Implementation and Development Call 20140403

Announcements

• Ontology Working Group: next call is Thursday, April 17 at noon EST/ 9 am PST – note proposed new time

• addressing persistent VIVO URIs and related issues

• next call will be focused on datasets and dataset ontologies, including options to engage with a W3C working group active in that area

• The next Apps & Tools call is April 15

• A great call with Violete Ilik from Texas A&M demonstrating  -- she has recorded special specific YouTube videos on how to ingest data into VIVO

• Find links to YouTube videos of all previous calls there

• Alex Rademacher (IBM Brazil) and getting specialized data into RDF and then into VIVO

• 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

• 2014 VIVO Conference Call for Paper/Poster/Panel Proposals is open – deadline extended to Friday, April 11

Upcoming Activities 

• First annual survey of VIVO sites

• See proposed project wiki page 

• Will be circulating to working group leads for review and will then put it out more widely

• designed to be one survey per site, that can be passed from one team member to another

• We are thinking of using this call next week as time for facilitated survey submission from participating sites  

Updates

• Brown (Steve) -- working on getting more pieces needed for release, and then on adding additional publications in prep for release in early May

• will let us know when we can take a look at it

• Cornell (Jim, Huda, Brian, Jon)

• Release 1.6.1 release candidate 3 -- finding some small bugs but we each have other projects -- looking to get this thing tested and out the door

• At this point we don’t anticipate another bug release before 1.7 -- sometimes difficult to determine when to defer the release for new bugs that crop up

• The current code is always in the 1.6 maintenance branch on GitHub

• Duke (Patrick)

• Initial feedback after rolling out to our A&S school.  Most of the feedback Julia and the provost office has been handling. We are going to be making a couple of tweaks. We have also gotten feedback on potential enhancements/changes to the search results. Still collecting those before making changes.

• Some faculty didn’t see the “more” button at the bottom of their publications

• Law School would like to see changes in some of the search results, to have only a named person to show up

• Julia: “Rollout and fallout”

• updating to 4.6 version of Elements API

• released our ontology extensions including artistic works (https://github.com/OIT-ADS-Web/duke_vivo_ontologies) and the vivo_mapper we use for our data ingests on Github (https://github.com/OIT-ADS-Web/vivo_mapper). We will email the group with more details.

• Florida

• Sending 3 folks out to American Medical Informatics Association Clinical Research Informatics/Translational Biomedical Informatics conference to present 2 posters on VIVO work.

• Added 6000 sponsors to our VIVO (NIH, NSF, etc…) and manually cleaned them up -- have categorized as companies, governmental organizations, etc.

• this might be useful to other people

• have also cleaned up the list of cities in the US

• See them here “Funding Orgs” https://vivostagingweb.vivo.ufl.edu/individuallist?vclassId=http%3A%2F%2Fvivoweb.org%2Fontology%2Fcore%23FundingOrganization 

• closed almost 280 “Data Quality” issues on our github DQ site: https://github.com/ufvivotech/ufDataQualityImprovement/issues?state=open 

• has really helped to have a directed effort towards improving data quality

• Adding building numbers & locations, ? Need help/advice with the best way to store LAT and LONG in VIVO. aka ontology+label examples?

• where would you put that? have people’s phone numbers and have the location in buildings based on network jacks

• Eric -- Profiles has latitude and longitude

• added a property so anything could have it

• may not be ontologically the best thing to do

• Do it through the VCard?

• Brian -- DBPedia uses the W3C WGS84 geo ontology that has properties for latitude and longitude http://www.w3.org/2003/01/geo/ 

• as long as those are pretty generic properties in terms of domain restrictions, those are likely the best bet

• Memorial University (John and Max)

• Are interested in following the discussion on tagging latitude and longitude to tag projects and other work that academics are doing, so they can be put on a map at some point

• testing VAGRANT on an Ubuntu install

• digging ourselves out -- summer is August 1 to August 20 -- a 50 centimeter snowfall in spring is now called a sprinter

• UCSF (Eric)

• Diving back into the cross-linking project and hopes to talk about at the project

• Crawling a bunch of data and switching over to a Fuseki back end from a relational one. Crawling about 20 institutions and putting in coordinates based on the institution, but Profiles has coordinates on the individuals

• Working with JSON-LD -- the crosslinks tool spits that out for the co-authors, and JSON-LD has advantages. If work with the JSON-LD raw, is not easy to work with, but if goes through a parser there are built-in functions that will do things like pull out all the people to make it easier to work with, and becomes a smaller data packet to send over the wire. Will have it live on UCSF Profiles soon -- in one case have found co-authors at over 20 different institutions

• Virginia Tech (Julie and Keith)

• Learning ontologies and SPARQL

• Elements project is moving forward and have first call with the Symplectic team tomorrow to plan implementation

• have Web of Science but not Scopus

• we have Digital Measures -- will be migrating data from that application to Elements

• had one preliminary meeting with local people on importing data from Banner

• Cornell has a pathway from Digital Measures (Activity Insight) to VIVO and from VIVO to Elements, and will be developing a pathway from Elements to Activity Insight as well as to the VIVO 1.6 ontology

• Weill Cornell (Paul)

• VIVO Dashboard (did I share this before?)

• code (authored by Miles Worthington): https://github.com/paulalbert1/vivodashboard 

• web interface: http://dev-vivo-dashboard.gotpantheon.com/ 

• hoping to support an arbitrary co-author network, if putting together a proposal or workshop

• we *think* we (Eliza) have succeeded in backporting cache awareness to 1.5.2 and committed the changes to the source; looking forward to promoting it to production before even before moving to 1.6???

• our performance test results in case anyone is curious - https://docs.google.com/spreadsheets/d/129EUW-ac46ok69g3UZHdfmDtvEMYGEyheSLM-kmYj5s/edit?usp=drive_web 

• the Ithaca team is loading Weill data, images, and code to try to reproduce timings on a server here – timings will be different absolutely but also may vary relatively

• it will be then more possible for the development team to instrument the application to detect where time is being lost as well as experiment with changes that could improve performance, especially on very large pages

• Harvester question

• sent an email on a Saturday -- several ways to use the Harvester to bring in data, with one being to directly match against records in VIVO and another to indirectly use a third source

• what is the prevailing practice?

• Patrick -- don’t use the Harvester but do match directly against the triples the data

• Cornell -- option B

• Florida does Amazon RDS that does real-time syncing, but could be done with MySQL

• database with 21 million triples is just 4 Gb so not necessarily large in scope in comparison

• and the rate of change in transaction input is not that high -- more like dozens per

• John Fereira will be the maintainer for the Harvester, and Ted and Chris Barnes have offered to facilitate the process; Stephen Williams is still available to answer questions and suggest changes

Notable list traffic

• 1.6.1 bug fix release candidate 3 being prepared for testing -- and more of the tests are being automated

• Where is the documentation on using the search indexer to only index certain URLs -- a new wiki page created

• Ontology questions

• Thanks for wiki updates by Patrick West from the Deep Carbon Initiative

• Still looking for someone with Active Directory experience for

• Should be able to issue LDAP queries against Active Directory as an LDAP source to get back username, affiliation

• Might be built into IIS 7 -- could do auth queries based on code built into the library

• http://www.iis.net/configreference/system.webserver/security/authentication/windowsauthentication 

• and probably have to write some .Net to pass back a token to Tomcat as a server variable in the session  for use in VIVO

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

• Funny Tweet of the day:  The right and wrong way to build incrementally. http://t.co/Tm7JbjEycq

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Call-in Information