Shortcut to temporal Google doc for meeting notes: https://goo.gl/pcvq1r

Announcements

Updates

  • Brown

  • Colorado

  • Cornell (Jon, Tim)

    • Jonathan -- new semantic/ontology engineer doing an independent analysis (Alex: “clean and sober VIVO review”) of VIVO Cornell extensions and their VIVO data sources, basic counts

    • Adding tool tips to labels (in public detail pages) for ontology properties in object editor (Public Description) will be in VIVO 1.8.1 release -- should also make this easier to customize by implementing sites

    • Jim has been working on fairly extensive test suite for group properties list (pulls together data for an individual page) -- needed to refactor this functionality -- not sure if will be in 1.8.1

    • VIVO 1.8.1 release planned for after VIVO conference with performance improvements for individual display pages which use extended FOAF properties -- Jim has add some caching of RDF on individuals and Tim has improved list view queries, but there is more work to do

    • General sentiment is to recommend installing 1.8 over 1.7 for most sites, rather than waiting for 1.8.1 -- caveat would be for sites starting with very large publication data sets

  • Dartmouth (Rodney)

    • Working on a tool to recommend eagle-i resources based on VIVO profile, publication, and grant data

      • coming up with a bag of words based on the vocabulary in eagle-i, and looks to see what words from the vocabulary are in the VIVO profile

      • uses cosine distance to find the most relevant resources it can

      • hoping to provide researchers recommendations of people they might like to talk with or resources they might not be aware of

      • also considering adding links from VIVO profiles to the resources they use in the eagle-i dataset at Dartmouth -- could also match up to other people’s eagle-i data outside of Dartmouth

      • Paul -- if you know people’s publications, you know their MeSH terms, and if eagle-i resources have been tagged with MeSH terms, there could be linkage there as well

      • Alex -- Violeta sent out a message that NLM has published MeSH as RDF (beta)

        • Paul F: Northwestern has been trying to map NLM publication types to VIVO publication types using local ontology extensions, but with the NLM publication types

        • Will also be trying to parse out the MeSH terms from PubMed using their URIs

      • Should we stay with UMLS service or switch to the NLM MeSH for VIVO?

        • Paul A -- UMLS has almost too many options, as an umbrella representing many (~150) source vocabularies, including more clinical terms)

        • In specifying the new Weill Faculty Information System will be using terms from MeSH primarily

      • In the context of linked data, what gets used may take precedence, which is likely to be the new NLM MeSH URIs

    • Using gensim library to find connections between resources and researchers.

    • Sparql queries to get information from VIVO.

  • Duke

  • DuraSpace

  • Emory

  • Florida

  • Fundação Getulio Vargas

  • George Washington University

  • IFPRI -- International Food Policy Research Institute

  • Memorial University

  • Northwestern (Paul)

    • Have VIVO installed on staging and production servers -- on track for public release by the VIVO conference -- hoping for vivo.feinberg.northwestern.edu

      • Awaiting public facing URL and opened ports

      • On track for production VIVO in time for conference

    • Some Lattice Grid visualizations have been added to our VIVO staging instance

      • 2 in now and 3 more to add

      • Alex -- will they be open source? yes -- continuing on the work from the Hackathon -- another app runs on the server to issue SPARQL queries and assemble the JSON data the Javascript visualizations use

        • Follows the University Florida model for add-in visualizations

  • Ontocale SRL (Brian)

    • Recently looking into the performance also -- has some effort to contribute to that so will be in touch with Jim and Tim

    • Will be very helpful to have Jim’s new test suite

    • In 1.8 we have something of the worst of both worlds -- a somewhat expensive query to get all the information for faux properties developed in 1.6, but also more complete support for faux properties in the low level data access objects

    • Hoping to work together that at the very least will only do one expensive things instead of doing that twice; may go for more radical rethinking of the hundreds or even thousands of very small queries

    • With Scripps have been trying to get very complete lists of publications from Pubmed to help people get their full list of publications for their NIH biosketch

      • Have added a search in Pubmed to help manage the NIH “my bibliography” -- pulling it from VIVO, which has significantly cleaned up the data

      • As an alternative to searching by name for my Bibliography

      • The NCBI batch citation manager was very helpful -- dramatically increased the number of publications in Scripps VIVO that have Pubmed ids

    • Moving on to additional publication types -- book chapters

    • Will be speaking at the German VIVO event September 9 or 10

  • Scripps

  • Smithsonian

  • Stony Brook

  • Symplectic (Alex)

    • Attended Community Leadership Summit in Portland this past weekend, held just before annual OSCON conference (next year will be in Austin, TX)

    • CLS 2015 attendees: http://www.communityleadershipsummit.com/attendees/ (nice to see Google, Microsoft, Amazon, HP and other large corps represented)

    • 2-day event with morning plenaries and unconference format for afternoons

    • Suggested and facilitated unconference session on “Surfacing expertise in your communities” with a 10-15 minute presentation on VIVO/ProfilesRNS. Had a half dozen+ attendees including someone from SWIFT representing Swiss universities, some industry folks, and a mental health support network in Oregon.

    • CLS is using Discourse for hosting their ongoing community discussion -- also has a wiki integration somehow (looks interesting): http://www.communityleadershipforum.com/

    • Others shared a related Q&A forum on  http://communitybuilding.stackexchange.com/ that might be useful resource for our community leaders

    • Geek tool for software development analytics worth checking out: http://bitergia.com/ (useful to evaluate open source projects you are considering, VIVO included)

  • RPI/Deep Carbon Observatory

  • Texas A&M

  • UCLA

  • UCSF

  • University of Maryland Baltimore County

  • University of Pennsylvania

  • University of Virginia

  • UNAVCO

  • Virginia Tech

  • Weill Cornell (Paul)

    • Posting a developer position on the VIVO project -- Eliza will be taking on a new role developing InfoEd for Weill Cornell

    • Continuing to work on ReCiter, an author disambiguation tool

    • Working on converting blocks of publications into structured PubMed records

    • Working on requirements and use cases for a Faculty Information System to replace the Office of Faculty Affairs promotion and tenure tracking system, with additional functions and tools -- separate from home-grown Faculty Review tool written in PHP-Zen, which will continue

      • will include validation step in workflow for certain data such as certifications, so that someone in Faculty Affairs can approve changes

      • looking at how to allow changes in underlying source systems

        • Elements has the ability to add a cloned manual record to overwrite the source system information in Elements, but it does not send notifications back to the source system

        • More applicable to internal data sources (at the institution)

        • Can always go back to the original record

      • VIVO likely to stay in the picture but primarily as a consumer of data

        • Have developed a methodology for segregating grants from a system of record from those that users may add

      • performance is much stronger now for non-logged in users, on Virtuoso

 

Notable List Traffic

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

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