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Calls are held every Thursday at 1 pm eastern time (GMT–4 in daylight savings, GMT-5 standard time) – convert to your time at http://www.thetimezoneconverter.com

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

Announcements

Upcoming Events

  • DuraSpace Sponsor Summit: March 11-12 in Washington DC

    • VIVO Project Sponsors that plan to attend in person or remotely should contact Kathryn by email if you have questions

    • people we know are attending -- Paul, Mike Conlon,

  • 2014 VIVO Implementation Fest: Wednesday & Thursday, March 19-20, at Duke University in Durham, NC

    • Draft schedule is online at https://docs.google.com/spreadsheet/ccc?key=0AoNlOCPPbx7MdG1KUXBySnJ0WFBxVWpWdmQ0M0ZtRmc&usp=drive_web#gid=0 for review and comment

      • Jim Blake would very much like to get feedback about the road map and relative priorities, not just among new development tasks, but among development, documentation, and more examples

      • Paul suggests offering people choices to react to

      • Alex -- are people interested in coming to the Hackathon for more than just coding

      • Chris -- absolutely want people to come to the Hackathon to work on things other than coding, such as writing requirements or user scenarios or re-organizing documentation

      • Happy to send out invites to the Hackathon if that facilitates getting travel approvals

    • Hotel block of rooms and advantageous rate of $101 times out on Monday, February 17

    • Please “register” by completing the online survey at https://docs.google.com/forms/d/1x3vj1JzKIJLsaWAo48zfVmIYIOavjko424NZa7bbR7E/viewform 

    • More logistics information at http://vivoweb.org/blog/2014/02/2014-vivo-implementation-fest 

    • 2014 VIVO Hackathon: on Tuesday, March 18 preceding the IFest at Duke University – Chris Barnes and Ted Lawless are soliciting input on possible development projects

    • 2014 VIVO Ontology working session (half-day) – morning of Friday March 21 at Duke University – will confirm point of contact; another potential option is a development roadmap half-day

    • Paolo Mangiafico at Duke has created a poll to determine interest in an Symplectic Elements-related meeting for other IFest attendees. He's included poll times that overlap with the iFest program, but suspects that the best times will be on Tuesday or Friday before or after the main VIVO program. There's also the possibility of organizing an informal/social dinner one of the evenings of the iFest, either in addition to or instead of a more formal meeting, so he included some evening times too. If you're interested in meeting, please indicate your preferences here: http://doodle.com/g88inmep6g63t7py

  • CASRAI U.S. Summit on Wednesday, April 9 at the American Psychological Association headquarters in Washington, DC -- will be discussing alignment of VIVO ontology and CASRAI as well as the european standard, CERIF, and the new U.S. SciENCV reporting format

  • Other VIVO-related events? We plan to centralize VIVO event listings/calendars in one place soon, and will link to this here

Annual survey of VIVO sites? (Good suggestion from Paul)

  • how many FTEs work on VIVO (and what is their domain expertise?)

  • what data are captured

  • what additional tools are used

  • (production environment specs/config?)

  • can put the results in http://vivo.vivoweb.org 

  • perhaps do a dry run at the I-Fest

  • (useful for DuraSpace to understand community growth, member prospects?) 

Updates

  • Brown (Ted)  Nothing too new -- waiting for a public VIVO rollout date.  

    • Updated the VIVO Vagrant image to install version 1.6 or 1.5.2 in preparation for the Hackathon, and is also putting together a list of tools

    • Hoping to have expressions of interest from Hackathon attendees in advance based on a possible list of topics.   

  • Colorado (Alex)

    • No WebEx audio at the moment (computer audio not working/mobile phone no charge) -- no major updates this week other than starting to help with IFest planning, no real time to spend on 1.6 upgrade past week

  • Cornell (Jim, Jon)|

    • Getting ready for 1.6.1 upgrade  -- timing unclear as we wait to see what people come up with as they adopt

    • preparing for upgrade of Cornell VIVO using the 3-tier build with some local modifications to login widget, etc.

  • Duke (Richard)

  • Florida

    • Looking at the 1.6 ontology as part of planning for the upgrade.

  • Memorial (John, Max)

    • still migrating from older Yaffle instance; bringing graphic design, developer, and usability testing teams together

    • hoping for a soft launch in the spring, with rollout to faculty in the fall and shooting for a public rollout in winter/spring 2015

  • RPI

  • Scripps (Michaeleen)

    • v.1.6 upgrade on hold: article ingest program won’t work with all the ontology changes; no funds for new contract to write a new ingest program

      • Jon -- could this be on GitHub for others to modify?

    • continuing QA/QC project: reviewing faculty profiles from individual CVs

    • will not be attending Implementation Fest due to funding issues

  • Stony Brook

  • Texas A&M

  • UCLA

  • UCSF (Eric) Being inspired by these calls for VIVO, are starting a monthly call for Profiles, and will be some overlap of topics and would like to get communication going in both directions.  Cross-linking authors across institutions is still progressing

  • Virginia Tech

  • Weill Cornell (Paul)

    • We released our “public beta” launch on the 31st of January

    • Tomcat has crashed on a couple occasions. Performance is slower than preferred on larger profiles with 7-800  publications (>20 seconds)

    • Hopefully contributing to Harvester upgrade to 1.6

    • Working on troubleshooting

      • upgrading Tomcat

      • upgrading Java

      • upgrading VIVO from 1.5 to 1.6 to take advantage of caching

      • investigating errors in the logs

      • lazy loading of publications?

    • Suggested an annual survey (see section above)

    • Eliza will be contributing as she has time to making the Harvester scripts compatible with VIVO 1.6

  • any others?

Notable list traffic

Multiple issues with the Harvester, some of which have been addressed and some which would benefit from a more active Harvester communication through the Apps & Tools working group meetings, sharing the vivo-dev-all list so we all stay informed

  • (Christian, Hannover) trouble even getting the Harvester running, documented at https://github.com/vivo-project/VIVO-Harvester/issues/14

  • (Eric, New Mexico) Success helping Isuru at Indiana University get past problems by switching to the National Library of Medicine's newer version of the jar file eutils_axis2.jar.  See this folder:  ftp://ftp.ncbi.nlm.nih.gov/pub/eutils/soap/v2.0/java/current/. This requires updating all Axis2 1.5.4 dependencies to Acis2 1.6.2, and switching to using the harvester-pubmedhttpfetch script instead of harvester-pubmedfetch (though you've got to make the termSearch value in pubmedconfig.xml URL-safe, and replace the space character with "+")

  • (Stephen) The Harvester infrastructure doesn't need changing to work with 1.6.  It could use changing to help it work with the API's better, but to get data in and out of VIVO it won't need any changes.  There are a couple of things an ontologist could probably do to help transition the example scripts from 1.5 to 1.6.  The main changes are in the XSLT and Score (which you define data properties to evaluate).

  • Ted used Jython to be able to write to the Jena database

  • On this Tuesday’s call, Chris will bring up the Harvester and ask for suggestions for a maintainer

Deleting multiple labels for classes

  • (Brian, Han) Since the ontology is in a different graph, removing extra ontology class or property labels requires including triples in the OWL namespace with the RDF being retracted

Fatal error when trying to replicate a VIVO in another location

  • (Jim, Anson) Looking into subtle Tomcat permissions issues and missing files that suggests that the VIVO portion didn’t get merged in correctly; trying to replicate a local instance in the cloud. The data are there but the display ontology seems not to be loading, so can’t browse the data.

Will the VIVO 1.6 ontology load in Protégé? – try Protégé version 4.3  

  • There’s an ontology visualization tool called jowl (http://jowl.ontologyonline.org/obi.html)  that could be very helpful, but it won’t load the VIVO-ISF ontology or VIVO 1.2, while it does load the eagle-i ontology, the pizza ontology 

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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