VIVO v1.6 Release Notes
What is this document?
The VIVO 1.6 Release Announcement covers the main features of the release at a high level but leaves out a number of helpful specifics. This document is intended to help those planning to implement the release as either a new installation or upgrade to learn more about new features and find pointers to more complete documentation elsewhere on this wiki.
The VIVO ontology has become VIVO-ISF
VIVO v1.6 incorporates major changes to the ontology that reflect a need dating back to 2009 to bring the VIVO and eagle-i project (https://www.eagle-i.net) ontologies closer together. NIH elected to fund two distinct projects focusing on the networking of researchers (VIVO) and research resources (eagle-i) but recognized the artificiality of the split and has encouraged collaboration, most recently by funding the CTSAconnect project (http://ctsaconnect.org) with Dr. Melissa Haendel of Oregon Health and Science University as principal investigator.
The new ontology is called VIVO-ISF, short for Integrated Semantic Framework. The full ISF ontology as published by the CTSAconnect project is freely available for download and includes technical documentation and its modules may be browsed online or downloaded. The VIVO 1.5 scope has informed selection of ISF modules appropriate for VIVO 1.6, with the anticipation that individual adopting sites may wish to include or exclude individual ISF modules based on their intended population of VIVO with data.
Documentation specific to VIVO-ISF lives on this wiki and will continue to evolve as the VIVO-ISF Ontology Working Group, led by Melissa Haendel and Brian Lowe, receives feedback from the rollout. Communities of interested are forming within the working group and will lead implementation of corrections, improvements, and expansion of the VIVO-ISF ontology for future releases. Please join the biweekly ontology working group calls.
To understand the VIVO-ISF changes from previous releases, we call particular attention to the VIVO 1.5 to VIVO-ISF change diagrams. Upgrading VIVO from version 1.5.x to version 1.6 includes an automated data migration process that should convert all existing VIVO content to the new ontology structure, but any local data ingest processes will almost certainly need to be modified to generate data compatible with the new ontology. We recommend backing up the VIVO 1.5 database and performing a provisional upgrade on a test server to confirm that the upgrade will complete smoothly – please see the VIVO 1.6 upgrade documentation for more details.
Internationalization
VIVO has gained significant adoption outside North America and internationalization of the application menus and other interface elements and ontology labels has emerged as a high priority, sometimes even in other English-speaking countries where even minor terminology tweaks have until now required modifying the VIVO application. VIVO v1.6 leverages Java resource bundles to separate all text strings embedded in menus, page templates, dialog boxes, error messages, and ontology class and property labels from the application itself so that translations can be accomplished without programming. Separating language-specific text from the code also minimizes the work of updating alternate language versions of VIVO for future releases; a comparison of the changes in the English text from one version to the next can pinpoint areas where text in another language would also need modification.
We characterize the internationalization in version 1.6 as read-only because significant additional work will be required to make interactive editing of all VIVO content in multiple languages possible. Content in the form of RDF bearing standard language tags and imported into VIVO will be displayed appropriately; VIVO will respect a user's current browser-based language preference settings to find the closest match based on BCP 47 standard language tags – for details see the W3C document on setting language preferences in a browser.
VIVO v1.6 does support editing each individual entity's primary label to supplement the default language with additional labels in other languages. While limited to labels, this would allow showing multiple versions of a person's or organization's name as well as including titles of books or other publications in multiple languages. Users whose browser settings indicate a language preference will see the appropriate language by default, with an icon to indicate that additional languages are available for that individual entity.
VIVO v1.6 still ships with U.S. English as the default language; a test bundle prepared using Google Translate for testing only is available and we expect an announcement soon of an contributed version prepared by VIVO community members.
Web services
VIVO 1.6 introduces important new functionality in the form of a web service designed to accept SPARQL update commands authenticated via username and password. One primary motivation for adding a write capability is to ingest data into VIVO that triggers updates to the search index as well as performing any needed re-inferencing. The VIVO Harvester has previously been able to write to the VIVO database directly by issuing Jena library calls, but using the VIVO web service will avoid the extra step of rebuilding the VIVO search index and re-computing inferences after each Harvester run.
The web service implements SPARQL 1.1 Update to allow other applications to write to VIVO via a well-documented standard. The write capability of the VIVO web service can be used in conjunction with linked data requests, VIVO's internal SPARQL query interface, or a SPARQL endpoint such as Fuseki to accomplish round-tripping of VIVO data in other applications ranging from lightweight JavaScript visualizations tools to full-scale web applications. Several VIVO community members leverage the native RDF capabilities of the Drupal open-source web content management system to create dashboards that re-purpose VIVO data, and with the new web service these independent applications will be able to create, update, and delete as well as read VIVO data.
Chris Barnes from the University of Florida is leading a new VIVO Apps & Tools working group highlighting existing tools via demos and discussions via biweekly calls.
