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Oct 19

Winchester, MA

The Fall 2014 VIVO Hackathon took place at Cornell University’s Mann Library in Ithaca, New York from Oct. 13-15. More than 30 enthusiastic developers from around the US and Canada in were in attendance. Fall colors, gorge hikes, trips to local eateries and opportunities for making friends around shared interests in leveraging the VIVO interdisciplinary semantic web! framework all contributed to a lively and successful event.

On Wednesday morning project teams participated in a closing session where accomplishments were shared with the group. “Show and tell” reports included slides and pointers to code contributions, issues being tracked, and new documentation. Slides and notes are available here at http://goo.gl/uWZU5c, including pointers to GitHub from projects producing code.
Here are a few highlights.

A data visualization hack team set out to identify and gather external authoritative data to help VIVO institutions understand their sources of grant funding. The aim was to populate a “bubble map” visualization that would highlight the location and level of support from organizations providing grant funding to universities using VIVO. It was no surprise that in the initial visualization of the map of the US many large bubbles appeared over Washington, DC, leading the team to look for more specific address information than can be found in existing data sources such as FundRef. Using federal tax id numbers, the team linked additional zip+4 and classification information to the FundRef data so that a registry accessible as linked data will make it easier for VIVO institutions to "follow the (grant) money".

The ontology! team tackled the challenges of sharing local ontology extensions to benefit other institutions and evolve VIVO ontology in concert. The team identified key requirements for a central ontology registry where VIVO installations could review available extensions and/or submit new proposed classes, properties!, or terms for review and possible adoption in subsequent VIVO-ISF ontology releases. The same platform could potentially also manage a registry of URIs for people, educational and funding organizations, journals, events, and vocabulary terms as persistent identifiers. By associating ORCID and/or VIAF records with registry entries wherever available, VIVO URIs from the registry could be linked to and/or added to Library of Congress and/or OCLC authority records used in library catalogs all over the world.

The principles of open data and linked data are central to the VIVO framework. Where and how to find the right authoritative data was a theme running through several hacks. Where do data come from? Where are data first generated? One team was concerned with how to include links to other, related things when publishing data on the web and proposed a simple version of a “VIVO requester” service that could use the vivoweb.org registry proposed above to determine who already has a persistent URI for a funding organization or the right vocabulary of equipment or research resource types for a particular purpose.

Anyone who has worked in a wiki knows that it can become unmanageable over time with many people contributing entries without a clear structure or editorial review. Making the VIVO wiki less wacky was the subject of a hack that sought to address a commonly perceived lack of documentation by improving the structure and tagging existing content and making it more clear to potential contributors where new content belongs. The DSpace wiki space demonstrates one approach to wiki structure that separates technical documentation varying with each release from introductory and explanatory documentation. Highlighting fewer topical categories, renaming files for consistency and moving technical documents into space-specific versions were among improvements made to the VIVO wiki.

Faceted browsing to support dynamic filters on browse pages or search results requires adding facets to existing page templates. The faceted browse hack added a faceted search of people by research area, and a start was made on building a more general capability that can be configured on a per-site basis without having to modify code.

Embedding Schema.org tags for SEO (search engine optimization) in VIVO requires only modest changes to page templates and will be an out-of-the-box capability in the upcoming release of VIVO v1.8. Google now builds its search results based on recognizing content and structure in Schema.org tags embedded in the HTML on web pages. This hack adds these tags to VIVO’s display pages and will make VIVO data more visible in Google and other search engines while also providing additional descriptive information in search results to benefit users.

Max Hu from Memorial University in Newfoundland demonstrated a Drupal CMS +VIVO data site: YAFFLE (http://www.yaffle.ca), where data developed and stored in VIVO is presented to users through Drupal pages providing additional entry points and help support.

Josh Hanna from the University of Florida worked on testing VIVO with the Stardog enterprise graph database (http://stardog.com) to see whether a commercial triple store could provide better performance with increasing amounts of data. Leveraging the VIVO community to negotiate academic Stardog licenses was discussed. Weill Cornell is also testing VIVO on other triple store platforms.
Patrick West reviewed the Deep Carbon Observatory Data Portal for the Deep Carbon Observatory (https://deepcarbon.net), a project led by RPI and funded by the Sloan Foundation. A Drupal front end with VIVO integration provides a variety of visualizations; persistent URI handles for every dataset link users back to VIVO as the primary metadata store. This functionality required a code modification in VIVO core to return the persistent data handles from the data repository at the time of dataset upload.

Northwestern University has offered to host the next VIVO Hackathon in 2015. More information to come.

Oct 1

August 12 - 14, 2015 in Cambridge, MA

Hyatt Regency Cambridge

The VIVO conference provides a unique opportunity for people from across the country and around the world to come together in the spirit of promoting scholarly collaboration and research discovery. This fun and exciting city will be the perfect backdrop for the 2015 conference. Join us to gain insight into the latest industry trends and innovations while enjoying all of the history, food, and culture Cambridge has to offer!

Be on the lookout for the Call for Papers coming soon!

If you have any questions, please do not hesitate to contact us.

Designing Events

+1-410-654-5525

 

vivo@designingevents.com

Sep 10

Reserve your hotel room before Friday to take advantage of special pricing.

The VIVO Project will be hosting  a hackathon event on the Cornell University campus in Ithaca, New York from October 13-15.  This event builds on the March, 2014 hackathon held in conjunction with the VIVO I-Fest at Duke University, and is open to anyone interested in actively participating in improving some aspect of the VIVO software, ontology!, documentation, testing, or related applications and tools. Chris Barnes and Ted Lawless, co-leads of the VIVO Apps & Tools working group, will be leading the event on-site, with logistics coordinated by the Cornell VIVO team.  

 Projects are deliberately open-ended and do not focus on competition — outcomes might include requirements gathering, review and prioritization of open issues, generation of sample data, developing more detailed business plans for VIVO search, generating proposals for new areas of the ontology, and writing or updating documentation, in addition to coding or working on data ingest.  Collaboration will be key, and a major goal of the event is to help grow a larger community of users motivated to contribute to one or more aspects of VIVO according to their interests, abilities, and priorities.

We encourage you to send one or more people to the event as a way to engage with other membership institutions and with a talented group of individual developers, implementers, and ontologists.

More information is available on the VIVO wiki at https://wiki.duraspace.org/x/Z4arAw, with logistics at https://wiki.duraspace.org/x/a4arAw.

Attendees are asked to register promptly at https://www.surveymonkey.com/s/9L5ZN3M, and the Hotel Ithaca room block (VIVO) is only guaranteed at the $129/night price through Friday, September 12 — 607 272-1000.

 

Sep 4

Pilot project to put relevant projects, collaborators, data at researchers’ fingertips

As observing instruments and computer modeling become increasingly refined, the amount of data generated by field studies has grown tremendously. Storing and archiving the data is a challenge in itself, but scientists also need the data to be easily accessible and connected to other relevant resources.

To help address this issue, UCAR is launching a project with two partners—Cornell University and UNAVCO—that aims to connect the dots among field experiments, research teams, datasets, research instruments, and published findings.

The two-year project, titled "Enabling Scientific Collaboration and Discovery through Semantic Connections," is funded by the National Science Foundation’s EarthCube initiative, which supports transformative approaches to data management across the geosciences (see original article here).

The project will demonstrate the benefits of a linked open data tool, known as VIVO, for managing scientific information and data. Developed by Cornell University Library in collaboration with a number of partners, VIVO is being used by over 100 organizations to create authoritative research profiles for faculty and staff as well as to link to their published studies and other relevant research. Other organizations, such as the Laboratory for Atmospheric and Space Physics at the University of Colorado Boulder, are extending VIVO to manage information related to scientific projects and research instruments.

The project aims to adapt VIVO so it can be applied to large-scale field experiments involving many investigators from a wide range of institutions. This would create a network of information linking field experiments with particular datasets, authors, publications, and even research tools that result from or are associated with each experiment.

"Someone coming from the outside would be able to find a particular paper that emerged from a field experiment and very quickly track down datasets, instruments, researchers, and so on," said Matthew Mayernik, an expert on research data services in the NCAR/UCAR Library who is the principal investigator on the project. "This is really about increasing the traceability of research and making it easier for people to find, assess, and use data."

To demonstrate the effectiveness of the approach, Mayernik and his colleagues will use VIVO for data from two sources: a recent NSF-supported interdisciplinary field program whose data archive is hosted by NCAR’s Earth Observing Laboratory (the Bering Sea Project), and a set of diverse research projects informed by geodetic tools, such as GPS networks and ground-based imaging, that are operated and maintained by UNAVCO.

If successful, Mayernik said such an approach would be expanded to other field experiments, including their data sets, researchers, publications, and research resources. 

Writer

 David Hosansky, NCAR & UCAR Communications

 

Collaborating institutions:

Cornell University

National Center for Atmospheric Research/

   University Corporation for Atmospheric Research

UNAVCO

 

Funder:

National Science Foundation (EarthCube initiative)

Aug 5

VIVO Caliente!

A few items for VIVO 2014

I didn’t have much time to sit in the Director’s Chair yesterday.  Like many people who are preparing for #VIVO14, I’ve been feeling like I’ve been playing “Whac-a-Mole” – a lot of different things to do to prepare for the VIVO Conference kept popping up.

There are a couple of things that I’d like to point out to those of you planning to be in Austin this week.  First, there will be a lot of focus on the VIVO-ISF ontology! and Data Standards (see blog post here).  Aside from a number of formal presentations and panels, you should also consider attending the Birds of a Feather VIVO-ISF ontology session with Melissa Haendel, VIVO Ontology Lead. It’s being held Friday, August 8 from 12:15-1:45 in Texas I. Come learn about what’s happening with the ontology, how to get involved, work efforts with various stakeholders, and projects of interest.  To follow ontology specific content on Twitter, use #VIVOISF! .

If you are new to the VIVO Community and would like to learn about becoming a member, a Birds of a Feather New Member session is being held from 12:15-1:15 in Texas III.  The session will focus on Member benefits and is geared to those individuals from organizations that are not currently Members.  If you’re interested in attending the session, Please RSVP to Layne Johnson at ljohnson at duraspace.org.

You’ll hear from some existing Members and you’ll have an opportunity to meet other new faces in the VIVO Community.

Last, but certainly not least, if you’re unable to be in Austin this week, we will miss you.  But, of course there will be plenty of people using Twitter, and you can follow at #VIVO14 .  

 

Here’s to a great week, virtually, or in Austin.  VIVO Caliente!

Jul 31

Symplectic Limited, a software company specializing in developing, implementing, and integrating research information systems, has become the first DuraSpace Registered Service Provider (RSP) for the VIVO Project. DuraSpace is a not-for-profit organization providing open technologies and services that promote durable access to digital data. Symplectic is a long-time supporter of the VIVO project, both as a founding sponsor and through continued support of the VIVO Conference  since it first began in 2010. Partnering with DuraSpace means Symplectic can provide VIVO services like installation, support, hosting and integration for institutions looking to join the VIVO network.

"As our first official Registered Service Provider for VIVO, Symplectic will help ensure that any institution, large or small, can fully participate in making research and institutional resources available for search, discovery, and analysis,” explained Jonathan Markow, CSO of DuraSpace. “We heartily welcome them to the RSP Program!”

VIVO, an open source!, semantic web! application and growing global community, is aimed at integrating and sharing information about researchers and institutions to support collaboration and discovery. As an incubated
DuraSpace project, VIVO institutions and DuraSpace members now have a greater opportunity to develop related technologies and services across broad academic and scientific communities.

“We are especially pleased to have been chosen as the first official Registered Service Provider for VIVO”, says Jonathan Breeze, CEO of Symplectic. “Working closely with the DuraSpace and VIVO communities will help us better serve institutions that wish to join the VIVO network, but do not necessarily have the capacity to do so themselves.”

Symplectic at the Upcoming 2014 VIVO Conference, Aug. 4-8

Join Platinum sponsors Symplectic at the 2014 VIVO Conference in Austin, Texas! The Symplectic team will be on hand to meet with the VIVO community, learn about exciting discovery network developments, and discuss the ways in which they can help institutions that want to join VIVO.

About VIVO

VIVO (http://vivoweb.org) is an open source, open ontology!, open process platform for hosting information about the interests, activities and accomplishments of scientists and scholars. VIVO supports open development and integration of science and scholarship through simple, standard semantic web technologies. VIVO was originally funded by Cornell University and the National Institutes of Health (U24 RR029822) and is currently a
community-supported incubator project under the DuraSpace umbrella.

About Symplectic

Symplectic (http://symplectic.co.uk) is a world-leading software development and service company specialized in the delivery of integrated research information management systems. Founded in 2003, the company combines years of experience in the academic sector with a collaborative approach to development to help research institutions collect, manage and showcase their research and scholarly activity. Their flagship system, Elements, is used by some of the world’s leading institutions including the University of Cambridge, Duke University, Cornell University and the University of Melbourne.

How Does DuraSpace Help?

The DuraSpace (http://duraspace.org) organization is an independent 501(c)(3) not-for-profit providing leadership and innovation for open technologies that promote durable, persistent access and discovery of digital data. Our values are expressed in our organizational byline, "Committed to our digital future."

DuraSpace works collaboratively with organizations that use VIVO to advance the design, development and sustainability of the project. As a non-profit, DuraSpace provides technical leadership, sustainability planning,
fundraising, community development, marketing and communications, collaborations and strategic partnerships, and administration.

FOR IMMEDIATE RELEASE
July 31, 2014
Contact: Sabih Ali <sabih@symplectic.co.uk>, Jonathan Markow <jjmarkow@duraspace.org>
Read it online: http://bit.ly/ULZoiB

Jul 30

There's been a lot of excitement and meaningful application of the VIVO-ISF ontology! and data standards in efforts across the globe. We’re thrilled with the overwhelming recognition by so many different groups about the power of data standards!  We’ve received a lot of interest from academia, government organizations, and the commercial sector to learn more about the standards and how to get involved in the meaningful work around the VIVO-ISF ontology.  

We hear you! You can see a full list of conference sessions at http://goo.gl/5EPqMO and be sure to follow all of the ontology sessions at the VIVO conference on Twitter at #VIVO14 and #VIVOISF!

Discuss the VIVO-ISF ontology and meaningful use of data standards:

Thursday 

  • 1:30-2:30 in Texas I Implementing VIVO and the VIVO-ISF Ontology - A Series of Real-World Experiences With Open Software and a Common Data Standard by Melissa Haendel (VIVO Ontology Lead, OHSU), Julia Trimmer (Duke), Don Elsborg (CU-Boulder). Panel moderated by Jon Corson-Rikert (VIVO Development Lead, Cornell)
  • 5:00-7:00 in Zilker Ballroom 3-4 Poster Session and Networking Reception offers a great opportunity to see practical application of the VIVO-ISF ontology by organizations form around the world

Friday

  • 12:15-1:45 in Texas I - Birds of a Feather VIVO-ISF ontology session with Melissa Haendel, VIVO Ontology Lead. Come learn about what’s happening with the ontology, how to get involved, work efforts with various stakeholders, and projects of interest.

Sessions about the power of data standards for integration, exchange, and discovery:

Thursday

  • 10:30-11:00: Integrating Symplectic Elements with VIVO 1.6  - Daniel Grant, Mary Walters, Michael Mitchell and Tim Morris (Emory)
  • 11:30-12:00: VIVO Team Recommender Based on Linked Open Data - Conforming to the VIVO Ontology - Noshir Contractor, Anup Sawant and Harshad Gado
  • 4:00-4:30: Linked data for libraries - Dean Krafft and Jon Corson-Rikert

Friday

  • 10:30-11:30: Invited speaker - Paolo Ciccarese, developer of Domeo, CiTO (Citation Typing Ontology), FaBIO (FRBR-Aligned Bibliographic Ontology, Open Annotation Ontology, Collections Ontology, and PAF (Provenance, Authoring, and Versioning Ontology)
  • 10:30-11:00: Reprsenting Arts Scholarship at Duke: Design, Development, and Migration of Artistic Works Data - Julia Trimmer, Damaris Murry and Patrick McElwee (Duke)
  • 1:45-2:15: The Case for Stable URIs - Melissa Haendel and Violeta Ilik
  • 2:15-2:45: The Semantic CV - CASRAI in VIVO-ISF - David Baker, Thorsten Höllrigl, and Albert Bokma
  • 2:45-3:15: De-Facto Standards Interoperating in the Real World - VIVO/ORCID/CASRAI - David Baker, Thorsten Höllrigl, Rebecca Bryant
Jul 27

I’ve been meaning to start this blog for some time, but until now, the time just didn’t feel right.  I was awash in unfamiliarity.  I knew only a handful of people from the VIVO Community, I wasn’t familiar with much of the technical jargon, I was uncertain about my leadership role, and simply put, I just wasn’t ready.

But now all of that is beginning to change. I’m beginning to recognize voices on teleconferences.  I’ve identified “go-to” people to help answer my questions.  I’ve begun to understand our priorities.  And most importantly, I’m starting to get to know many of you and experience what I consider to be one of VIVO’s greatest strengths: the unselfish nature of the VIVO Community and the unfettered willingness to share and help others.  It is with this backdrop that I introduce to you From the Director’s Chair.

Why this blog?

I’ve come to realize that there are so many moving parts associated with the VIVO Project that it is next to impossible to keep up with everything that’s going on.  That’s a bit scary, considering that my full-time job is all things VIVO, which might lead one to conclude that I see and hear it all.  Not so.  My thinking is that if I have a difficult time keeping up with all of VIVO’s activities, how do others in the VIVO Community keep apprised of what’s happening?  My hope is that this blog will serve to communicate VIVO Veritas.  Yes, that’s right.  This forum should serve us by communicating truths about the current happenings related to VIVO.

What should you expect From the Director’s Chair?

You should expect a weekly installation on VIVOweb.org on Monday mornings.  You should not expect a restating of the obvious.  You should expect to be involved – I will encourage contributions from our community.  My first guest blog will include a feature by Ted Lawless from Brown University.  I really have no idea what Ted might share with us, and I will have no hand in that.  What my guests share with you will be untouched by me.  You should expect content to be unfettered, unfiltered, and unrivaled.

I commit to you that posts From the Director’s Chair will be short and sweet.  They will be passionate.  They will be from the writer’s perspective.  They will be fun.

Your comments and suggestions are important and encouraged.

If you like what you read here, great!  If you don’t, I’ll need to know about that.  Have a question about something VIVO-related and want to see it addressed in the blog? Just let me know.  I’m only an email or tweet away: Layne at VIVOweb.org or @Layne Johnson.

See y'all in Austin!

Layne Johnson
VIVO Project Director

Jul 24

Join us at the annual VIVO Conference in Austin to connect with colleagues, new and old. This year's conference will continue the tradition of bringing together conference attendees with dynamic speakers.

VIVO is happy to announce this year's keynote speakers:

  • Carole Goble: Full Professor in the School of Computer Science, at the University of Manchester
  • Peter Fox: Tetherless World Constellation Chair, Professor of Earth and Environmental Science and Computer Science, and Director of the Information Technology and Web Science Program at Rensselaer Polytechnic Institute  

Along with these insightful keynote presentations, invited speakers include:

  • Dr. Paolo Ciccarese: Assistant Professor of Neurology at Harvard Medical School; Assistant in Neuroscience at Massachusetts General Hospital; Senior Information Scientist, MGH Biomedical Informatics Core; Co-chair of the W3C Open Annotation Community Group
  • Katy Börner: Professor of Information Science, Indiana University
  • Elaine Collier: Senior Advisor to the Director, National Center for Advancing Translational Sciences

Come Meet The New VIVO Project Director

The VIVO team is proud to introduce Layne Johnson as the VIVO Project Director under Duraspace. Layne began this role on May 1, and is working full-time to help us bring VIVO to the next level. Layne will be attending the VIVO conference, and is looking forward to meeting members of the VIVO community.

 

VIVO is about LEARNING

And here are just a few topics you will see presented at this year's conference:

    - Creating Dynamic Micro Portals within VIVO

    - Enriching Researcher Profiles with Altmetric Data

    - Bringing Together Cancer Researchers in India and South Asia with VIVO

    - New Tools for VIVO Developers

    - ...And much more

Jul 7

The 2014 VIVO Conference and the VIVO Apps and Tools working group are sponsoring a competition for applications using data coming from VIVO systems to support research communities.

Eligibility

Applications can be written in any language. To qualify applications must:

  • Consume VIVO data (linked open data in the VIVO ontology!) from more than one VIVO site.
  • Be accessible from a single persistent URL, accessible on the public Internet without authentication.
  • Available as open source! via a standard open source license.

Criteria for Success

Applications will be judged on the following criteria:

  1. Value to the research community.
  2. Functionality: The application performs as described.
  3. Presentation: The application is well organized and attractive.

Prizes

The first prize winner will have registration refunded, receive a cash prize and will be awarded a plaque at a recognition ceremony during the conference. Second and third prize winners will receive certificates.

Submissions

To submit your application, please send an email to Apps & Tools Working Group Chairs Ted Lawless (tlawless@brown.edu) and Christopher Barnes (cpb@ufl.edu). Applications are due July 31, 2014. Winners will be announced at the conference.

Submissions must include:

  • Names, academic degree(s), affiliations, and locations of all authors. Brief (500 words or less) description of the application and its value to scientists.
  • A URL for the application.
  • Instructions regarding operation. The judges will execute the application from the URL provided without assistance from the authors.

Additional Resources

VIVO uses Linked Data standards for data access via Resource Description Framework (RDF)!. See http://linkeddata.org for more information regarding Linked Data, RDF and data processing.

VIVO enjoys a robust open source, open community space on DuraSpace at http://wiki.duraspace.org/display/VIVO with content that supports implementation, adoption, and development efforts around the world. The VIVO software and ontology are publicly available at https://github.com/vivo-project/VIVO.

For more information on the Apps and Tools Working Group please check out the wiki at https://wiki.duraspace.org/display/VIVO/Apps+and+Tools+Working+Group