Calls are held every Thursday at 1 pm eastern time – convert to your time at http://www.thetimezoneconverter.com
Ontology Working Group: next call is Thursday, May 15 at noon EDT
Agenda to be determined -- look for an announcement
Apps & Tools Working Group: next call is May 13th at 1pm EDT
April 29th call: 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
Violeta Ilik from Texas A&M will be there
- the organizers (including Violeta) are looking for another representative from the VIVO community
First annual survey of VIVO sites
see Paul's email to the lists: What does your site care about? Participate in the 2014 VIVO Annual Survey
The survey is live: https://www.formstack.com/forms/?1704676-gIMWlsYzom
Next themed weekly call topic – May 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
Patrick: we used a special JDBC setting to control for special character garbage created by ingest
in deploy.properties, add some configuration:
VitroConnection.DataSource.url = jdbc:mysql://localhost/dev_vivo?useUnicode=true&characterEncoding=utf-8
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
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
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
in middle of annual budget process so will fill out VIVO survey after budget deadline
kudos to Brown
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?
Information, Interaction, and Influence -- Digital Science workshop organized by Amy Brand (VP Academic & Research Relations) at University of Chicago on May 19-20: “Research Information Technologies and their Role in Advancing Science”
Free to attend for academics. Invited speakers include friends of VIVO: Kristi Holmes (Northwestern), Bill Barnett (Indiana), Simon Porter (Melbourne), Griffin Weber (Harvard), Leslie Yuan (UCSF), Rebecca Bryant (ORCID), Daniel Hook (Digital Science), Euan Adie (Altmetric)
More info at http://www.digital-science.com/events/information-interaction-and-influence -- link to Eventbrite registration
the ORCID Outreach Meeting is May 21 and 22, immediately following – https://orcid.org/content/orcid-outreach-meeting-and-codefest-may-2014
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
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)
Performance? Gave Brian and Jim the Weill code and data to install on a Mac and a VM in Ithaca; Jim has been helping install VIVO on a new VM at Weill and are seeing better performance with that installation. Currently looking at fine tuning and documenting settings in detail.
A Google Doc for the emerging performance documentation (based on last week’s themed call) while it’s still in flux -- will then go on the wiki
Wiki home for performance guide will be https://wiki.duraspace.org/display/VIVO/Performance+Troubleshooting+Guide
Temporal doc linked from there for collab edit https://docs.google.com/a/symplectic.co.uk/document/d/1ylp9HEzJiBsBP6vx1vd-Irf8o3Ff-5vDhytOVTI5_Ho/edit#heading=h.vdtjwwvnjdn7
Notable list traffic
- VIVO Harvester, Pubmed Sample Issue
- Cache map of science
- OpenVis Conf in Boston this week
- Harvester 1.5 Code
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