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View and edit this page permanently at https://wiki.duraspace.org/x/JfcQAg, or use the temporal Google Doc for collaborative note taking during the call.
DuraSpace is seeking a dynamic and entrepreneurial Project Director for the open source VIVO project (www.vivoweb.org), a world-wide community focused on creating software tools, ontologies, and services. The VIVO Project Director will have the opportunity to play a major role in a collaborative movement that will shape the future of research.
See full posting – applications are scheduled to close on or near October 23rd. Note that there is no requirement to be a U.S. citizen.
No release candidate has been created yet – progress each day.
Notes from Sept. 24 meeting recorded as this webcast showing a Python data checker for VIVO developed at the University of Florida.
Next meeting on Tuesday (October 8) at 1pm Eastern – Stephen Williams from the University of Colorado will host. Stephen has posted an agenda to the vivo-dev-all mailing list.
Paul -- great that you are recording the sessions and posting them to YouTube.
Brown (Ted)
finalizing import of data from existing research profiles
hope to have a public release date set soon
created a Vagrant bootstrap script for VIVO. Will install VIVO on an Ubuntu server image.
Colorado (Alex & Stephen) In the middle of Elements curation and behind on listserv responses
Working on Elements publications curation for 2013
Stephen will be catching up on VIVO emails after recovery from flooding
Cornell (Jon, Jim, et al.)
1.6, 1.6, 1.6, 1.6, 1.6…
Duke (Richard)
reloading grants data from our source system. we put grants into their own graph and then wipe/reload that during a full grant load process. most days we just do an incremental load.
search re-indexing process taking a really long time >5h, sometimes ~1.5h -- doesn’t seem to correspond to the number of new triples -- looking forward to incremental re-index
UF had an issue with bad characters taking a long time to fail
new version of Solr in latest VIVO repo
Jon -- any correlation to inferencing? Richard indicated no, not running inferencer as they ingest all triples to not require it -- using a Ruby script that they could possibly extract and share
Florida (Chris)
Had a second successful run of people ingest from people soft
Developing a weekly process
Deploying ingest from git repository
Working on visualizations with d3js (http://d3js.org/) and JSON -- which can be generated from within VIVO -- Javascript visualizations seem fast! Probably demo in last October Tools call.
NYU (Yin)
talking to production group about graduation project -- been working as a dev/research project
been using an intermediate data format for getting data into VIVO, but prod group wants to connect VIVO (?) to enterprise data warehouse -- are there best practices for this? Jon clarified if they want a realtime connect vs ETL -- suggested that the closer the transformation gets to RDF, the easier it is to bring it into VIVO -- Ted happy with Python and RDFlib, UF been using Python and starting to use RDFlib
https://github.com/ufvivotech/ufDataQualityImprovement/tree/master/vivotools
question about not using front end, rather back end RDF via XML or URLs, and Solr search?
Also suggested VIVO hardware requirements? Chris suggest AWS specs on wiki.
AWS Specs for UFL VIVO Hosts:
X-Large-Memory
17.1GB (ram)
6.5 EC2 (cores)
420GB
64-bit moderate
m2.xlarge
2X-Large-Memory
34.2GB (ram)
13 EC2 (cores)
850GB
64-bit high
m2.2xlarge
Scripps (Michaeleen)
Stella has a working version of the grants ingest from NIH Reporter. Ingest program written for 1.5.1. Not sure if she should share for that reason?... Jon: it would be helpful to post regardless!
Stella is also working on authorship representation.
Representing patents
Stony Brook (Tammy)
Using JSON to integrate at data interface between Java and Python dev efforts
UCSF (Eric)
Bringing in grants from NIH Exporter -- Jon mentioned concern of annual updates to long running (25y) NIH grants -- Stella’s looked into how to best represent these in VIVO ontology
Author registry idea; would be compatible with ORCID and include ORCID ID -- aim for lower policy hurdles
Anyone look at Project Honeypot tools to keep bad traffic away from site? HTTP Blacklist catch around 10k HTTP requests per day. UF also blocked access to CPU heavy pages like the visualizations, for web spiders that don’t honor robots.txt.
Weill Cornell (Paul)
reconciling self-reported publication data with data from VIVO instance -- very few pubs rejected, many were duplicates already in VIVO -- Ted offered some good advice
template updates
See the vivo-dev-all archive and vivo-imp-issues archive for complete email threads
1. PubMed Harvester doesn't like particular records (Lynda, Andy)
The Harvester is essentially unusable with PubMedFetch, due to bugs in code from NIH. Some records in PubMed have data which is not correctly handled by the NIH code. It's possible to work around these bugs by using PubMedHTTPFetch instead of PubMedFetch. However, you need to URL-encode your search request if using the HTTP version.
2. ExternalAuthId and named graphs – fixed by Jim and tested by Ted VIVO-305 - Matching property should work if the triple is in a named graph (not just kb-2) - RESOLVED
3. VIVO and TDB (Michel, Ted, JohnF) – have VIVO working with a TDB database, instead of SDB (so a relational database back end store is no longer needed)
Ted: Fuseki 1.0 was released last week and I was able to get that to connect to an instance of VIVO 1.5 using the same endpoints you specified:
VitroConnection.DataSource.endpointURI = http://localhost:3030/tdb/sparql
VitroConnection.DataSource.updateEndpointURI =http://localhost:3030/tdb/update
Michel: I now want to write a java program with Jena, where I insert data into the TDB. I want to use the Jena api, with model.createResource and resource.addProperty and so on.
Ted: I use Python and RDFLib [1] for VIVO data loading. RDFLib, as of version 4, supports SPARQL 1.1 so you could use that to write directly to Fuseki
As for learning about the VIVO ontology, one technique that I've heard recommended and find useful is to use the VIVO admin to create resources that you want to load (FacultyMember, Book, etc) and then inspect the RDF that is generated to see how the data is modeled. VIVO will serve Turtle for a resource (e.g. n1234) by pointing your browser at http://localhost:8080/vivo/rdf/n1234/n1234.ttl.
JohnF: Specifically, take a look at the org.vivoweb.harvester.utilrepo.JenaConnect class. It's an abstract class that is extended by SDBJenaConnect and TDBJenaConnect. It should give you a good idea what you'll need to do to insert RDF into VIVO using the Jena API.
4. Finding grants via investigator name (Michaeleen) – having an investigator relationship with a grant is not sufficient to make the grant show up in the results for a search on person name.
5. Uploading image when editing a property of an individual (Yu, Huda, JohnE, PatrickW, BrianC)
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