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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?

      ...

      • 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

      Updates

      • 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 PagedSearchController.java 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.  https://gist.github.com/lawlesst/6300573 

        • 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 - https://github.com/vivo-project/VIVO/pull/7 

        • 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: https://github.com/OIT-ADS-Web/vivo_widgets 

      • Johns Hopkins

      • Memorial

      • RPI
      • Scripps
      • Stony Brook
      • Texas A&M
      • UCSF
      • Virginia Tech
      • Weill Cornell

      • (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 (?)

        anyone else

      Notable list traffic

      Restricting user access to data from named graphs (Eliza)

      ...

      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

      ...