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VIVO Updates March 12 -- ontology, implementation, camp, conference

What's hot?  Ontology is hot, that's what's hot.  Interested in the ontologies that drive VIVO?  So are we.  Here's some newness around the VIVO ontologies:

  • Muhammad Javed of Cornell has written a VIVO Ontology Explorer.  Give it a try!.  Javed's tool shows which VIVO ontology classes and properties come from which underlying ontology used by VIVO.  That's very cool!  Javed's tool links to the LODE representation of the VIVO ontology, and uses the existing domain diagrams from the VIVO ontology.  All in a very clear and clean presentation.  A great addition to the VIVO tool set.  Interested in learning more about the VIVO ontology and the ontologies VIVO uses?  Spend some time with the VIVO Ontology Explorer.
  • The Ontology Improvement Task Force is up and running!  The task force will develop a domain definition for the VIVO ontology, as well as propose processes for making ontological changes.  Some changes are minor and can be done without effecting running VIVO systems.  Other changes would have consequences for existing VIVO systems.  The task force will consider both. The task force will have a call Monday, March 13 at 11 AM US Eastern Daylight time.  The US went to daylight savings time Sunday morning, moving its clocks forward one hour.  If you are planning on joining the ontology call, please check your time zones.  Here's the WebEx Link.
  • Protege Training.  Stanford University will be hosting a Protege short course regarding Protege tool for ontology development and management, March 29-31 on the Stanford campus in Palo Alto.  Mike Conlon will be attending – hope to see you there.

Implementation Call this Thursday  Join Paul Albert on the Implementation Interest Group call this Thursday at 1 PM US Eastern Daylight Savings Time.  Here's the Webex link.  The call is a great place to start for those planning VIVO implementations, those in the middle of creating VIVO for their institutions, and those taking care of systems already implemented.  The group takes questions, shares tips and tricks and provides a home away from home for those setting up VIVO.  Project managers welcome!

Upcoming events – Camp and Conference  VIVO Camp and the VIVO Conference are coming up:

  • VIVO Camp will be held at the Hyatt Regency Hotel, Albuquerque New Mexico, April 6-8.  Register now!
  • VIVO Conference will be held at Weill Cornell Medicine, New York City, New York, August 2-4.  The Call for Proposals is open.  Submit your proposal now!

Go VIVO!

Mike

Mike Conlon  VIVO Project Director Duraspace 

VIVO Updates -- March 3. Development, ontology improvement, conference proposals, vivo camp, vivo registry

Development call this Thursday.  The Development Interest Group will meet this Thursday at 1 PM via WebEx.  The WebEx link is here.  Graham Triggs will lead a discussion of development in progress and planned future development.  Are you a developer?  Please consider joining the call.

Ontologists Unite! The Ontology Improvement Task Force is looking for you.  The task force will create methods for improving the VIVO ontology.  As some of you may know, the VIVO ontology is a subset of VIVO-ISF, the VIVO Integrated Semantic framework.  No changes have been made for several years.  But there are reasons to improve the ontologies used by VIVO (what are they?) and there needs to be a way to update the ontology (what might that be?) If you are interested in change management in the context of open source communities, this is the task force for you.  The next call of the task force will be Monday, March 13 at 11 AM US Daylight time (US clocks "spring forward for daylight savings time the day before the call).  Here's the webex link.  All are welcome! 

VIVO 2017 Call for proposals closes March 26.  The 2017 VIVO Conference (http://vivoconference.org) will be held at Weill Cornell Medicine August 2-4.  Do you have work you would like to share with the VIVO community?  VIVO 2017 is accepting submissions for posters, panels, workshops, and talks.  Please consider submitting your work.   We make it easy.  The conference is a fantastic opportunity to meet people in the community, and organize new things for the VIVO community.  Submit your work.  See you in New York City!

Not too late for VIVO Camp.  We are going to have a great time in Albuquerque, New Mexico, April 6-8 at the Hyatt Regency Hotel learning about VIVO.  It's not too late to join us.  Register at http://vivocamp2017.eventbrite.com

Do you have a VIVO site?  Is your site in the VIVO Site registry?  If not, please add your site.  It is very important to the VIVO Project to help our sites across the world and to share information with our sites.  If your site is already listed, that's great!  If not, please follow the directions on the page to add your site.  If your site is listed, but the listing needs to be updated, please update your listing using the instructions on the page.  Oh, one more thing.  If you know of a VIVO site or site(s) that are not listed in the registry, please let us know so we can contact them and have them added.  Thanks to all for your help maintaining the VIVO Site Registry!

Go VIVO!

Mike

Mike Conlon  VIVO Project Director Duraspace 

 

 

VIVO Updates Feb 26 -- Camp, Ontologies, Strategy, Outreach

VIVO Camp Registration extended.  We have a great group signed up to learn about VIVO at VIVO Camp, April 6-8 in Albuquerque, New Mexico.  Registration has been extended and will remain open until we're full.  Register today for Camp here.  An itinerary is available.  Drop us a note at info@vivoweb.org

Improving the VIVO ontologies.  We'll have a call Monday, February 27 at 11 AM regarding improving the VIVO ontologies.  If you are interested in the ontologies, particularly in change management regarding the ontologies, please consider joining the call.  Here's the Webex link.  Here's an agenda.

Put your thinking caps on.  Ready for some strategic planning?  VIVO has a strategic plan (available here) for the period 2015-16.  We're drafting a plan for 2017-18.  We need your help.  In particular, what can the VIVO community do over the next two years to make VIVO the obvious choice for everyone?  We'd love to hear from you on the VIVO Google Groups or contact one of the Steering Group members.

Outreach and engagement call this Thursday  Interested in building community around VIVO at your institution?  The Outreach and Engagement Interest Group shares experiences, answers questions, and discusses building support for VIVO.  The call will be this Thursday, March 1 at 1 PM US Eastern time.  Here's the WebEx Link.

Go VIVO!

Mike

Mike Conlon  VIVO Project Director Duraspace 

VIVO Updates for Feb 19 -- camp, wiki, ontology

VIVO Camp Registration deadline Feb 24.  (that's this Friday!) Considering VIVO?  Planning a VIVO implementation?  Need to learn more about VIVO?  Maybe you're the new person on an existing project and need to catch up.  Register today for Camp here.  An itinerary is available.  Join colleagues leaning about VIVO in Albuquerque, April 6-8. Questions about camp?  Drop us a note at info@vivoweb.org

Collaborative editing in the wiki.  You know how Google Docs supports multiple people editing a document at the same time?  Every sees who editing. The VIVO Wiki, hosted by Duraspace, was recently upgraded to Atlassian Confluence version 6.0.  You can read about new features here.  One new feature is collaborative editing.  Yay!  Now task forces, governance groups, interest groups, technical writers and others working in the VIVO wiki and the VIVO documentation wiki can invite their friends and write and edit together.  Do you have an account for editing?  Just ask and you shall receive.

Improving the VIVO ontologies.  As you may know, VIVO uses ontologies to describe the relations between things, and the data that can be recorded about these things.  Vitro, the software underlying VIVO, is a "domain free" ontology-driven application.  That means Vitro can be given any ontology, and it can create instances and record data about the instance, presenting web pages for each entity and supporting search over the entities and their data.  In addition, Vitro provides an ontology editor to add new classes, object properties and data properties to the ontologies it is currently using.  Vitro has been used to store data regarding library catalogues, clinical trials, space craft, and other collections of things defined by ontologies. You will be hearing more about Vitro over the course of the year.

VIVO inherits all this capability from Vitro, and uses a collection of ontologies to represent scholarship and research.  Using ontologies proves an open data model that can be used by others, and provides a common exchange format for data about scholarship.  VIVO then provides visualizations and other interface elements to make use of information about scholarship compelling and useful.  Do you have ideas about how VIVO could be more compelling and more useful?  We are always looking for exciting ideas.

All that VIVO records is based on the ontologies it uses.  As with most human creations, ontologies change over time.  We find gaps in what we are able to present.  We find that ontologies we are using have been improved.  We find technical issues in the ontologies resulting in VIVO behavior that could be improved.

But improving ontologies can have significant impact on the VIVO community.  VIVO sites use their knowledge of the ontologies to transform data from other systems into data that can be used by VIVO.  When the ontologies change, these transformation may need to be changed.  Many sites use VIVO data in reports and web sites, and visualizations that they have created.  These pieces of software use their knowledge of the VIVO ontologies (typically in the form of SPARQL calls) to get data from VIVO.  When ontologies change, these peices of software must change, and that can be difficult, time-consuming and expensive.

I'd like to start a conversation about ontology improvements.  There are a number of questions I think we may wish to consider:

  • What is the purpose of any ontology improvement?  What kinds of improvements are there?  Why would any improvements be needed?  What impacts would ontology changes have on the community?  How can we know the impact of any particular ontology change?
  • If we were great at ontology improvement, what form would that greatness take?  What would be included?  Can you picture a world in which we were great at ontological improvement?  What would that world look like?
  • How would we get from where we are now to what we want?  What would we do first?

I'm sure there are many other questions to be asked about ontological improvement.

But you might be saying "what ontologies are there" and "why do I care".  You can find documentation on the ontologies used in VIVO in the VIVO documentation.  You can find a representation of all VIVO classes, object properties and data properties here.  You may find some things you think may need to be improved.

Apps and Tools call this Thursday  Interested in tools and applications that work with VIVO?  The Apps and Tools Interest Group call will be held this Thursday, February 16, at 1 PM EST.  Join us in a discussion of software that can be used with VIVO.  We have a catalog of apps and tools here.  We are always eager to hear of more.  Do you have a tool to be shared with the community?  Tell us about it. Here's the WebEx Link.  See you Thursday!

Go VIVO!

Mike

Mike Conlon  VIVO Project Director Duraspace 

VIVO Updates -- Feb 12 -- VIVO 1.9.2, Helping each other, VIVO Camp

VIVO 1.9.2 Released  VIVO 1.9.2 is a maintenance release addressing several bugs.  Upgrading to 1.9.2 should be straightforward, there are no ontology or functional changes.  Bugs fixed:

  • ORCiD integration fixed
  • GEMET vocabulary service now uses SSL
  • LCSH vocabulary service repaired
  • Creation of secondary entities in web interface fixed

You can get version 1.9.2 here.  Release notes are available here.

Helping each other  The VIVO community has a long history of helping each other.  Recently we had two outstanding examples of community members responding with great help:

Both responses will be used to improve the VIVO technical documentation.

VIVO Camp  Considering VIVO?  Planning a VIVO implementation?  Need to learn more about VIVO?  Maybe you're the new person on an existing project and need to catch up.  Register for Camp here.  An itinerary is available.  Join colleagues leaning about VIVO in Albuquerque, April 6-8. Questions about camp?  Drop us a note at info@vivoweb.org

Implementation call this Thursday  Considering, planning, working on a VIVO implementation?  The Implementation Interest Group call will be held this Thursday, February 16, at 1 PM EST.  Join Paul Albert with questions and comments regarding your implementation.  No previous experience with VIVO or with VIVO calls is needed.  We are always looking to help each other.  Here's the WebEx Link.

Go VIVO!

Mike

Mike Conlon  VIVO Project Director Duraspace 

VIVO Updates -- Camp, Conference, Microsoft Academic

VIVO Camp April 6-8.  Albuquerque, New Mexico.  The Camp will be a great opportunity to learn about VIVO.  New to VIVO?  This is the place to start.  Considering VIVO?  Even better – VIVO Camp will engage attendees about the why and how of VIVO implementations.  Click here to register now!

VIVO 2017 Conference August 2-4.  Weill Cornell Medicine, New York City.  The conference brings together VIVO enthusiasts from all over the world.  The Call for Proposals is open now.  Click here to submit your proposal to the VIVO Conference.

Microsoft Academic – a new data source for VIVO?  We are always looking for new data sources for VIVO – places where you might be able to get information on the golden query.  Like Google Scholar, Microsoft Academic is the result of large scale automated harvesting of web sources.  Unlike Google Scholar, which expressively disallows use of the data by software, Microsoft Academic has an open API and documentation encouraging reuse of the data they have assembled.  Their API meets several important criteria for VIVO:  1) It is "open" – you can make open queries up to some limits and then pay fees for higher volume.  2) It identifies works, people and institutions using its own internally consistent keys, 3) Given information about a person, or a collection of people, it can find publications that have a high probability of being authored by those people.  You get the Microsoft Academic probability estimate and can make your own decisions about cut-off values for particular applications.

Microsoft Academic appears to be useful.  You may want to take a look at http://academic.microsoft.com At the present time it is difficult to determine what fees might apply for use of the API in particular institution settings.  

Disclaimer – Microsoft Academic is not a supporter of VIVO, and to our knowledge, has no interest in VIVO.  The interest in Microsoft Academic is that of Mike Conlon based on the needs of the VIVO community and the features offered by the service.

Outreach and Engagement this Thursday.  The Outreach and Engagement Interest Group will have its call this Thursday at 1 PM EST.  Click here for the webex meeting.  See you there!  

Go VIVO!

Mike

Mike Conlon  VIVO Project Director Duraspace 

 

 

VIVO Updates Jan 22 -- VIVO Camp, Triple Pattern Fragments

Learning is fun!  Register now for VIVO Camp, April 6-8, Albuquerque, New Mexico. Join Julia TrimmerVioleta IlikPaul AlbertMike Conlon and Graham Triggs for an introduction to everything VIVO.  If you are considering VIVO, planning a VIVO implementation, have started and need to know more, please plan to join us in Albuquerque!  Modeled after the highly successful Fedora Camps, VIVO Camp will offer high quality instruction, breakout sessions, opportunities to have your questions answered.  Should be a great way to meet leaders in the VIVO community, share experiences, and learn more. 

Triple Pattern Fragments coming to VIVO.  A triple pattern fragments (TPF) server has been added to VIVO for the next release.  You can try it now on OpenVIVO at http://openvivo.org/tpf (OpenVIVO is a VIVO anyone can use.  The VIVO Project uses OpenVIVO to demonstrate VIVO and features coming to VIVO.  Do you have a profile in OpenVIVO?  You should – just sign on to OpenVIVO using your ORCiD username and password.  A profile will be created for you.  Don't have an ORCiD username and password?  You should.  Just go to http://orcid.org and sign up.)

What is TPF?  At the 2016 VIVO Conference, Ruben Verborgh of Ghent University gave an outstanding talk on Triple Pattern Fragments, "The Future is Federated."  You can find his talk on OpenVIVO here:  http://openvivo.org/display/doi10.6084/m9.figshare.3680310.  Ruben has many papers and presentations on triple pattern fragments and the semantic web.  His OpenVIVO profile has an extensive bibliography with many links to full text and presentations.

The basic idea is intriguing.  Triples are great for representing data, but SPARQL is not that great for sharing data.  Open SPARQL endpoints (servers providing open access to a collection of triples) are rare.  SPARQL can be difficult to learn and write, and it is very easy to make mistakes that produce the wrong data, or lead to very excessive demands on the SPARQL server.  Institutions running open SPARQL endpoints often must reset their servers due to such queries.  The maintenance of such servers becomes a burden to sharing data.

TPF provides a solution.  TPF servers provide data, but only to very simple queries that can be quickly resolved.  In this way, TPF servers can easily be maintained.  The simple queries can be combined by applications to get answers that might have required complex SPARQL and significant processing time for a SPARQL server.  

Following Ruben's talk, it became very clear that VIVO and Vitro are outstanding platforms for sharing data via TPF.  A TPF server has been added to OpenVIVO.  It responds to TPF requests for triples.  We will explore opportunities to use TPF in OpenVIVO.  TPF has the potential to "leave data at rest." Software using TPF can query data across a collection of VIVOs, rather than gathering data into a central place to make cross site searches.

Apps and Tools  We'll continue discussion of TPF at this week's Apps and Tools Interest Group call with a demonstration and some sample JavaScript code for making queries of the OpenVIVO TPF server.  The call is at 1 PM US Eastern Time. On WebEx.  Hope you can join us.

Go VIVO!

Mike

Mike Conlon  VIVO Project Director Duraspace 

VIVO Updates for January 8 -- 2017, Camp, 1.10

Happy New Year.  We are looking forward to 2017!  Here's a few things we can look forward to in the coming year:

  • New Leadership Group members.  Each year we fill positions on the Leadership Group according to the VIVO charter.  We have new members and with new members comes new opportunities for leadership.
  • New Steering Group members.  We will have three openings this year to be appointed by the Leadership Group. Please consider serving.  The Steering Group provides leadership for the project.
  • A new strategic plan.  Our existing two year plan, needs an update.  We will have more about this in the coming weeks.  
  • VIVO Camp.  The VIVO project is holding its first ever training event April 6-8 in Albuquerque, New Mexico.  If you are just getting started with VIVO, this could be a great way for you to learn more!
  • VIVO 1.10.  Due this summer, VIVO 1.10 will have many new features and improvements.  See VIVO 1.10 Release Planning for on-going description of features being added and discussed.
  • Open Repositories, Brisbane, Australia, June 26-30.  
  • 2017 VIVO Conference, Weill Cornell Medical College, New York City, August 2-4.

There will be many more events, and announcements over the course of the year.  Here are some ways you can help:

VIVO Camp April 6-8, Albuquerque, New Mexico.  Need to learn more about VIVO?  VIVO Camp is the place for you!  VIVO Camp will provide an opportunity to cover the full range of VIVO topics with experienced instructors.  New to VIVO?  This is a great opportunity to get a head start.  No VIVO experience required.  Registration will open shortly.

Coming in Release 1.10.  VIVO 1.10 is expected this summer.  All software dependencies in Vitro will be fulfilled from Maven Central.  This means that we will no longer be distributing versions of dependencies that can not be found at Maven Central.  All dependencies in Vitro are now actively maintained by their respective projects.  The Vitro distribution can be a bit smaller, but more importantly, Vitro is no longer dependent on software that is not being maintained.  This is a big step forward for Vitro.

Development call this Thursday. The Development Interest Group will hold its call this Thursday at 1 PM US Eastern Time.  The call is open to all and focuses on software development for VIVO and Vitro, and in particular, issues related to the development of version 1.10.  If you are a developer and would like to contribute to version 1.10, you are encouraged to review the GitHub repositories and the VIVO 1.10 Release Planning.  Use the Webex link to join the call.  We hope to see you this Thursday! 

Go VIVO!

Mike

Mike Conlon  VIVO Project Director Duraspace 

VIVO Updates for Dec 18 -- New Members, VIVO Camp, Happy Holidays!

Two new members!  Dartmouth College and Université du Québec à Montréal are new VIVO members!  Thank you!

For a complete list of VIVO members, see VIVO members.  Becoming a member is easy.  See Become a member.  We look forward to hearing from you!

Announcing VIVO Camp April 6-8, Albuquerque, New Mexico.  VIVO Camp is a new effort to help organizations explore, adopt, and implement VIVO.  Designed for new sites – those considering VIVO and those starting a VIVO implementation, VIVO Camp will provide a fun, instructional, interactive environment to learn more about VIVO and the VIVO Community.  The instructors will be:

  • Paul Albert, Weill Cornell Medical College
  • Mike Conlon, VIVO Project Director
  • Violeta Ilik, Northwestern University Feinberg School of Medicine
  • Graham Triggs, VIVO Technical Lead
  • Julia Trimmer, Duke University

Registration for this ticketed event will open early in 2017.  Seating will be limited.  Discounts will be available for member institutions and students.  More information about the camp is available on the VIVO web site.  If you are new to VIVO, considering VIVO, have heard of VIVO and would like to know more, here's a great opportunity to learn more.

Last update of 2016.  The holidays are approaching and the year is waning.  This will be the last VIVO Updates of the year.  VIVO Updates will return January 8.  Until then, have a happy holidays, and a joyous New Year.  See you all in 2017 with lots of updates from VIVO!

Go VIVO!

Mike

Mike Conlon  VIVO Project Director Duraspace 

 

 

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Announcing VIVO Camp, a training event in Albuquerque, New Mexico, April 6-8, 2017

The VIVO Project will hold its inaugural, multi-day training event designed specifically for new and prospective users. VIVO Camp will be held April 6-8, 2017 at the University of New Mexico in Albuquerque. Over two and a half days, VIVO Camp will start with an introduction to VIVO and gradually develop a comprehensive overview by exploring these topics:

  • VIVO features

  • Examples and demos of VIVO including customizations

  • Representing scholarship

  • Loading data

  • Introduction to the ontologies

  • Managing a VIVO project

  • Engaging communities

  • Using VIVO resources

Participants can expect to gain a broad understanding of all aspects of implementing VIVO, including scoping and planning, development and data ingest, user engagement and customizations. This event will be an opportunity to meet and consult with key VIVO community members and to benefit from the experience of many successful VIVO implementations. The curriculum will include multiple opportunities to address current challenges, so participants will be instructed in advance to bring specific problems and implementation barriers to VIVO Camp.

 

VIVO Camp instructors provide years of experience holding VIVO events, managing VIVO implementations, and participating in the VIVO community.

  • Paul Albert, Weill Cornell Medical College serves as chair of the VIVO IMplementation Interest Group

  • Mike Conlon, VIVO Project Director and served as the principal investigator at the University of Florida on the NIH grant to create the VIVO community

  • Violeta Ilik, Feinberg School of Medicine, Northwestern University serves as program chair for the 2017 VIVO Conference

  • Graham Triggs, VIVO Technical Lead

  • Julia Trimmer, Duke University manages the Scholars@Duke team and serves as the Co-Lead of the VIVO Outreach and Engagement Interest Group

 

Join us in April to learn all about VIVO and consult with this group of VIVO experts. Registration is limited and you must register by February 17 to reserve your place at VIVO Camp!

Registration is open. Register now!