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CU Boulder is closed today due to severe flooding in the area – we hope all is well with Stephen, Alex, and Liz and their colleagues.

Release update

There are still open blocker issues for the 1.6 release – and we expect to need about 3 weeks for testing, so look for a mid-October release.

Apps&Tools Group

Notes from Sept. 10 meeting and WebCast:

Next meeting: Tuesday, September 24 at 8 AM Eastern, 10 pm Melbourne, 1 pm London, 2pm Amsterdam and Rome


  • Colorado (Alex)

    • Starting publications curation using Symplectic Elements for 2013 faculty reporting cycle -- Google Scholar and Researcher ID have both come up

      • can do an author search in your university’s domain and find several hundred faculty, a number of whom have curated their entries

      • Elements has the ability for users to import RIS (from Endnote) or Bibtex (from Google Scholar) -- but Google Scholar doesn’t give you a batch export capability for a group of authors (just 1 item at a time)

      • Can possibly scrape a Google Scholar record of DOIs and then go to the CrossRef publication search

      • Paul -- should be aware that the quality of the data harvested in Google Scholar may come from a variety of sources of uneven quality, so the citations may not be as pristine as a PubMed record

    • Planning how to test 1.6 data migration to test 1.6 and prepare for modifying our Harvester ingest

  • Cornell (Jon, Jim, Tim, BrianL)

  • Duke (Patrick) -- Still moving forward on artistic works, with mockup data in a test instance and working on display in VIVO; still working on how to get the data in from Elements; will push back Arts & Sciences rollout for a bit

  • EPA

  • Florida (Chris) -- Apps & Tools 2nd meeting Tuesday -- demo of Vagrant virtual machine for VIVO to make it easier to build and test VIVO. Has a new template for a SPARQL query example with a link to test on the UF SPARQL endpoint -- the first sample tests getting a person’s positions via their email address -- all the information is in the meeting notes on the wiki, and recorded the call as a webcast posted to YouTube, including the demos

    • next meeting on the 24th at 8 am to attract international collaborators to the call

    • will continue to refine the working group goals

    • will hope to have more SPARQL examples to show

    • will hope to have a working Vagrant virtual machine with sample data, that will be much smaller than the current virtual machine

  • Memorial (Max) -- working on the front end with a web developer and back end mapping the Yaffle database schema to the VIVO ontology

  • NYU (Yin) -- couldn’t make call. no updates.

  • RPI

  • Scripps

  • Stony Brook (Tammy) -- recruiting more developers to semantic web projects (Java developers) in their IT group -- data integration for additional projects. Trying the total immersion technique.

  • Texas A&M

  • UCLA

  • Virginia Tech (Julie) -- no special update, but working with central IT to get software installed and configured; going well.

  • Weill Cornell (Paul) -- faculty evaluation tool in use for first time -- giving faculty the chance to accept or reject pubs, and they were pleasantly surprised to see very few rejected publications and many of those were dupes -- Ted at Brown mentioned the CrossRef test file submission feature that returns DOIs, so can test a batch pasted in by a faculty member more easily against what have in VIVO already

    • Question for the group: Is it legitimate to have multiple labels for an individual?

    • Certainly for multiple languages; but in other circumstances? When there is a semantic difference, it seems like another property should be used; otherwise there’s no reason to have a 2nd label

    • Sometimes duplicates occur where one is an untyped literal (better for adding labels in different languages) vs. a literal types as a string (less flexible)

Notable list traffic

Language deployment and change to the 3-tier build (Jim)

VIVO's implementation of linked data (Jim)

  • A linked data best practices document indicates that sending a license statement is recommended. VIVO has a Terms of Use statement that included a statement about content in linked data, and we will add that to each linked data response.

    • Sites should be aware of this text and make sure they agree with its terms: To the extent copyrightable, the information presented on the VIVO website and available as Resource Description Framework (RDF) data from VIVO at [ your institution name ] is intended for public use and is freely distributed under the terms of the Creative Commons CC-BY 3.0 license which allows you to copy, distribute, display and make derivatives of this information provided you give credit to [ your institution name ]. Any non-copyrightable information is available to you under a CC0 waiver.

  • This is the tutorial:, referenced from

Content negotiation for VIVO and for VIVO's SPARQL endpoint

  • Should VIVO redirect a request for to when there's no accept header?
  • BrianL: You can't request Mike Conlon himself over the Internet, so if you issue a request for his URI, VIVO redirects you to an HTML page (information about Mike Conlon) that is not the same as Mike Conlon himself. If you request RDF (in your HTTP request's accept headers), VIVO redirects you to still another URL for RDF data (
    • The question is whether search engines get confused by this – is this causing practical problems?
    • Where this might make a difference is when we generate an HTML VIVO page, should we show links to other pages in VIVO in the /display form (HTML), rather than the /individual form of the true URI?
    • VIVO sends a 303 redirect ("see other") – and search engines can't assume that the 303 they are redirected to will be the same every time they come to the /individual URI, so they can't cache it.
  •   VIVO-282 - Getting issue details... STATUS  will implement content negotiation for VIVO's internal SPARQL endpoint

Configuring Fuseki

Image upload – see  VIVO-287 - Getting issue details... STATUS

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