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Please add additional agenda items or updates --

Updates

  • Stony Brook – upgrading VIVO to jdk1.7 – has it working on the dev site with but connection pooling is not working with 1.7 the SUNY REACH site. Needs this for his WebID development. We should then change the documentation from saying it won't work with 1.7 to saying it will.
  • Florida – Chris is focusing on CTSAconnect and trying to add clinical expertise data into VIVO using a harmonized version of the VIVO and eagle-i ontologies, supplemented by clinical information such as number of patients they see with different diagnoses, the procedure codes they have used, and board certifications – moving towards tag clouds showing clinical expertise.
  • Weill - Thanks for all the help from Cornell Ithaca on troubleshooting the performance issue. Demoing a product call new relic (question) – trying to improve long listings of publications, and putting up a copy of Cornell VIVO so can compare rendering times on Weill and Ithaca servers using the same code and data.  Brian sent Eliza a note about a command line tool called SDBprint that will write out the SQL produced from translation of a SPARQL query, as a way to debug what appear to be inefficient queries.
  • UCSF – 
  • Duke – upgrading VIVO from 1.4 to 1.5 and want to export publications en masse and re-load them, vs. re-importing them from Symplectic Elements, which can take as long as a week.  They are also finding issues around which publications are marked to be visible in VIVO – trying to work out a way to flow through this kind of preference from Elements down to VIVO as a downstream.  Some colleges such as Medicine only want representative publications to come through.
  • SUNY Buffalo – Doing a project that involves a student instance of VIVO as an e-Portfolio system connected with the institutional repository (DSpace at Buffalo and also SUNY-wide) and expose them to open access patterns of scholarship. Purchasing a new server and wanting to use jdk1.7 since support for 1.6 is going away. Looking to recruit students for a pilot that would use the SUNY-wide DSpace and back-feed individual campus institutional repositories.  Alex: the Library at Colorado is looking at an open repository.
  • Scripps – Planning for a contract project with Stella to bring in grants from NIH Reporter and possibly from NSF
  • Cornell – Jim has been working with the build script and data getters and multiple language support. Tim will be introducing horizontal tabs to control the display of each property group, based on user feedback on the length of the scrolling with the more vertical pages in the current VIVO. Had tried to use collapsible property groups, but are finding the horizontal tabs preferable, especially for entities with very little data. Will be factoring this as an optional template to include in the individual person page template for the next release.
    • Huda – working on additional search facets for Datastar, and has everything but the type and time facets done – getting equivalent classes on the types facet; time is tricky because there can be either single dates or time intervals.
  • Colorado – working on concatenations of lists in cases where people have multiple positions in an organization or multiple degrees from one organization and don't want them showing up several times on the organization page.  Trying to figure out how the file download mechanism works so people could do a .csv file of contacts of people they want to list on a grant proposal or for similar purposes. It's the faculty reporting time window at both the Boulder and Colorado Springs campuses, so are trying to do frequent updates.  Presented VIVO to a campus interest group including some research centers (university and federal) in the area, including a person from NASA; discussion focused on general semantic web questions as well such as strict or loose ontologies, the practicality of using sparql, etc. Alex encourages others to find others on campus who may be interested in using VIVO/Vitro technologies, even if for other purposes including research.
    • Alex is also exploring Alchemy (http://www.alchemyapi.com), a local company that will provide free licenses for their search engine (up to a maximum number of queries per day)
  • NYU – 
  • Johns Hopkins --
  • Indiana --
  • Brown – working on cleaning up data produced by the vendor from faculty CVs; trying a data feed from CrossRef; working on custom forms and are trying out the 3-tiered build for local changes. Just getting started but have been able to track down the forms.  Interested in expanding to the medical school in the 2nd phase of the project, and would be interested in certifications and potentially clinical data as well.
  • other --

Other updates or topics

  • Implementation Fest dates and tentative agenda
    • Tentative dates are April 15-16th OR April 22-23, both being Monday-Tuesday – hoping to finalize by early next week
    • One thought was to have a balance between content oriented to early-stage evaluators and helping to gel and support existing users. Are leaning toward inviting new adopters but including activities focused on addressing challenges on the technical and ontology side as well.
    • This might lead to a schedule with intro presentations the morning of the first day leading into hands-on session working on documentation
    • There could also be a third day focusing on a development project such as internationalization where a group of people might be able to make significant headway together in one day
    • Who might come
      • Brown – like the working session idea, and expect to be able send 1-3 people
      • UF – would be helpful to address remaining gaps; Nicholas Rejack as the official VIVO data steward would be a good person to come
      • Weill – willing to share feedback on the requirements and data cleanup, completeness, and performance
      • Buffalo – would like to have some intro sessions to get people fired up, but also people interested in real nuts and bolts discussions
    • Could also be a way for people from different sites to get together and develop workshop materials for the conference
  • Simon Porter is experimenting with Joseki over Oracle as a semantic triple store at Melbourne
  • Internationalization – Jim has worked out the framework and recommends a pattern that has been tested in a couple of proofs of concept, but extracting the English out of all the templates and in some cases the controllers as well is a fair amount of work.
    • Can we put out out the template and request others to help with one template/controller pair at a time?
    • Jim has checked in the examples completed so far and is creating wiki pages to document the recommended approach.
    • This might lend itself to be a collective distributed path, including participation from native speakers of other languages

Notable development list traffic

  • When it's not possible to access a source database directly, what VIVO tool supports harvesting data via that source's API?
  • Mainimage inverse extension (to point from the image back to the person) – the inverse relationship would be helpful in finding the way from an image to the person as part of batch image uploading
  • Rebuilding the search index from a crontab after adding data (presumably not interactively but via ingest)
  • Change in deploy.properties for developers (developer.defeatFreemarkerCache=true) - Jim did this to make an undocumented developer-focused feature more visible when making changes to templates and not wanting to have to restart Tomcat – becomes a 1-minute default cache for templates so they get loaded faster
  • A new, generalized approach that will allow you to define a DataGetter and associate it with the Freemarker template of your choice – triggered by a request to put a global variable into the footer of every VIVO page; this can be done through configuration with only having to make changes in the templates, not the Java code.
    • An example where people might like to cherry-pick the commits in the development branch
    • Colorado keeps a test instance with the current dev branch and will deploy to production with the next release
  • The recent update of Solr from 3.1 to 3.6 in the dev branch appears to require replacing the Solr index, not just a rebuild – "I couldn't rebuild the index, because Solr wasn't responding to commands. However, I did fix it by deleting my [vitro-home]/solr/data directory, restarting VIVO, and then rebuilding the search index
    • This same issue has been experienced at Colorado as well as Cornell
    • The Solr upgrade was about 5 different point releases
    • We might something in the build that would remove the files automatically with the upgrade if still running Solr 3.1 – a bit scary, but should at least be in the

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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