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Calls are held every Thursday at 1 pm eastern time (GMT-5) – convert to your time at – and note that the U.S. is on daylight savings time.

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


    • Brown (Joe and Ted)

      • still debugging the issue with application becoming unresponsive on login -- it looks like what Jim had thought it was in his last email is true -- the Java model lock is not released because the write to the database is never finishing, so when a user logs back in s/he can’t connect. Can replicate that with a script here -- only locks if the connection is idle for more than 60 minutes (can log back in successfully after 45 minutes), but are at a bit of a loss as to how to proceed -- has been in touch with local database administrator to help determine the root cause.

      • DOI editing problems - HTML tags or XML from MS Word copying/pasting making it’s way into data and makes building links troublesome.  Interested in turning off WYSWIG editor for this property. The WYSIWYG editor does try to filter out Microsoft Word garbage HTML and check for cross-site scripting, but also likes to put a paragraph tag around the text you entered so that you’re not getting only the text you type.

        • you can turn off JavaScript on that page (?)

        • could try pasting into TinyMCE using the the HTML mode, but end users doing self-editing will most likely not do this

        • could make a custom form for the DOI property that presents a different page template that doesn’t have TinyMCE activated, or could configure it differently than it normally is, or you could do additional post-processing with it

        • using class to disable TinyMCE for a single text area? editor_deselector : “noeditor” 

        • if you hire students, you may be able to get them to use the Chrome browser’s “paste as plain text” option

      • importing data from existing local researcher profile system

      • preparing for conference presentations.  Looking at other VIVO’s Journal and University resources for possible constructing owl:sameAs links.  

    • Colorado (Alex)

      • wrapping up installation related tasks for Symplectic Elements, e.g. firewall configuration, publications data sources, etc

      • designing experiments for publications ingest using Symplectic Elements to then feed to VIVO

      • Stephen working on VIVO 1.6 contributions

      • running daily data load using new and much faster Harvester process, loaded into production VIVO for Boulder and Colorado Springs on Mondays and Thursdays -- still babysitting this process, hope to automate further in next iteration

      • met with our med school’s CTSA team (CCTSI) who have implemented Profiles RNS the VIVO ontology version) about linking and collaborating in the future, e.g. on ORCID rollout and sharing/linking data

    • Cornell (Jim, Jon, Brian Lowe, Tim, Brian Caruso)

      • VIVO 1.6 updates: BrianC working on RDF web service... As an alternative to using eitehr XML or JSON, is hoping to use the Jena SPARQL ARQ library that accepts updates in a standard way... looks promising. Hoping to find a way to run the W3C’s SPARQL update test suite to confirm that it is working correctly, but is having trouble finding simple reusable code to do that.  There had been a number of comments on the wiki page on a proposed RDF web service (Stephen and Ted) so is hoping there would be people willing to test and/or help find a test suite

        • Ted already has libraries that can do SPARQL update on the client side, so likes this approach

      • Mann Library has been hosting the IAALD international agriculture conference all week, which included a workshop on VIVO (slides) and uncovered additional developments related to VIVO around the world:
        • There will be a workshop on VIVO at the Semantic Web in Libraries Conference in Hamburg, Germany Nov 25-27, 2013
        • A number of international agriculture organizations are planning and/or starting VIVO pilot projects, including INRA in France and the World AgroForestry Centre (ICRAF) in Kenya
        • The Inter-American Institute for Cooperation on Agriculture (IICA) has commissioned work on a Spanish version of VIVO using the VIVO v1.6 internationalization capability, with support from the USDA, and has received expressions of interest for adoption from Brazil, Colombia, Uruguay, Paraguay, Argentina, and Mexico, as well as many library members of the SIDALC consortium
        • The Global Forum on Agricultural Research (GFAR)'s AgriVIVO project will be adding new content, including researchers from CABI
        • The U.N. FAO's OpenAGRIS bibliographic database has a disambiguated list of 40,000 journals available as linked data; they also have an excellent demonstration of a linked data mashup of linked data from AGRIS itself, DBPedia, the World Bank, Google, GBIF,, and FAO fisheries statistics

RPI (Patrick)

      • Worked out the DOI generation issue. I do not know the specifics, student has not yet checked in the code changes to our git repository. We now generate a DOI for each individual created in VIVO

      • next big task is migrating user information (circa 500) from Drupal to VIVO, mapping between the user information tables in the Drupal relational database with user-defined fields to the VIVO ontology. Then harvesting that data, since can’t customize the RDF that can be generated automatically by a Drupal view on a node.  Can pick and choose what information is needed.

      • then integration between Drupal, CKAN, and VIVO. CKAN is a data repository used by the British site, the USDA -- can store documents, images, data products, charts & graphs, and has a nice mechanism for keeping track of revisions of the documents and some lineage. So want to tie into CKAN the ability when a user creates a data object in CKAN to automatically create a VIVO entry for it where can do searching and reporting.

      • Does VIVO have the Prov ontology yet? no, but waiting for a use case

        • Documentation was made public mid-May

        • Jon sharing PROV-O May 17 diagram -- they’re thinking the ontology structure should be quite compatible with VIVO

      • Is there an ontology, or part of the VIVO ontology, that represents awards (grants for example)?

        • Yes there is. Tied to project, person.

      • The CKAN connection is relevant to DataStar

    • Stony Brook (the Crew) -- Hoping to discuss an issue with the WebId implementation where are wanting to use blank nodes rather than assigning a URI; have worked around that by giving URIs to what would typically be blank nodes, but should VIVO be able to accept blank nodes. The triples are in the triple store and show up in any graph other than the default kb-2, but don’t show up in the public graph (kb-2). (The remove blank nodes command is useful for deleting graphs containing blank nodes.)

      • Tammy has been getting a model from the VitroRequest object, but Brian suggests getting an RdfService from the same VitroRequest

      • will sort out by email offline

    • Texas A&M (Violeta) -- Looking for help with ingest strategies and is meeting tomorrow with business intelligence group with hopes for being able to develop automated ingest. Everything else looks good and enough data has been entered to be useful in convincing others at Texas A&M that VIVO is the way to go. What is the suggestion for handling co-authors that are not members of Texas A&M -- what class should be used? Jon@Cornell is recommending FOAF:Person and then hiding them from listings/search results, and will followup offline.

    • Weill Cornell (Paul and Eliza) -- Graphs issue -- last week Paul asked about how we could separate data into different graphs with the Harvester. Stephen W. had suggested doing that by setting the Score parameter, but the way they do ingest at Weill is to bypass the scoring and namespace mapping stages since use Scopus author ids that don’t need disambiguation.  So given that, would like suggestions on how to do the separation by graph; could put all the data in any one graph, but want to put authors in one graph, articles in another -- or graphs by source such as grants in one graph, education data in another, but may be harder to separate out one set of data during a single ingest into several graphs (e.g., Scopus vs. PubMed).  Stephen indicated he had a script to do it so a post to the list should work to raise the issue Monday.

    • UCSF (Eric) -- continuing to look at the ORCID integration as an OpenSocial gadget with Boston University diving into that.  A couple other things happening, too -- two conferences before the VIVO conference where will be talking about research networking and linked data:

      • a UC-wide conference where won a competition this year for app development

      • and a W3C conference where will be talking about OpenSocial and other social networking platforms on the Web -- and there will also be someone talking about the JSON-LD serialization format for linked data -- we should be happy that the linked data message is getting out and expanding to other communities -- ALEX: is this the Workshop on Social Standards (Aug 7-8

    • Eric will report on what he learns

VIVO 1.6

  • VIVO 1.6 release code freeze has been delayed to allow for integration of the new Integrated Semantic Framework ontology and preparation and testing of the necessary data migrations. Stay tuned at our weekly meetings for updates.

  • See the VIVO 1.6 release planning or VIVO 1.6 JIRA issues and please comment

VIVO Apps Contest

  • Entries are due July 31 – see Call for Applications for more information
  • Is anyone here submitting an entry? Does anyone want to collaborate on one?

VIVO 2013 Conference

  • List of sessions and poster posted here (PDF)
  • Register before July 19 for best rate and conference hotel availability
  • Conference hotel is Hilton St. Louis at the Ballpark Hotel
  • Wednesday night baseball game (Cardinals vs Pirates) and cold beer!

Notable implementation and development list issues

  • Creating a custom list view that includes a variable-length list (Paul reopened) thread
  • Adding link to institutional repository (Giuseppe) thread
  • Current Develop Branch (Stephen) thread 
  • VSTO Ontology Slowing Down Web App (Tyler) thread 
  • VIVO import data (Veslava) thread 
  • Connection pool issues (Mark) thread 
  • Model Listener, and Listeners in general (Patrick) thread 
  • VIVO unresponsive when editing / logging into the system (Joe) thread 
  • Heads up - line endings (Jim) thread
  • 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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To join the audio conference only

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