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Calls are held every Thursday at 1 pm eastern time – convert to your time at http://www.thetimezoneconverter.com

 

Announcements

  • Ontology Working Group: next call is Thursday, May 1 15 at noon EDT/ 9 am PDT

    • Agenda to be determined -- look for an announcement

    • addressing persistent VIVO URIs and related issues

    • today’s call was focused on datasets and dataset ontologies, including options to engage with a W3C working group active in that area

    • The Health Care Life Sciences working group new draft standard for dataset description

    • We’re trying to think how VIVO can contribute

      • Submitting use cases on how we represent datasets in VIVO

        • Patrick West: DCAT ontology is what we’re using at RPI for the Deep Carbon project. Also have our own DCO ontology that we’d be happy to share. Integrating with CKAN for data flow and management.

      • Making people aware that VIVOs will have extensive contextual data around datasets

      Also discussion of how VIVO relates to ORCID iDs and the distinctions between an ORCID iD, a VIVO URI, and the set of statements about a person in a VIVO

  • Apps & Tools Working Group: next call is April 29 at 1 pm EDTMay 13th at 1pm EDT

    • April 29th call:

    • Find links to YouTube videos of all previous calls there

    • On April 15 call: Chris talked about FundRef and funding org data and stable URIs -- match with citizen(something).org and then visualize this

    • Alexandre Rademaker (IBM Brazil) and getting specialized data into RDF and then into VIVO -- video will be on YouTube soon

      • did his whole presentation with Emacs

    • Had a call with David Wood yesterday about Callimachus

      • he spoke at the VIVO conference last year

    • Apps and Tools workshop at the conference. Looking for participants to do demos -- looking for the best ways to create, use, visualize VIVO data and would love to have additional authors and help

  • VIVO Bootcamp at ELAG 2014 (June 10 at University of Bath, United Kingdom)

    • Violeta Ilik from Texas A&M will be there

    • the organizers (including Violeta) are looking for another representative from the VIVO community

Upcoming Activities 

  • First annual survey of VIVO sites

  • Next themed weekly call topic – April 24thMay 8th: VIVO End User Documentation – for supporting end users who will be editing in VIVO, whether individually or as proxy editors for a whole department (requested by University of Florida) -- can we make templated documentation where individual sites can put in tips or extra information? Rumor has it there’s a good document underway -- can this be shared on GitHub using GitHub pages? (Alex: GitHub being used by non-coders for local political campaigns and other collaborative writing projects)

    • Are there examples from other projects that do documentation better?

    • Format of themed calls could be a mix of presentations and working session

    • Note that we are seeking volunteer facilitators for each themed call -- let Alex, Paul, or Jon know directly or via the listserv(s)

    • May 22 -- will resume discussion of performance

Updates

  • Colorado Brown (Don)

    • focused on effort to roll out Orcid iD’s to our Faculty and PRA’s

      • sending a pre-registration email next week

      • collecting those over the summer and will be added to the Faculty Information System (FIS) database

      • inclined to wait for 1.6 since the ontology changed slightly in its representation of ORCID iDs with 1.6

    • looking at upgrading to VIVO 1.6 prior to ingesting Orcid iD’s into VIVO

      • big challenge will be to upgrade our harvest process. If there are any links to harvester code that has been converted to 1.6 I would like to see this to help bootstrap my process.

        • John Fereira <jaf30@cornell.edu> has volunteered to be the VIVO Harvester project maintainer

      • LASP -  ontology complete.

      • Other people seem to be using other tools -- have other organizations done the upgrade with other tools?

        • a mix -- the Harvester can be seen as a framework designed to have modular steps where the code used for each step may be Python just as well as VIVO

    • mention of BESSIG April 16 meeting with LASP VIVO team? Attendees from local labs including a USGS (?) group

      • LASP is thinking of putting up a SPARQL endpoint

  • Cornell (Jon, Jim, Brian, et al)

    • VIVO 1.6.1 released -- not a lot of feedback yet

    • We have a number of other projects that may use all or elements of VIVO

    • Working toward a 1.7 release, keeping it modest, to get on a schedule of two releases a year in accordance with discussions at the DuraSpace Sponsor Summit in DC in early March

      • May and November seem to be the logical times to not get involved in the summer vacation and winter holiday periods

      • looking for a code freeze the end of May

    • Question: will there be major ontology changes with 1.7?

      • Answer: No.  Just any bug fixes or improvements/clarifications that we receive feedback have been problems with 1.6

      • We do hope to produce the VIVO-ISF modules for 1.7 from the master ISF ontology in a more automated way, as is being worked on for eagle-i

  • Duke (Patrick)

    • Question about how to add book or artistic work reviews -- helpful reply from Michaeleen (using “featured in” predicate) -- starting to look into how to represent this as “review of” (BIBO) in VIVO, as well as in Elements

    • Upgrading Duke’s Ruby-based “Mapper” interop to Elements 4.6 API

    • Released core of “Mapper” and Duke ontology extensions on GitHub -- will send some info to list -- contact them with questions -- started this process at Hackathon

  • Florida (Chris)

    • Starting our 1.6 migration planning -- hoping to be migrated over before the Conference

      • Have a lot of data ingests built around the 1.5 ontology that need some re-working

    • Presented 2 posters (on figshare?) at American Medical Informatics Association (AMIA) Clinical Research Informatics Meeting.

      • dChecker (on github) - Sem Web data quality tool that is based on SPARQL and python.

      • Enterprise Data 2 RDF - PeopleSoft to UF VIVO RDF

        • have started to understand more of the test cases that have to check for in the ingest -- dual appointments, etc

    • Working on universal list of funding organizations (aka, NIH, Sloan, etc.) with URI’s and geospatial location data and IRS non profit data associated.

      • Wants to create a map showing the organizations funding active grants at UF

      • About 6,000 funding organizations have DOIs, and each of them has an EIN (employee identification number) from the IRS -- an important linking variable since is in FundRef also

    • Link to Mike’s Python tools on GitHub https://github.com/mconlon17 

    • Apps & Tools group has been recruiting presenters -- not necessarily just on finished products -- starting to have working discussion sessions

  • IBM Research and FGV (http://www.fgv.br) (Alexandre)

    • Interested in VIVO+CKAN (datasets and people, along the lines of what the Deep Carbon Observatory at RPI has done). IBM Research and City of Rio de Janeiro project can be a very interesting use case.

    • Involved in the implementation of VIVO at FGV (unfortunately, the VIVO instance is not yet public. it has 23k people and 72k research instances). Problems and questions about VIVO Performance! -- a good topic for a themed call in May

  • Memorial University (Max)

    • have been trying to find documentation on migrating from 1.5 to 1.6 -- to be able to migrate their 1.5-era Knowledge Mobilization Ontology to be compatible with 1.6

    • had a session on Friday at the I-Fest with Melissa and Brian -- but Max’s hard drive crashed subsequently so is looking for notes

    • Brian -- can re-send the ontology file that were working on in Protégé, and instructions about how to download the ISF again

    • Yaffle update -- have been communicating with University of New Brunswick (UNB) and CNA (College of North Atlantic ) about sharing the Yaffle code

      • Thinking about separate instances for now

      • Have a front end design and have been doing usability tests

      • Have a Drupal front end that has been hooked up to VIVO, using MilesW’s Drupal RDF extension (link?)

  • Smithsonian (Alvin)

    • Meeting with Institutional stakeholders/funders to address their specific needs

    • Identifying data sources for import and writing RFP for contractor to import and establish method for updating/reporting per user needs

    • Jon: DuraSpace VIVO project starting to work on list of Registered Service Providers -- please let any contractors interested in VIVO work about DuraSpace’s RSP directory.

  • Symplectic (Alex)

    • attended UCSF-hosted Profiles developer call last Friday

    • joined SHARE Technical Working Group (SHARE webpage) -- attended call this past Tuesday 

  • RPI (Patrick)

    • Upgraded from 1.5 to 1.6 and migrated to a new machine all in the same step.

    • Changed the URI of the DCO ontology. This caused an issue with the JENA index. Basically it was corrupt. So we would have to query using the old URI <http://deepcarbon.net/ontology/schema#projectAssociatedWith> but the result of the query would show the new URI <http://info.deepcarbon.net/schema#projectAssociatedWith>

      • Basically had to export all the RDF as n-triples (ingesting RDF/XML is broken in VIVO 1.6). Dropped the mysql datbase, created a new empty database, re-installed VIVO, started tomcat and let it fill in. The ingested the n-triples file. It’s still working (105,000 statements to work through)

    • Integration with CKAN broke with upgrade to 1.6. Fix to be installed later today

    • Still trying to work through the ontology changes in 1.6. The obo ontology is the focus of this. Since the predicate URIs are, um, not as self explanatory as you usually find.

    • Issue on Tuesday with MySQL creating massive temporary files (16GB each) given more complex SPARQL queries. This caused a file system full issue that had to be resolved by changing the MySQL configuration to point to a different temp directory.

    • Still having issues with Server Status … huh … actually, not seeing those issues at the moment. Perhaps it was tied to the index problem we were having.

    • Single Sign-on integration using shibboleth is completed in the test environment. We’re running tests now and hope to have in production by the end of the month.

    • We now have over 1000 individuals, and each one of those will be able to log in to VIVO and add/modify content given a certain set of permissions.

    • We’re starting to create some really, really cool visualizations using data from VIVO using our faceted browser, using Drupal, Google Maps and Google Earth, and using simple web pages.

    • Don in chat window: Hi Patrick - have you had a chance to sit on the VIVO ontology calls? We talked about the HCLSdataset w3c working group. Curious about your dcat extensions and this: http://htmlpreview.github.io/?https://github.com/joejimbo/HCLSDatasetDescriptions/blob/master/Overview.html 

  • UCSF (Eric is out of the office today)

  • Virginia Tech (Keith)

    • Implementing Symplectic now and about 4 weeks out from getting data ingested into VIVO -- starting with 1 or 2 departments but are planning to expand to the whole of Virginia Tech

  • Weill Cornell (Paul)

    • Performance

      • Still struggling with downtime and slower performance of larger profiles

      • Brian was able to get our code/data performing well on his instance

      • Goal #1: test Brian’s instance with our load-testing tool

      • Goal #2: try installing VIVO on a dedicated server

      • Goal #3: install VIVO on a dedicated VM at Cornell Ithaca for performance testing so that we have an instance instrumented for test data coming from Weill and other orgs

    • Where do sites store their official organizational hierarchy including official name, type, sub/super organizations, leadership, etc.?

      • Chris -- at UF, VIVO is now the only place where there is a complete organization hierarchy

      • Believe this is the case at Brown as well -- dealing with research institutes and programmers

Notable list traffic 

  • Steve)

    • The Brown site is live http://vivo.brown.edu and also redirects from http://research.brown.edu

    • Patrick: we used a special JDBC setting to control for special character garbage created by ingest

    • Did CVs come from another source? Were attached to the old site but also from other sources. Faculty members submitted CVs manually at the start of the process, but there was a legacy system for making them available and where new ones had sometimes been updated.

      • The CVs are held within the VIVO system itself

    • Next -- working on the publication layer and building that out -- a foundation to build more and more stuff on

    • Ted put together a Django app for editing as part of the umbrella management application -- Faculty will use the same system for editing/adding publications, updating the overview, adding pictures, etc.

      • Wired into 1.5 for the moment but will use web services in VIVO 1.6 -- communicating with SPARQL endpoints for now using add and remove requests

    • Thoughts of migrating to 1.6? Also on the docket -- would simplify the process of updating from the Django interface

  • Cornell (Jon, Jim, Tim, Brian, Huda)

    • We start the migration to 1.6 on May 8, Slope Day -- estimating one week to complete migration and plan to disable editing during that time

    • Has been using the 3-tier build along with Florida and Colorado, where local changes are added on top of VItro and VIVO  

  • Duke (Patrick, Sheri, Richard)

    • Working on putting together plan for your next phase of work. This includes adding the following: non-faculty opt-in, collecting additional professional activity data, report by year and a news feed section.

      • The News site will include references to Scholars

    • Big task is to support reporting data out of the system

    • Adding artistic works to our widgets tool

  • Florida (Chris)

    • Ingesting Grants Data and Continue to work on Sponsors data for sharing related to FundRef.org

    • update to dChecker software. Now adds links to bad data in the email report. Code release soon on GitHub.

      • Figure: Image of Data Quality Report

      • Screen Shot 2014-05-01 at 1.23.03 PM.pngImage Added

  • Memorial University (Max Hu)

    • We just had an internal site running (Drupal), the old Yaffle accounts have been migrated. It’s available for testing and hooking up to VIVO.

    • The graphic design (Ver.02) will be  completed by Friday (May 2rd.)

    • Continue working on the KMyaffle ontology to meeting vivo 1.6 ISF requirements.

    • Prepare data to ingest to VIVO 1.6

  • Scripps (Michaeleen)

    • no update

    • in middle of annual budget process so will fill out VIVO survey after budget deadline

    • kudos to Brown

  • Smithsonian (Alvin)

    • Have a pilot VIVO set up as a proof of concept -- upgraded to 1.6.1 this week and has suggested edits which he’s entered on the wiki

    • Met earlier in the week with people from EPA and IFPRI (Cristina Perez) on practical examples of getting data in.

    • Will be looking at ingest options and will share questions with the list

  • Stony Brook (Tammy)

    • Also working on uploading grants data -- interested in Chris’s work on shareable sponsor URIs at UF

      • Chris wants ontology advice on how to represent the data

      • a DOI for each of 6,000 sponsors in the US, but not shared as RDF on the Internet with URIs

      • idea is to have a single URI referencing the Sloan Foundation across multiple VIVOs

    • Needed to remove data, so pulled it out (confirmed by logs) but all appeared to be there in SPARQL queries

      • Does add/remove go to a scratchpad model?

      • Brian: any of the asserted triples that you’re directly deleting should disappear from KB-2, but not the inferred statements. Those get removed by the inferencer are put in a scratch pad that should be deleted after the processing completes; if the inferencer doesn’t complete it’s removal, there may be a scratch model still left hanging around

      • Tammy -- would a problem in the course of retraction abort removal of the remaining RDF included in the retraction?

  • Symplectic (Alex)

  • RPI (Patrick)

    • An engagement team for the DCO project has taken a look at the interface in general and has several questions and concerns -- can we have a dialog?

      • Sure -- let’s have a themed call to discuss, or can discuss offline

      • 1. Project displaying issue on person’s page - when adding people to projects through the “other research activities” property on person’s page, the project is shown as “missing activity”, and this “missing activity” node is not associated with the project. Go to http://info.deepcarbon.net/vivo/display/da5b50ce3-2877-4e9f-9ba4-f645d811bf43 and click on the Research tab.

        • Tim -- has been in correspondence with Han about this -- relates to the most specific type

      • 2. There is no custom form page for adding people to projects from a project’s page. That’s why we had to do the other way around and ran into issue #1. Any progress on this?

      • 3. Two weeks in a row now we’ve had to restart tomcat due to out of memory issues. We’ve upped the memory numerous times, and there should be enough memory. Looking at the vivo log file we’re getting GRIDLOCK issues. Once the gridlock issue happens we run out of memory. https://scm.escience.rpi.edu/trac/ticket/2130 

        • Brian -- the out of memory error is related to the permgen setting, not the heap -- did you update both heap and permgen

        • Patrick -- updated both; not a lot before the error in the log that looks like a problem

        • Brian -- let’s pursue offline

      • 4. Our Publications page, which used to show information, now simply displays the page that says “This page is not yet configured. Implement a link to configure this page if the user has permission.” http://info.deepcarbon.net/vivo/publications . It is working in 1.5.

    • Our plan is that hundreds of users will be able to create, edit, delete instance data from our VIVO site. We’re not ingesting data from anywhere and users simply view the content, users will actually be able to create content. And we’ll be creating various policies for different groups of users. Are there any sites that currently do this?

    • The Engagement Team of Deep Carbon Observatory is requesting a usability study for VIVO. They have concerns with what they’ve seen so far (related to the previous bullet).

    • Patrick: to what extent do sites enable self-editing?

    • Jon/Chris: both our sites allow self-editing

    • Patrick/Jon: let’s have a themed call on usability

  • UCSF (Eric)

    • Just last week released a new version of Profiles code with the latest OpenSocial engine -- seems to be fast

      • Have a gadget to pull in grants that somebody else has adopted

    • Still scraping together data about co-authors, pulling in part from VIVOs

      • with Fuseki, speed is good but then runs off a cliff at a certain amount of data -- is it likely to need more memory?

    • Will be working with Symplectic to pull in publications from sources other than PubMed, including Scopus (Paul -- talk to Weill about their experience and scripts)

      • might try the Harvesters built for VIVO

  • Virginia Tech (Julie)

    • Keith right in the middle of Symplectic Elements implementation -- installation and configuration and connecting to data sources that require institutional subscriptions

      • Anticipate working with Symplectic’s VIVO connector about the middle of May

    • Interested in other institutions’ experience with user engagement

      • Committees of researchers to make decisions about ontology extensions, for example? -- Duke has a set of power users who help with training but also provide feedback from users

      • Would this be a good topic for a themed call?

  • Weill Cornell (Paul)

Notable list traffic 

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

 

Call-in Information

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