2014-04-03 Implementation and Development Call

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

• 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