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

These calls now use WebEx – see the "Call-in Information" at the bottom of this page.

Please add additional agenda items or updates --

Updates

  • Brown – (Ted) – Still cleaning up data that has been loaded; met with people who maintain the local faculty information system and will be getting current faculty positions and titles from that.
    • Also created new local object properties to display service to the university and other types of service in line with how they typically appear on faculty CVs – looking at how to display date ranges using custom list views
  • Buffalo – (Mark) Has VIVO installed on a new production server and configuing mod-jk
  • Colorado --
  • Cornell --
  • Duke – (Richard) Upgraded test environment to VIVO 1.5 but had a question about exporting a large model – kept running into memory problems, so tried exporting data in chunks by getting a handle on a dataset vs. a model – there are a few ways to get a query in there.  Brian – definitely want to use the actual SDB dataset object, not Jena models, or will miss out on the optimization that SDB does for limit queries.
    • Also found that when had been using named graphs, with 1.5 the graphs have to have real URIs, not just strings.  Modified the graph names in the SQL table and reactivated the graph again, and seemed to work. Brian – Yes, going forward the graph names have to be valid URIs
  • Florida – (Matt) Fixed the indexing problem – had to use a Java debugger and go through the SQL tables to find the source; a manual index would fail, and incremental indexes had not been working for a while.  A single form feed character pasted into VIVO from a PDF in March of 2011; cannot reproduce the error by pasting the same file back into more recent versions
    • Now working on getting the logs to reflect manual edits, that previous versions used to log in the vivo.all.log – Brian suggests modifying the auditor, since none of the logging functionality is built into VIVO that was locally modified at UF; with 1.5 have one central place to listen to all the changes via the new RDF API, and the image editing must not yet be using that which is why it still shows up in the logs.  By switching to logging from the auditor in the RDF API, you should see all the edits again, but will have to filter out the inferred triples that are also inserted by the application at the same time. (See dev list messages)
  • Indiana -- 
  • Johns Hopkins --
  • Memorial University of Newfoundland – (Lisa) 
  • NYU – (Yin) Looking at the VIVO development model and came up with a nice way of saying synchronized with the development master branch as checking in local changes to the search indexing and results display. Substantially replacing some sections of code as converting VIVO to search people only – redefining how the indexing and the weighting goes, using what is now still a prototype; now wants to be able to keep up with whatever changes continue in the dev version so won't have to continually. Will write it up and solicit feedback from others in comparison.
    • could be straightforward to swap out the way that indexing is done for people, but less clear how alternative indexing would work on other types of entities like publications, events, organizations, etc.
    • is there a branching model that is recommended?  Jim – holding pretty close to the Gitflow model; Yin – use that in-house already
  • Scripps --
  • Stony Brook – (Tammy) Erich has WebID working on sample code and still looking to bring into VIVO and will contribute the module.  Upgraded to the latest Tomcat 7 and JDK 7 and Erich is working with both of those.
  • UCSF – (Eric) Getting ready to release the RDF version of Profiles, that is compatible with the VIVO ontology, this weekend.  Will be doing a panel presentation on OpenSocial at the upcoming AMIA conference.  Not sure whether anybody else has gone live with the OpenSocial additions to VIVO?  Alex – has discussed features like the slideshare gadget at some meetings and gotten positive feedback. Eric – reviewers for the panel liked the concept of bringing content in from industry.  Right now are storing the data in a relational model but now sees how to store RDF from working with the RDF version of Profiles – wondering what should be in RDF vs. relational – some content wants to be available as linked data, while other data might be more private and/or just transactional support.  Has there been any thinking about that on the development team?
    • Jim – so far all the discussion has involved in storing as RDF; Jon – VIVO user accounts are stored in RDB, a different data store from where the public data is stored (SDB)
    • Eric – Loki stores everything in RDB and exports on request as RDF for linked open data; Profiles is more of a hybrid, in part due to its transition from a purely relational product, but also perhaps for performance reasons and because it uses a .Net stack. Profiles has kept passwords in RDB, for example.
  • Washington University – (Kristi) Interested in discussions about the Implementation Fest
  • Weill – (Paul) Still working to a deadline of getting publications clean enough to be used as the basis for a separate faculty reporting exercise. Are making very specific Scopus queries for each faculty member rather than relying on general Harvester queries.
  • other --

Other updates or topics

  • Implementation Fest dates and agenda
    • still working on reserving spaces, which may be easier to schedule on Thursday or Friday at the Law School where the I-Fest was held last year
      • could then potentially have recreation like skiing on Saturday
    • may check with a few others spaces including LASP
    • hotel in walking distance from the Law School has a rate of $84/night
    • might be able to do a code sprint with a smaller group at a local startup; open source projects have sometimes done that
    • we'll look for good snow ...
  • Visualization sprint at Indiana
  • Upcoming presentation February 7 on Karma, a data integration tool used to map USC faculty data to VIVO
    • Powerpoint from 2012 VIVO Conference presentation by Pedro Szekely of the USC Information Sciences Institute

Notable development list traffic

  • Resolution of search indexing problem at Florida, and remaining questions about how to trap for the data issue involved (a form feed character pasted in from a PDF)
  • Exporting large models – a Jython script to call Jena with Harvester libraries, specifying a particular model, as developed by Ted at Brown
  • Modifying VIVO to allow authentication with WebID while still using modules in Apache httpd to support authentication
    • from Erich at Stony Brook: 
      When you try to log onto a site that accepts WebID, it will ask for your certificate.  That site will then look in the certificate for the URI of your foaf file then grab your foaf file and reference it to get your public key.  The server will then check the signature of your certificate with the public key to verify that you have the private key to the public key.  If they match, you are logged on, and, as a bonus, the server now knows basic information about you from your foaf file.  Also realize, there are no commercial certificate authorities involved.  If you suspect your private key has been compromised, re-key your foaf file and local certificate...you're done.  No running around to numerous sites.  Change the picture in your foaf file and sites accepting WebID can update from your updated foaf files, as well as, other information.  Cool eh? :-) 
  • VIVO 1.5.1 logging – how to log all edits made through the application and ignore all changes made to the inference graphs
  • Prefacing URIs with a non-numeric character (and an issue in VIVO to fix for 1.6)
  • Desire to combine multiple positions/titles for one employee when seen from the department's page
  • Jim: show me your code – "When I get your code, I'll 'diff' it against the original release code to see what you had to change, and how hard you had to work to make it happen. I'll summarize for the team, and we'll talk about ways to make it easier."

Call-in Information

Topic: VIVO weekly call

Date: Every Thursday, no end date

Time: 1:00 pm, Eastern Daylight Time (New York, GMT-04:00)

Meeting Number: 641 825 891

To join the online meeting

To view in other time zones or languages, please click the link: https://cornell.webex.com/cornell/globalcallin.php?serviceType=MC&ED=167096322&tollFree=1

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