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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/uvkQAgIfwQAg, or use the temporal Google Doc for collaborative note taking during the call.

VIVO is hiring!

DuraSpace is seeking a dynamic and entrepreneurial Project Director for the open source VIVO project (www.vivoweb.org), a world-wide community focused on creating software tools, ontologies, and services. The VIVO Project Director will have the opportunity to play a major role in a collaborative movement that will shape the future of research.

See full posting – applications are still being accepted -- the sooner the better. Note that there is no requirement to be a U.S. citizen.

Release update

Current blocker issues

 

So close we can just about smell it!

Join the release test mailing list if you wish to be informed of release candidates, plus the final distribution -- and we’d love to have help testing -- subscribe here: https://lists.sourceforge.net/lists/listinfo/vivo-release-test

Apps and Tools Group

Next call is October 22 – look for an announcement from Chris Barnes with the time and connection info.

Upcoming Events

2nd Annual CASRAI International Conference, October 16-18 in Ottawa
  • Conference streams: Reconnect Big Data, Reconnect the Library, and Reconnect the Machine
  • http://reconnect.casrai.org
  • Jon C-R will present on VIVO
    • Memorial University will present their recent work –  "An innovative university-community connecting tool, Yaffle, is being rebuilt using the VIVO framework allowing it to interoperate with other VIVO sites and platforms using the VIVO ontology for search and/or data integration across multiple institutions and university-public intersections. 

    • 1st Annual UCosmic Conference, October 31 in New York
      • Collaborative Software Development to Address Strategic Challenges in Higher Education: Kuali, VIVO and UCosmic 
      • http://www.ucosmic.org/Conference.aspx
      • Deep discount for VIVO community members
    • VivoCamp pre-conference at SWIB13 conference, November 25-27 in Hamburg https://sites.google.com/site/vivocamp13/ 
      • short presentations and demos on a number of topics by a couple of experienced people, followed by discussion, Q&A, panels etc.
      • Organized by Valeria Pesce, Lambert Heller, and Lukas Koster
      • John Fereira from the U.S. will be attending

    Updates

    • Brown (Ted)

      • waiting for a public rollout date to be set.  Hopefully prior to Jan 1, 2014

      • CV data has arrived for hospital affiliated faculty.  Reviewing that and prioritizing what should go into VIVO first -- things like licensing and credentials

    • Colorado (Stephen and Alex)

      • Debugging an issue related to Solr searches -- may need some features added to VIVO deployments to keep Solr from using the 8080 port that Tomcat uses and working off port 80 instead -- have to include the port to connect to Solr. May be an issue with Apache rewrites?

        • Richard -- we at Duke do run Solr on a separate VM from what VIVO is on -- were able to configure it through the deploy.properties file and had to have the correct files on the Solr server -- can share that part of the file

      • Does anyone have a heartbeat monitor for Solr to detect a corrupt Solr index?

    • Lab for Atmospheric and Space Physics at Colorado (Don Elsborg)

      • We have a standalone Angular app that polls a Fuseki endpoint which resides on our database server. Data is returned in JSON. We¹ve found the performance to work very well this way.  VIVO remains largely behind the scenes, with a set of JavaScript apps providing front end services.

      • Currently we just developed an Angular relationship assignment page which relates people with skills. The post currently calls the harvester to ingest. We¹d like to speed this up but we¹re waiting to see what happens with VIVO 1.6 and the potential REST interface before we invest much time into Java Jena calls or wrestling with updates in the latest Fuseki endpoint.

      • We have other reports using the Google API that work very well for our needs.

      • Near term I envision doing more work with Angular and perhaps D3 to create new methods for updating relationships between various items. This would be used more for an editorial type of interface with small amounts of updates so we won¹t wreak havoc with the inference engine.

      • The nice thing about the relationship assignment page we made is that we can easily extend it to created triples between most subjects and objects.

      • Our skills view has just been demo’d to our institution and it seems there’s a lot of enthusiasm for it. So we¹re about to define our next 2 week sprint and release the initial skills website to our institution.

      • Could do a short demo as screenshare in the near future.

    • Cornell (Jon, Jim, BrianL, Tim et al.) 1.6 1.6 1.6 1.6 …

      • Also updating our HR ingest as a result of Cornell shifting from PeopleSoft to Workday, with a quite different alignment of organization units

    • Duke (Richard, Patrick and Sheri)

      • Providing a way to allow faculty to remove the sparkline from profile.

      • Have some more rollouts in the works, working college by college.  So far VIVO is successfully pushing cleanup in source systems of record, as for example cleaning up working titles in upstream systems -- have strong Provost backing to do that

      • Happy with Julia’s support page and their custom “edit mode” that links to other data sources external to VIVO’s edit functionality, like faculty titles.

    • Florida (Nicholas) - Have some personnel changes coming up so are documenting server configuration, etc., and debugging person ingest code.  

    • Memorial (Max and John) Working with the Knowledge Mobilization Ontology and playing around with the UI -- does anyone else have experience re-using and exporting data to populate other web pages. Have looked at Miles Worthington’s RDF api

      • John Fereira’s semantic services

      • Google linked data api -- implemented in Elda (java) and also in PHP

      • JSON-LD has a number of implementations in different languages

      • Looking to test 1.6 since don’t yet have a production instance

    • RPI (Patrick)

      • Have “direct deposit” working, being able to upload files in VIVO, have it deposited automatically in CKAN with the assignment of a DCO-ID, add the appropriate properties into VIVO.

        • can do a demo on a future call -- also the Drupal module below

      • Also, we have a Drupal module that allows us to specify a SPARQL query and an XSL translation to use to query the VIVO sparql endpoint and display the information inside of a Drupal page. We’re also working on modularizing the module so that it can also be used in a simple web page, or in MediaWiki pages, or Confluence, etc, etc...

      • Having issues with cloning a VIVO site onto a test server, connection to solr was the initial problem. This is on a virtual server. Logged in, we go to Site Admin, click on class hierarchy, then Add New Class, and get a stack trace “HTTP Status 500 - org.apache.jasper.JasperException: org.apache.jasper.JasperException: org.apache.jasper.JasperException: java.lang.IllegalStateException“. The vivo.all.log file says “2013-10-10 13:08:39,012 ERROR [VclassRetryController] VclassRetryController could not forward to view.” (westp@rpi.edu)

    • Scripps (Michaeleen) -- would like to post the local ontology extensions to the wiki (Jon will set up a page).  Will be continuing to add articles and update grants, but will be waiting for new funding to update ingest scripts from 1.5 to 1.6.

    • UCSF (Eric) -- Followed up with Scripps about the ontology extensions for representing NIH grants (grabbing extra data about annual updates) - will hope to add that to the Profiles product.

      • And starting to work on UI things in Profiles so can link to the profiles of authors at other institutions, using the service Griffin Weber has developed at Harvard for disambiguating authors centrally out of either Recombinant or Harvard. Anyone would be welcome to use the service.

      • UCSF hopes to jumpstart by hosting USC and UCSD Profiles and starting cross-linking of authors among their 3 institutions

    • Virginia Tech (Curtis) Just received a notice that the server (a virtual server running CentOS = open source fork of RedHat Enterprise Linux) is ready to start loading the software -- hopefully will have news from that next time.

    • Weill Cornell (Paul and Eliza)

      • Custom styling of publications -- modifying the SPARQL query to see the authors as well on a person’s profile page, plus Freemarker scripting to order the authors according to their ranking

        • (see also vivo-dev-all message from Stella)

      • Working to understand why PubMed is not happy with DOI-based queries.

      • Still working on a way to offer users the ability to sort publications by journal name, date, publication type, etc. as they wish 

        • Short demo next Thursday during weekly call

    • any others?

    Eliza’s Demo

    Extending and customizing the VIVO functionality for listing publications in Weill-Cornell researcher profiles.

    Eliza shows the way they have customized the publications list on the individual profile page. It required modifications to three template files, and the use of the TinySort plugin for JQuery. Some of their functions are based on data that they get from Scopus (number of citations), and they can create links to Scopus information because their library is a subscriber to Scopus.

    Eiza will post the code on the Duraspace Wiki.

    Questions? Feedback? 

    Updates

    • Brown (Ted)

      • ironing out details for feeds from campus sources and VIVO sync processes

    • Colorado (Stephen and Alex)

      • preparing for annual faculty reporting cycle, continuing with publications curation in Elements to feed into

    • EPA (Laura) - no update, back in the office

    • Cornell (Jim and Brian) – Jon at CASRAI International Conference (http://reconnect.casrai.org). Working on 1.6

    • Duke (Richard and Patrick)

      • Not much to report. Deciding whether to pull data on artistic works (about a dozen types, e.g. performances), and the different kinds of roles, from Elements or from other (local) systems.

      • Here is our current list of artistic work types:

        • ceramic

        • composition                    

        • costume design                 

        • dance                          

        • decorative art                 

        • digital media                  

        • drawing                        

        • exhibit                        

        • film                           

        • graphic design                 

        • illustration                   

        • installation                   

        • lighting design                

        • motion graphics                

        • new media                      

        • painting                       

        • photograph                     

        • print                          

        • sculpture                      

        • set design                     

        • theatrical performance         

        • video

      • Here is our current list of artistic roles:

        • actor

        • casting director

        • choreographer

        • conductor

        • consultant

        • creator

        • director

        • juror

        • musician

        • narrator

        • performing artist

        • producer

        • restager

        • vocalist

        • writer

    • Memorial (John) – presenting on VIVO and Yaffle at CASRAI International Conference

      • Jennifer is at CASRAI with Jon C-R. New staff member working on cleaning and updating the data. Looking at options for customizing the UI. Waiting for 1.6

    • Scripps (Michaeleen and Catherine)

      • In maintenance mode. Adding data, and waiting for 1.6

    • Stony Brook (Tammy)

      • Getting data into the Stony Brook site. So far, so good. Still need grant data. Moving along.

    • Virginia Tech (Julie)

    • Weill Cornell (Eliza)

      • Eliza's demo

    Notable list traffic

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

    How do you create a list of authors for publications on individual researchers' profiles? (Paul, Stella)

    • Look for a demo from Eliza next week

    Uploading image when editing a property of an individual (Yu, Huda, JohnE, PatrickW, BrianC) 

    • Adds a file to CKAN and brings back properties to add to VIVO

    • Will be having a WebEx call between the RPI grad students and Cornell developers to discuss various ways that this could be accomplished

     

    Is there a way to limit the number of labels for an individual, on editing in ingest

     

    • Lukas Koster at the University of Amsterdam still has a question about the Java requirement, given this statement: "We recommend starting with Java 7 since Java 6 is no longer supported." But in the Vivo 1.5 installation guide it says: "Java (SE) 1.6.x... VIVO does not work with Java 1.7"
      • Jim Blake replied seeking clarification – is anyone running 1.5 with Java 7 in production?
      • Stony Brook is using Java 1.7 with VIVO 1.52 in production, and 1.6 will require Java 7.
    • Han at RPI asked about querying against the VIVO built-in sparql endpoint by sending an http GET request.
      • Jon and Brian Caruso responded with some of the options, including 1.6 support for specifying credentials
    • Patrick at RPI followed up about issues with a cloned VIVO site. 
      • Jim and John Fereira provide feedback... Java debugging ensued... Jim provided a revised source file for [vitro]/webapp/web/error.jsp. The page may still fail under some circumstances. However, it will write the original error to vivo.all.log before doing anything else.
      • Running into a known cascading issue with the JSPs, with a fix targeted for VIVO 1.7. Hotfix available from Jim to help with debugging errors thrown in JSPs in 1.6 and 1.5.x.
    • Jon checks in with Michel in Netherlands about his progress connecting VIVO to a TDB triple store, and data ingest options.

    • Paul asked about support for multiple labels -- Jon mentioned that in 1.5 (?) the additional labels aren’t overwritten/lost as required by multi-language support, but only the first label is displayed -- VIVO editor ability to see multiple labels and to choose the one that is displayed (1.5 or 1.6?)

    • Would it be arbitrary to limit what can be done with a given predicate, when the RDF standard does not impose that constraint?

    • Ted -- a SPARQL query added to your ingest process could detect multiple labels, or could be run against the existing data. With 1.5 the VIVO application does alert a logged-in user when multiple labels exist and allows them to select the one to keep

    • Alex -- could this be a “best practice” (or “good practice”) topic for a wiki page?

    • Nicholas has added a nightly check at UF for duplicate labels

    • Nicholas at UF was just running that “report” today

    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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