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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.

VIVO 1.6

  • VIVO 1.6 release standup meetings are held every weekday noon – likely primarily of interest to those committing code for this release, but open to all

  • Given the ontology and directory layout changes, should this be version 2?
    • Pros: this is a bigger jump than a normal point release, especially with the ontology and data migration, but also with the RDF initialization files rearrangement

    • Cons: there are other features we consider important for 2.0, such as completing multiple language support for content entry and editing and not just the menu and content display; this is the first release of the ISF/VIVO ontology and of internationalization so doesn't feel mature enough for 2.0
    • Road map consideration – we need an updated technology road map and defining goals, features priorities, and resource requirements for 2.0 might be the best way of framing that discussion
  • For background, see the  VIVO 1.6 release planning  or VIVO 1.6 JIRA issues and please comment there or here

Apps & Tools Working Group

Chris Barnes would like to talk to us about his plans for the new VIVO Apps & Tools working group and get your input on topics, timing, and frequency of calls.

  • Proposed Bi Weekly call time Doodle Poll
  • Apps&Tools Birds of a Feather meet-up Agenda and Notes from 2013 VIVO Conference
  • Proposed First Meeting Agenda
    • Create list of goals and action items for working group
    • Decide on recurring meeting time.
    • Discuss creating working group Github site and NAME
    • Discuss finding the first 4 tools presenters for meetings
    • Other / Updates

How do we discuss what should be included in core VIVO?

Jim has proposed and Stephen has echoed a desire to look at what we include in core VIVO.  Stephen makes the following points:

However, I don't think they should just flow in. I think they should get code reviewed and community approved.  This is for two reasons.  
    1. Some things should stay local, albeit very few things in my opinion.
    2. Everyone needs a little recognition sometimes, discussing contributed features helps us all understand who is working on VIVO and feel more apart of the community and not just users.
This isn't the vivo-user-group list, it's the vivo-dev-all list and we should embrace community contributions by discussing them in our meetings.

VIVO 2013 Conference

  • If you gave a poster or talk and it's not yet on the VIVO 2013 materials page, please send Tim Worrall your final copy or a link to SlideShare or similar online service, or add the link to this page or the Google Doc


  • Brown (Ted)

    • interested in the Policy implementations that Eliza and Jim have been discussing on the list -- are making use of named graphs and want to hide the editing icons for that data

    • changed to restrict Coauthors (local class) from appearing in paged search results.  Previously we had added not been indexing this class (via vivoSearchProhibited.n3) but this was preventing the coauthors from appearing in the autocomplete in the editing forms.

    • tested the Sparql Update feature in progress and was able to create, modify and delete data via a Python script using the standard SPARQL library. 

    • focusing on updating and cleaning publication data for fall or early next year public rollout - merging coauthors, merging different instances of same publication, etc.

  • Colorado (Stephen and Alex)

    • Adding a feature to VIVO - 

    • Working on updating the harvester for the ontology changes

    • Preparing to test VIVO Release Candidates

    • Working on our Elements test instance installation and publications curation

  • Cornell (Jon, Jim, ...)

  • Duke (Patrick, Sheri and Richard)

    • Adding initial start to ontology changes for artistic works into our test instance -- data will be entered into Elements

    • Working on pulling in some additional data from Elements like Book Section, Conferences and others.

    • Finishing up a campus production sparql endpoint for use at Duke (to start with will require an API key) -- replicating the VIVO MySQL db to avoid impact on production VIVO

    • VIVO Widgets repo: 

  • Johns Hopkins

  • Memorial (John and Max)

    • Working on cleaning up data from existing Yaffle database for data ingest testing - developing templates to help data cleaning staff effectively move data from current SQL database and clear unneeded entries and elements.

    • Initial stages of UI planning and development, planning for starting work with a design team and front-end developer beginning in mid-September.

  • UCLA (Vivek)

    • Evaluating VIVO and VIVO Harvester -- the Harvester crashed, modified code to work around this, and wants to contribute this back -- Stephen asked Vivek to email the dev list and he’ll followup on contributing this

    • Trying to populate a test VIVO with CSV… found CSV-to-RDF code related to Ingest Controller in 1.5 code, but method is commented out? Will include this info in his email to the dev list

  • UCSF (Eric)

    • a question for the Duke team -- saw the widgets at the conference for grabbing data from VIVO to add to other web pages. Are these open source?

      • Richard -- yes, they’re out on GitHub and fairly recently updated, with a few more local changes still to push up

    • will try and do hosting for Profiles; interested in the SPARQL update service for VIVO.

    • Expects to be seeing a need to indicate that a publication in multiple systems -- how to de-dupe this? Would a DOI not be enough? Stephen noted this had been suggested in the old VIVO IdeaScale

  • UF (Chris and Nicholas)

    • Working on python tools for doing Person and position data  into our vivo. Getting ready to put the tool into production. Soon to follow will be courses. Tool take csv files as input and then make ADD/Subtract rdf files that can be  loaded into VIVO via the admin interface.

    • Wondering if anyone has a deploy to production from Git strategy they would be willing to share. Stephen can share the wiki pages, and Ted will also.

  • Weill Cornell (Paul)

    • Making changes to the template such as combining multiple publication types in a single list and allowing the end user to sort by, say, citation count.

    • Eliza is (almost?) finished with a tool that allows for piecemeal updates of certain properties/classes without having to do a complete reingest.

      • Need for some data needs to be updated usually 1-3 months after being published: publication type, funding, PMCID, MeSH

    • Early stages of tool that infers UMLS expertise -- getting data from a variety of sources, not just pubs -- can feed the tool a CSV with any kind of data

    • Jon: NIH Reporter request for more tools to (?) load profile URIs into Reporter (?)

Notable list traffic

Restricting user access to data from named graphs (Eliza)
  • Jim is developing a wiki page on the Policy implementations that differentially govern authorization to edit anything in VIVO based on the class of the data involved and the level of privileges of the user, and Eliza will be looking at making a change that may look directly at the graph any given publication belongs to
VIVO Sparql endpoint requires login
  • (Patrick&RPI) At the moment, in order to issue a sparql query against VIVO, it looks like you have to actually be logged in. We want to be able to allow anonymous users to be able to issue sparql queries. I don't see anywhere in the documentation that details anything about configuring or managing the endpoint. Is there a way to allow anonymous users to issue sparql queries?
    • Jon: how many people would like to expose SPARQL queries to unauthenticated users? Some risk of denial of service or unintended data updates?
    • Stephen: planning to follow UF and Duke's plan for a SPARQL endpoint using a replicated db

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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