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VIVO Updates May 7

VIVO 2017, NYC, Aug 2-4.  The VIVO Conference has some changes this year, changes we think you will like.  First, workshops are included in the registration price.  You should come for Wednesday, the workshop day, and stay for Thursday and Friday.  The workshops have no extra registration fees.  This is a big savings and one we hope will encourage additional participants in the workshops.  Second, registration prices have been lowered.  The conference has the same benefits as always, but at lower registration fees.  How did we do that?  Well, that's the third thing – the conference will be not be held at a hotel.  Weill Cornell Medicine is hosting the conference and they have done a spectacular job lining up space and support for the conference.  So plan now to attend what promises to be a different, yet familiar VIVO conference.  Register now before the early bird rates end.  http://vivoconference.org

Ontology domain definition.  Last week we described the work of the Ontology Improvement Task Force and their interest in creating a "domain definition" for VIVO.  The domain definition answers the question "what does the VIVO ontology describe?" You can find a draft of the domain definition here:  https://goo.gl/vRkQl4  The draft is completely open to all for comments and editing.  We've received quite a few very good comments and suggestions and the document is much better as a result.  Please help!

Who should have a profile?  We are often asked this question.  Our answer is that the institutions doing VIVO projects decide for themselves.  That said, many institutions explore the question and many come to similar conclusions.  The question is the topic of a first column in what I expect to be a monthly series, exploring topics of common interest to those engaged in creating profiles.  Please see the inaugural column "Who should have a profile?" available here.  The piece is about 800 words long and non-technical.  Let me know what you think.  And what you think might be good topics for future columns.

Go VIVO!

Mike

Mike Conlon  VIVO Project Director Duraspace 

 

 

Who should have a profile?

May 2017
 
The VIVO community is creating profiles for people engaged in the creation, transmission, and preservation of knowledge and creative works.  These works take many, many forms.  In some cases, the works may be stored in an institutional repository.  In other cases, the works may be ephemeral, as in the case of performances of music or theater.  Some works are openly accessible.  Many are not.  The works may be well identified by a DOI or other persistent global identifier.  Many are not.  And regardless of the nature of the work, its archiving, and its identification, the relationship of people engaged in the work varies considerably.  Some people are “authors.”  The cultural norms for authorship vary significantly across disciplines, domains and activities.  Other people may have contributed in a wide variety of other ways.
 
And this leads to a fundamental question for the VIVO community and for all those across the world creating and supporting profiles for people — who should have a profile?
 
For social networking sites, the answer is simple — whoever wants one.  And there is significant pressure from the purveyors of the sites to increase the number of people using their services.  The services are supported largely by two mechanisms — selling the data of the people using the service, and advertising to the people using the service.  In both cases, the more people using the service, the more valuable such sales will be.
 
The situation is different for systems such as VIVO.  VIVO is not supported by advertising or by selling data.  VIVO data is generally available (we will elaborate on this in a future column), and advertising is not part of the business plan for VIVO.  VIVO is member and institutionally supported.  Through the generous support of members, the VIVO project is able to organize community efforts to advance the software, and support and grow the community.  Through institutional efforts, VIVO infrastructure and data are created in support of the members of the institution.  To date, about 150 institutions have VIVO infrastructure, and about 25 are supporting the VIVO project through membership.
 
For VIVO, institutions answer the question “who should have a profile?”  They answer this question in a variety of ways.
 
Most institutions include only faculty.  This provides a simple, bounded definition of who is in the profiling system and who is not.  Of course, there are some edges here — are temporary faculty included?  Clinical faculty?  Are librarians faculty?  Do you include non-tenured faculty?  Instructors?  These institutions typically include all faculty that meet the local definition.  Many do not support “opt out” — removal or hiding of a profile, and very few support “opt in” — faculty get a profile only if they approve the creation of the profile.  The most common case is that the institution defines who is a faculty member for the purpose of creating profiles, and then creates a profile for everyone meeting the local definition.  But take a look at the first sentence of this essay.  VIVO is about “people engaged in the creation, transmission, and preservation of knowledge and creative works.”  Are the faculty the only people such engaged?
 
Some institutions have more inclusive answers to the question.  Some include post doctoral associates, visiting and other temporary faculty, and graduate students.  These people are often engaged in appropriate activities.  And many times, their participation in these activities goes unrecorded and unrecognized.  There are numerous current difficulties in including these people in profile systems.  Their contributions may not be “authorship” and our ability to track non-authorship contributions is generally poor.  We need better vocabularies, shared understanding, improved reporting and other policy and practice changes to recognize the work of all the participants in the work.  Some sites have objected to the notion of inclusion on the grounds of “density” — some of these people may have contributed little.  Multiplying the number of people in the profile system by five or ten times to include these people may not be seen as cost effective for the institution. And there may be privacy concerns for including students who may not be employees of the institution. 
 
Some institutions go even further and include professional staff such as lab technicians, software developers, data managers, writers, crafts people, project managers, administrators, and many others.  Think of the last time you saw a list of movie credits.  What kinds of people are included?  Each of the people in the credits had a role in creating the movie you watched.  Is the situation somehow different in the creation, transmission, and preservation of knowledge and creative works?  Should we have the means to recognize everyone’s contribution?
 
I hope the VIVO community can serve as a forum for the discussion of the question raised here — who should have a profile?  Let’s discuss!
 
 

VIVO Updates, April 30, 2017 -- Conference, Camp, Ontology, Outreach

New York State of Mind.  Summer is coming and with summer come thoughts of New York and the VIVO Conference.  The conference will be held at Weill Cornell Medicine, August 2-4, 2017.  Conference registration includes half-day workshops, invited speakers, keynotes, posters, and presentations by your colleagues in the VIVO community. Join us for the premier VIVO event of the year.  Registration is open! http://vivoconference.org

VIVO Camp.  The first VIVO Camp was held in Albuquerque New Mexico, April 6-8.  We had a great group of attendees from del Rosario University, Stanford, the University of New Mexico, MIT, Fred Hutchinson Cancer Center, the University of Auckland, McMaster University, and UNAVCO. Lots of learning and sharing about VIVO and VIVO projects! Thanks to the instructors Julia TrimmerVioleta IlikPaul Albert, and Graham Triggs who joined me in presenting material and leading discussions.  

When and where should we hold the next camp?  Drop us a note a let us know what you think.

Ontology Domain.  We all know what VIVO is about, right?  Kinda sorta?  But sometimes we are surprised by what we find and don't find in the VIVO ontology.  There might be things we want to say about our faculty and our experts that are difficult to say, or are missing.  And conversely, people who study the ontology (you know who you are) find things in the ontology that might not be relevant to the work of VIVO.  Nothing is perfect.  That's why we have an Ontology Improvement Task Force.  The task force is working on a draft "domain definition" describing the domain of the VIVO ontology.  Domain definitions are often accompanied by "competency questions"  – questions that should be answerable using the ontology.  The draft domain definitio, competency questions and some observations are available here: https://goo.gl/vRkQl4 and is open for comments and review.  

Please take a look.

Outreach call this Thursday.  This Thursday, May 4 at 1 PM US Eastern time, the Outreach and Engagement Interest Group will have its monthly call.  everyone is invited to share thoughts about engaging people with VIVO.  This is a non-technical call.  All are welcome!  Here's the  WebEx Link

Can't make the call?  Share your thoughts, questions, comments, and concerns on the VIVO Community Google Group (web) vivo-community@googlegroups.com (email)

Go VIVO!

Mike

Mike Conlon  VIVO Project Director Duraspace 

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