, and workshops.  Make your plans to attend and meet up with your VIVO colleagues!

Conference rates go up May 30.  Register today!

May 30 is the final deadline for late breaking posters for the VIVO Conference.  Have work to share with others?  A poster is  great way to share your work!

This year, the conference planners have included "unconference" opportunities for people to organize small informal (5-7) groups of people around particular topics.  Similar to focus groups, each unconference meet-up will provide an opportunity to gather information about the interests and needs of the community and share with others.  Stay tuned for more information about how to sign-up and organize an unconference meet-up.

Interested in learning more about VIVO development?  A workshop at the conference Wednesday will provide an introduction to the code.

Apps and Tools on Thursday The Apps and Tools Interest Group will meet Thursday at 1 PM.  See the group page for call info.  The group is open to all and discusses apps and tools that can be used with VIVO.

Sprint 2 starts Tuesday  Sprint 2 has a kick-off meeting Tuesday at 11 AM.  See the sprint page for call-in info.

Spring cleaning in GitHub The VIVO Project on Github was getting a bit cluttered.  There were repositories for software not actively being developed, and repositories for software actively being developed by community members as adjuncts to the core VIVO software.  So we did some spring cleaning.  We now have three github organizations, each with their own repositories:

  • This is the project organization and contains repos for VIVO, Vitro, Harvester, Jenatools, sample data, and languages.  These are the components of VIVO, and are actively maintained.
  • This organization contains repositories for software associated with VIVO that are under shared maintenance and development by community members.  It includes VIVO Vagrant, and work of the VIVO Product Evolution effort.
  • This organization contains repositories for projects no longer under active development and is offered for historical purposes.  Code here is unlikely to be currently useful but may indicate ideas the project has had in the past.

We hope this is an improvement and will help each us better understand what is ready to use, what is community-developed, and what we have worked on in the past, but are no longer working on.  As always, all feedback is welcome!

Debra Hanken Kurtz will join Arizona State University in June.  Debra Hanken Kurtz, CEO of Duraspace, is taking a position at Arizona State University.  Erin Tripp has been named interim CEO.  See  Debra and I started the same day at Duraspace, back in March of 2015.  Debra has worked tirelessly in support of VIVO and has significantly strengthened Duraspace in her time at the helm.  I have worked closely with Debra for the past three years.  She is a friend and colleague and I wish her all the best in this next chapter in her life.  VIVO is stronger as a result of Debra's work.  Thank you Debra!

and go VIVO!


Mike Conlon VIVO Project Director