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View and edit this page permanently at https://wiki.duraspace.org/x/FoVjAg, or use the temporal Google Doc for collaborative note taking during the call.

Announcements

  • Release update – Current blocker issues
    • Testing release candidate 5
  • Apps and Tools Working Group
    • Chris Barnes records the Apps & Tools call for viewing asynchronously – check for the latest recording.
  • Upcoming Events
    • Duke will be hosting the 2014 VIVO Implementation Fest from March 19-21, with a hackathon starting Tuesday the 18th (see below) – reserve your hotel room today and stay tuned for more information in coming weeks

Updates

  • Brown

    • faculty testing beginning this morning.  About 70 faculty using this system and reviewing profiles.

    • reconciling journal names with ISSN  via JournalTOC API and Pubmed.  

  • Cornell -- Brian, Tim, Jon -- still working on v1.6

  • Duke - Sheri -- still working on the artistic works feature and pulling in keywords from the Library of Congress -- not immediately obvious which LCSH terms to bring in -- e.g., a search for “textbook” will bring back 4 different unique ids

  • Florida - Nicholas -- have been running an updated version of course ingest, that is also linked closely to the updated people ingest. Are finding that a number of grad students get brought in through courses, which if they have a UF ID, can be supplemented with directory information.  Still progress on the organizations visualizations using d3.js

  • Memorial

    • I am wondering if some could help us with issues in running harvester:

    • Q1:  with  Harvester 1.5. the whole process: dataDBclone, fetch,… ran well until the “diff’ process, the below is what I got .

      • Invalid config file: contains

      • >> non-value map (paramName=paramValue) value for parameter '( d / dumptofile )'

      • >> 2013-12-09 09:06:20.183 DEBUG [o.v.h.d.Diff] Stacktrace:

      • >> java.lang.IllegalArgumentException: Invalid config file: contains non-value

      • >> map (paramName=paramValue) value for parameter '( d / dumptofile )'

      • Q2: I also followed the video tutorial to try harvester1.0. The whole process was fine, checked log file and no issue at all. But could not get data populated. Is there any possible reason?

    • Q3: I have loaded our local ontology RDF/OWL from admin-page. This file was generated via protégé. Some local extension classes were inherited from VIVO core, some our own classes and relations. But it seemed it still need to re-add new class / properties/ from Ontology Control Panel.

      • Q4: For an instance, I have a class:Project in our Ontology(is subclass of VIVO core: project), I added our local extension property: “KMY: Research Theme”. This has been reflected in Protégé. Do I still need “add new data property” from “ Ontology control panel”. How about those properties that we inherited from VIVO core? Do I still need manually add in same way.

    • Q5: I was hoping if someone could explain some terms:  Internal name (RDF local name), inverse internal name , Display tier  in Ontology Control Panel.

    • Contracting with Miles for front-end Drupal work

  • Stony Brook - next on the “to do” list is to disambiguate the authors in the current data set. Getting the data in JSON format and is hoping to sort the input to group papers with common authors together; had earlier gotten information in spreadsheet format that was easier to sort.

  • RPI -- at the AGU conference in San Francisco this week

  • Scripps -- (frost on the windshield this morning and getting into the 30’s at night). Have started the quality control project to review 330 faculty profiles to find any mis-assigned faculty publications, comparing against the CV or a definitive list on faculty lab pages. For someone with an unusual name, found 1 error in 400 publications. But another person who came from industry in neuroscience who had a lot of book chapters that had not been indexed well in PubMed or Web of Science, but were found in SciFinder (40 more). A person with a common name had 22 articles that had been mis-attributed to him. Hoping to finish for March 1 rollout.

  • UCSF -- Eric -- still percolating the idea of the co-author registry. Questions -- do we have any idea how many of our users at various sites are using mobile devices. At UCSF have been measuring for a few years and are now up over 10%; BU has found that they have over 20% mobile. A responsive design approach would likely take a middle course between the full-length profile.

    • Also saw an open source network visualization tool called cytoscape (used Gladstone institute at UCSF) that has an add-on that will go to Pubmed and pull down a person’s publications and co-authors to dynamically generate a network graph

Hackathon planning

Chris Barnes is soliciting input on possible development projects for a hackathon to start the Tuesday of the Implemention Fest week (the main event begins Wednesday) ...

Will have a room on Tuesday the 18th with networking; will start with getting each participant up to speed on a basic tool set of VIVO virtual machines with data already loaded. Will provide a 5-page small presentation format to be able to give a mini-update on their ideas and progress. At the end of the 2nd day will present what has been done to the rest of the I-Fest audience. Work can continue on Thursday or could shift to workshop activities.

Would like to provide some generalized themes from the community on what people would like to see coming out of the hackathon -- e.g., faceted search, tools for lightweight visualizations  using HTML5/Javascript.  If you had a group of the best hackers for VIVO, what would you like to see created?

  • what do we mean by faceted searching? have seen examples in the past where a search for cardiology with 272 results relating to people could be broken down further by other characteristics

    • Griffith’s ResearchHub builds out a web of terms that might help you

  • anything that enhances search and discovery, such as relevance ranking

  • adding schema.org tags to our HTML based on the underlying RDF

  • Looking into using Griffin Weber’s disambiguation service -- nothing about it is specific to Profiles.  By default works with Pubmed but Griffin has an extension developed to link to Web of Science (if your institution has a license)

    • His implementation is built on more than name matching

    • A lot of people have experience with edge cases and if we put all our heads together we could challenge some of the more challenging cases

    • Harvard Disambiguation Service Based on paper about disambiguation

  • Pulling together ingest tools to provide a modular, end-to-end functionality that leverages the best part of the Harvester while taking advantage of other tools

  • Building a mobile app for VIVO in a day or two using lightweight JavaScript frameworks

    • Start from mobile first

    • Support search and a scrollable profile

Notable list traffic

  • Guidance for using the Harvester – calling for those with experience to share tips and update documentation
  • Ingesting CSV in general
  • SciENCV is up and running
  • Glassfish 4

    • does it work with (or require) Java 1.7?

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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