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Calls are held every Thursday at 1 pm eastern time (GMT-5) – convert to your time at http://www.thetimezoneconverter.com – and note that the U.S. is already on daylight savings time

These calls now use WebEx and have no limit on the number of attendees – see the "Call-in Information" at the bottom of this page.

Updates

  • Brown – (Ted) Wanting to display results by a "truncation" of the label. How have others done it? One idea: add a new data property to the individual and to the search index.
  • Colorado – (Alex) Preparing for the Implementation fest. Stephen still working on using the Harvester instead of legacy scripts for ingest.
  • Cornell – (Jim) Working on multi-site search, chatting with Arve about caching. (BrianL) Working on the application configuration ontology. Related to the CTSA project, trying to simplify the ontology where classes or properties have been created strictly for display distinctions.
  • Duke – (Richard) Going live with School of Medicine in early May. Doing the rollout with "stubbed" profiles for faculty. [Threats of impending SPARQL questions to the list]
  • Florida – 
  • Indiana – Having some success finding out why the display doesn't happen. Concurrency issue. It's difficult to isolate in the code.
  • Johns Hopkins – 
  • Memorial University – 
  • NYU – 
  • Scripps – (Michaeleen)
    • Imported all Grants for Scripps Research Institute and Scripps Florida from years 2008 through 2013.  Still need to decide how to handle multiple occurrences of the same project number (different suffixes) and whether to include subprojects. Would appreciate guidance on how to represent which campus (Scripps Research Institute or Scripps Florida) received the grant. Currently using local extension properties tsri:receivedGrant/tsri:grantRecipient. We don't think Reporter has data about what department administers the grant but it might be useful to add in order to see grant productivity by department.
    • Bug with ‘manage authors’ dialog incorrectly reordering authors (this operation happens just as a result of going to that page - can't cancel out). When we went to edit the authorship for articles having more than 100 authors using ‘manage authors’ the application would spontaneously reorder the entire author list and reordering by hand was unmanageable. Problem is in edu.cornell.mannlib.vitro.webapp.beans.DataPropertyComparator failing to find the datatype of the property (vivo:authorRank). Have temporary local patch on Scripps.
    • Enhanced publications list view in place: author names as they appeared in the citation and in the order in which they appeared in the citation, limited to first 12 with et al. at the end if more than 12, followed by article title, followed by journal, followed by volume and page, followed by doi (if present) as link to publisher's page with full-text options, and pmid (if present) as link to PubMed record. For an example, scroll to Publications at http://vivo.scripps.edu/individual/CravattBenjamin
    • For rdfs:labels with certain characters (double quotes, html tags), editing the label causes the label either to be not shown at all in the editing box or not shown in its entirety. When editing the label for an article such as [ “Chiral amnesia” as a driving force for sold-phase homochirality / http://vivo.scripps.edu/individual/endnote19713 ], we can re-type what we want to appear but the existing text isn’t available to modify (i.e., it doesn’t display on the edit screen). For a doi with a </br > at the end in the underlying data (must have been entered with a cut-and-paste) the resulting doi link did not work, but the edit screen (even Edit HTML) just displayed the doi number and not the extraneous hypertext tag.
    • Handling reprints of articles: Although this is question best addressed on the Ontology call, I wonder if anyone can provide a brief answer for how to handle original research articles that are reprinted in another journal. Many faculty include citations to these reprints on their CVs as some indication of the significance of the original article. An example title is at http://dx.doi.org/10.1016/j.tet.2008.03.086 : Reprint of “Allene-alkyne cross-coupling for stereoselective synthesis of substituted 1,4-dienes and cross-conjugated trienes” [Original article appeared in Tetrahedron in April 2008 and the reprint was published in the July 2008 issue as “dedicated to Professor John Hartwig on his receipt of the Tetrahedron Prize”.]. Each publication has a distinct DOI and at least different issue and page numbers, but sometimes the same publication year and volume.
  • Stony Brook – (Erich) Getting access to two institutional systems. May soon go public with StonyBrook VIVO, in addition to existing Reach implementation. Developing an app to monitor RDF requests, even the failed ones. Will be open source soon. Getting close with WebID integration with VIVO.
  • SUNY Buffalo – (Mark) Identified the search index problem as stemming from a Tomcat bug. How to back up a VIVO system?
  • UCLA – Nobody on the call, but they are coming to the IFest workshop.
  • UCSF – (Eric) Working on their Profiles implementation and OpenSocial items for that. Attended AMEA(question) - hoping to preset some of that at the VIVO conference.
  • WashU –  
  • Weill Cornell – We'd like to write some documentation on configuring the VIVO database for special characters. Anyone knows of a specific page to edit this? 

Upcoming events

2013 Implementation Fest – April 25-26 at CU Boulder

  • community hands-on development day is planned as an optional additional activity on Saturday the 27th, e.g. working on internationalization
    • We have interest from Costa Rica, Mexico, and France in principle – there's one room choice option that has H.323 videoconferencing
    • Please sign up as an attendee (also can register as a remote attendee) and indicate here whether you plan to be involved in the development day activity
  • 2013 VIVO Implementation Fest page has information on transportation and hotels
  • Registration page – note that there is no registration fee for the workshop
  • A DRAFT schedule is available for preview on sched.org (including for mobile view) and as a Google Doc

2013 VIVO Conference Call for Submissions released

Security issue 

Update from Jim Blake on the issue discovered by Arve Solland from Griffith last week. Also: what Griffith is doing with page-caching.

Are you using Java 7 yet?

 (Jim) It's time. It's past time. I just modified the build script to require Java 7. So if you are working from the "develop" branch, get out there and start using diamond notations, try-with-resources, multi-catch clauses, and all of that fine stuff. Go wild.

Notable implementation and development list traffic


New
  • (Rohan) Query efficiency in Map of Science visualization – getPublicationsWithJournalForAllSubOrganizations
    • (Tim) The Map Of Science visualization does not include any date-time information for the user, but the query retrieves the publication date.  Are the publication dates being used in the background somehow -- for example, do you only map publications from the last 10 years? If you're not using the date, there's no need to get the date information. If the publication date is being used somehow, you might want to consider removing the optional clause, which makes the query more inefficient.  The query won't return publications that have no date, but you may not be mapping those anyway. Similarly, do you need to get the journal uri and label inside an optional clause?  Since publications are mapped based on the journal name, there doesn't seem to be a reason to fetch those which haven't been linked to a journal since they can't be mapped. One other question: are you using SPARQL constructs to build a model and querying against that? Or are you querying directly against the database?
  • (Mark) Bug in Tomcat 7 for Ubuntu – source of the "There is no <whatever> content in your VIVO" problem from last week
    • (Jim) Re-installing an old Tomcat should fix your current problem.  Or you might look for a newer version of Tomcat. Such an egregious bug will surely be fixed quickly. I'm glad that this turns out to not be a bug in VIVO, per se. However, it's obvious that we need to make it easier to isolate and diagnose this sort of problem. As a first step, I have started a wiki page with suggestions for troubleshooting this sort of issue.
Still open
  • (Kelly) Harvester duplicates and speed issues for pulling from PubMed

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

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