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Calls are held every Thursday at 1 pm eastern time (GMT–4 in daylight savings, GMT-5 standard time) – convert to your time at

View and edit this page permanently at, or use the temporal Google Doc for collaborative note taking during the call.


  • Release update – Current blocker issues
    • Working toward release candidate 4
  • Apps and Tools Working Group
    • Chris Barnes records the Apps & Tools call for viewing asynchronously – check for the latest recording.
  • Upcoming Events
    • Duke will be hosting the 2014 VIVO Implementation Fest from March 19-21, with a hackathon likely to start the 18th (see below) – reserve your hotel room today and stay tuned for more information in coming weeks


Eric Meeks presented a 10-15 minute demo of Open Research Networking Gadgets (ORNG) to lead off the call.

  • enabled gadgets to read Linked Open Data a while ago -- converted LOD to JSON-LD which is very easy for the gadget to parse and deal with

  • but the gadgets themselves never produced any LOD -- and that’s now changed

  • Kirsten Bibbins-Domingo ( has worked with the ORNG gadgets to highlight certain publications, weblinks, featured videos, news articles, mentoring, global health, tweets, and notes

    • About half the data you can now add via gadgets

    • And about half of the UCSF Profiles users have added at least one gadget

  • the gadget for publications looks the same as anything else in VIVO because the data is added to the RDF rather than being stored separately in the application database

    • have a tiny OWL file that’s mostly an extension of FOAF, though are using some VIVO properties that found to be handy

    • starts with a class called the ORNG Application -- one per gadget, or about a dozen in all (e.g., one for Twitter, Youtube, etc)

    • further down have another class that’s an Application Instance, that connects a foaf:Person to a gadget

      • when the user adds a gadget to her profile, the Application Instance is added -- so will have several thousand in the database

      • points to the researcher it belongs to, with then a specific property linking to each type of gadget -- hasLinkGadget, hasMentoringGadget, etc.

        • the property is generated based on the gadget filename

  • in the application, a link to the gadget points to the Linked Open Data produced by the gadget, which is then rendered into HTML

    • each embedded chunk of data -- e.g., a featured publication -- is also available and pulled in as LOD, structured as name-value pairs. When the name-value pairs include JSON objects, it may get hard to read

      • people consume the data on Drupal sites and now get core application data and gadget data in via LOD

    • as a next step, are hoping to store the date within each gadget as RDF -- with each gadget type defining its own little ontology which would semantically define the content now generically stored as name-value pairs

    • when would it make sense to just bring the data into Profiles or VIVO as RDF in the VIVO ontolgy?

      • Eric sees gadgets as a way to extend the ontology -- less intimidating than going into the larger VIVO ontology

      • would have an OWL section embedded within the XML that defines the gadget

      • can add or remove without doing any surgery on the source code or the core ontology

      • value: expands the base of developers willing to go in and create extensions

    • want to get rid of the awarded grants gadget because grants data now is part of Profiles

    • if a gadget becomes really popular, then it probably should be rolled into the core product -- but this is a way to explore and extend without a major commitment

  • Is the OpenSocial community ( going in this direction?

    • Looks like they are involved with W3C Social Web Working Group

    • beginning to consider LOD -- it started in the consumer space, but is now setting down into settled areas where there are extensions being built

      • ORNG, but also Huddle and Ford (workflow gadgets) -- and may not look anything like ORNG

        • these solutions tend to be good for one industry space

      • ORNG has done more real work with LOD than any others in the OpenSocial community

    • alive and well but different from the original vision

    • the whole concept of a social network as a platform is healthy

  • Will hope to conduct an ORNG stworkshop at the Implementation Fest if schedules work out


  • Brown (Ted)

    • Org structure work; created local classes to group organizational units as required/desired here at Brown.  Replaced default org browse that pulls from these local classes, could demo this in the near future

    • Faculty testing will start any day now.  

  • Colorado (Alex)
    • Stephen has been working on 1.6 testing and preparing for upgrade; feeling pretty good about release candidate 3
  • LASP (Don)

    • Skills app is live now -- VIVO behind the firewall using a custom ontology that integrated with VIVO, showing a skill and proficiency. Uses an Angular.js app for entry and edit -- right now the Harvester injects the data into VIVO, so are eager to start using the SPARQL update in 1.6. Led to a discussion about the next project, and consensus that can spin up a public VIVO instance and SPARQL endpoint in their DMZ and share data with their public website and other parts of the university

    • All developed with undergrad labor

    • Will continue to work with the dataset/instrument/spacecraft ontology from RPI

    • Can demo on a future call (CHRIS: notice i’m staying quiet about Alex taking my demo , lol) ;)

  • Cornell (Jon, Jim, et al)

    • Most of the focus is on VIVO 1.6 release progress -- hope to have RC4 out shortly

    • Joe who works with Activity Insight and Elements has been prototyping bringing in that data in VIVO 1.6 format

  • Duke (Sheri, Richard)

    • Patrick gave a presentation on the artistic works and it went well; also working on pulling in Library of Congress subject headings, and are revamping the way users can add and remove keywords

  • EPA (Laura, Zac, MaxF, Tian)

    • Still working on revising process for ingesting publications now that will be pulling in all co-authors and not just EPA ones

    • Have had some briefings within the organization and are getting positive feedback as well as awareness that not everyone’s data is complete -- thinking about how to involve users in supplementing data

  • Florida (Chris, Nicholas)

    • Finalizing testing of our Course Ingest.

    • Testing pulling out all data as N3. Found Fuseki fails to return the LIMIT query the same way the VIVO sparql interface does. IE, Fuseki fails to return query at all.

    • VIVO apps and tools call hosting and HACKATHON planning.

  • Memorial (John, Max)

    • We've had issues loading our ontology file from filegraph/tbox - it has been causing tomcat to fail and then hang on restart. With general troubleshooting, we could tell the it seemed to be a database issue - tomcat would start fine without mysqld running, but would hang on restart with mysqld running. We can get tomcat running using this boot sequence, but once we start mysqld and try to reload our web app via the tomcat manager the web app fails to restart.

    • We ran a msyqldump and retrieved our (possibly corrupt) DB file, then loaded it into a clean install, but our vivo app would still not properly boot.

    • We tried loading RDF/XML from site admin page, and it worked.

    • A couple of questions:

      • Should we be loading the ontology file into a clean DB install?

      • Should the ontology file be in rdf/xml format?

    • Are there any backup instructions available? We’re going to be establishing a regular backup regime for our development instances, and are wondering if there are any tricks and tips.

    • Is there any updated harvester manual available? We are beginning the data ingest process using harvester, and if anyone feels they could offer any advice (as needed) we would appreciate it!

  • RPI (Patrick)

    • Preparing a demo on the Deep Carbon Observatory for the American Geophysical Union conference in SF ( -- Drupal, VIVO, CKAN, and the unique identifiers (handles) that are generating. The basic idea is to do a data deposit, starting on a Drupal site and moving to VIVO to add datasets and linkages, and then start an upload in VIVO that deposits the data in CKAN; VIVO then gets the handle for the deposited datasets

      • also have tools outside of VIVO that pull data out of the triple store

      • e.g., a map of the different researchers

      • a faceted browser using an opensearch description document -- publications and datasets

      • and display information from VIVO in their Drupal site, using a Drupal module that grabs information from a SPARQL endpoint and displays it in Drupal

      • question from Don at LASP -- using the Solr tools for the faceted browser? No -- using tools written in house by students

        • can drag facets up and down, close or add facets, change out widgets for facets

        • can go from the faceted browser directly to VIVO

        • Is the code on Github or elsewhere?

    • CHRIS: VIVO Apps and Tools would love to have you DEMO on 12/17 1 PM eastern Call. (thanks so much. email me at if you need anything)

      • I’ll add it to my calendar, and will demo 12/17, yes

    • One issue we’re working with Jim Blake at Cornell is the Policy work. We have a workaround, but want something more permanent.

  • UCLA (David)

    • Doing some research and learning more about VIVO, and will be trying to install 1.6 release candidate 3 to explore the UI

  • UCSF (Eric)

    • Some movement on the author registry -- Griffin has sent out a straw man web service model that could be created, and will be giving him feedback on that

      • Would be good to have someone from VIVO involved in the conversation -- have someone from Knode involve

      • somewhat agnostic as to ontology

      • trying to think through the authority aspects of it

      • will enable clicking around to co-authors at different institutions

  • Weill Cornell (Paul)

    • Working on our Publications 2.0 approach

    • Sorry had to leave early….

Hackathon planning

Chris Barnes is soliciting input on possible development projects for a hackathon to start the Tuesday of the Implemention Fest week (the main event begins Wednesday) ...

Email if you want to send ideas! Also, come to the 12/17 VIVO apps and Tools call.

Notable list traffic

See the vivo-dev-all archive and vivo-imp-issues archive for complete email threads

Call-in Information

  • Date: Every Thursday, no end date
  • Time: 1:00 pm, Eastern Daylight Time (New York, GMT-04:00)
  • Meeting Number: 641 825 891

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