VIVO Release 1 V1.4 Announcement
- - December 10, 2011 - -VIVO Release 1 V1.5 Announcement
+ July 11, 2012 +-
+
+
Overview
-VIVO 1.4 introduces two significant new features as well as - extending development begun in previous releases. Proxy - editing allows any VIVO user to designate another user as his - or her proxy for review or update, a much-requested feature, - and VIVO 1.4 also includes the ability to annotate VIVO - entries with terms from controlled vocabularies using external - terminology services.
++ Overview +
+VIVO 1.5 introduces a number of new features addressing + extensibility and interoperability, reasoning, page customization, + and a first step toward internationalization. VIVO's profile + management has been improved with a number of new custom forms, and + there are significant improvements to ontology browsing and editing.
-Proxy - editing
VIVO now allows anyone with a VIVO profile to - delegate editing privileges for his or her entry to another - user, or proxy. Proxy-based editing facilitates adoption and - updating of VIVO in settings where researchers do not have the - time to maintain their own entries and wish to delegate - editing to specific persons. Proxy editing also supports - granting a VIVO user the rights to edit other entities such as - specific organizations, furthering sustainability by - controlled distribution of editing responsibility. Proxy - privileges can be managed by VIVO administrators on behalf of - multiple users or by an individual user on his or her own - behalf.
+The VIVO 1.5 development cycle has also included extensive + design work on features anticipated for implementation beginning + with version 1.6, including increased modularity, the introduction + of a separate ontology for display and editing controls, and the + addition of a graphical ontology class expression editor.
-Linking - to external vocabularies
Many people have requested - support for associating terms from established controlled - vocabularies with people, publications, grants, organizations, - and other types of data in VIVO. While small taxonomies or - vocabularies may most easily be imported in their entirety - into VIVO, a number of the more popular controlled - vocabularies are very large in proportion to the number of - terms likely to be referenced within a single VIVO - instance. Incorporating terms by reference helps keep terms in - sync as these vocabularies continue to evolve and is more - consistent with linked data principles. -
++ Extensibility +
+Since version 1.2, VIVO’s use of the Jena Semantic Web + framework (1) has allowed implementation sites to use any database + supported by Jena, including MySQL, PostgreSQL, and Oracle. VIVO + Release 1.5 extends this flexibility a major step further by making + it much easier to extend VIVO to use any triple store, and include + an experimental feature that supports connecting to any triple store + that exposes a SPARQL endpoint that supports SPARQL update. Initial + tests with Sesame are quite promising.
-- Stony Brook University's Department of Medical - Bioinformatics, led by Dr. Moisés Eisenberg, hosts an RDF - version of the National Library of Medicine's Unified - Medical Language System or UMLS - (http://www.nlm.nih.gov/research/umls/). Through - a 2011 VIVO mini-grant, Stony Brook has developed a web - service that accepts incoming term requests from VIVO and - returns one or more matching UMLS concepts with stable - URIs. VIVO displays the label associated with the UMLS - concept but the concept's URI ensures that references remain - unambiguous, even across multiple VIVO instances at - different institutions.
++ VIVO + is now an OpenSocial container +
+The OpenSocial standard (2) defines a web-based container + environment for hosting third-party components in a web application + and provides a set of common application programming interfaces for + developing these components by leveraging the Google Gadgets (3) + framework. Eric Meeks and colleagues at the University of + California–San Francisco and other institutions have developed + OpenSocial gadgets designed to work with RDF expressed using the + VIVO ontology. For VIVO 1.5, Eric has adapted the Apache Shindig (4) + OpenSocial reference implementation to communicate with VIVO and + collaborated with the VIVO development team in extending VIVO itself + to support OpenSocial gadgets referencing data in VIVO or bringing + additional data to VIVO based on page being viewed.
-- The interface from VIVO to the UMLS service has been - implemented to allow linking to additional vocabulary services such as - GEMET (http://www.eionet.europa.eu/gemet), and we will - offer additional choices in upcoming releases.
++ Reasoning +
+The simple reasoner built into VIVO now has support for sameAs + reasoning to allow joint display of statements associated with two + URIs that have been asserted or inferred to be sameAs each other. + The VIVO reasoner will also now maintain inverse property statements + based on presence or absence of inverse property declarations in an + ontology. Although the VIVO application has previously added and + removed property inverse statements during interactive editing, this + feature had been requested to simplify the preparation of data for + ingest with the VIVO Harvester or other tools. Recomputing + inferences will trigger the reasoner to supply any missing inverse + property statements.
-Visualizations
-The VIVO 1.4 release features a novel science maps visualization that supports the comparison of publication profiles of up to three organizations.
++ New page types +
+The VIVO 1.5 release expands the flexibility of VIVO as a web + application by adding additional dynamic content features. Sites may + create arbitrary HTML pages or web pages that display the results of + SPARQL queries and link to those from any template in the + application; these new pages may optionally be top-level menu pages + and may include multiple sections featuring the results of + parameterized SPARQL queries and static HTML content as well as data + filtered by class group and type. New page specifications are + typically paired with page template modifications to provide the + desired level of control over display of dynamic content. These + changes significantly augment VIVO's native reporting capabilities + and enable sites to demonstrate aggregation, interconnectivity, and + network effects in VIVO data. Queries and report templates will be + useful to share across sites and a SPARQL resource page has already + been established on the VIVO wiki (5).
-All science map visualizations also now feature the updated - basemap of science that uses 10 years of publication data - (2001-2010) from Elsevier's Scopus and Thomson Reuters' Web of - Science. The UCSD map was originally created by the Regents - of the University of California and SciTech Strategies in - 2008. It was updated by SciTech Strategies, L'Observatoire des - sciences et des technologies, and Indiana University's - Cyberinfrastructure for Network Science Center (CNS) in - 2011.
++ Customized + short views +
+Site maintainers may also customize the way that individuals + are displayed on VIVO index pages, browse pages, or search results - + all without modifying the basic VIVO code. Custom templates, + populated by custom queries, can be assigned to classes of + individuals in any of these contexts.
-Ontology changes
-Ontology changes from 1.3 to 1.4 were relatively minor, - including an update to the Geopolitical Ontology and changes - to support linking to external vocabulary references as - described above. Changes for each release are documented on - the VIVO wiki on Sourceforge - at http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology.
++ Language + filter +
-With version 1.4, the VIVO ontology will be submitted to - the Bioportal (http://www.bioontology.org/bioportal), an - open repository of ontologies hosted by the National Center - for Biomedical Ontology, to facilitate access and - dissemination.
+VIVO 1.5 will respect a user's browser language preference + setting and filter labels and data property text strings to only + display values matching that language setting whenever versions in + multiple languages are available. This is an important first step + toward internationalization of the VIVO application, an effort we + expect to continue in future releases.
-Freemarker conversion
-VIVO 1.4 continues the major effort begun with version 1.2 - and continued in 1.3 to convert VIVO's entire user-facing code - base from Java Server Pages (JSPs) to FreeMarker, the Java - template engine library - (http://freemarker.sourceforge.net/). FreeMarker - more cleanly separates internal application programming logic - from page display, making the VIVO application more - understandable and extensible, especially for developers new - to VIVO. The entire user-facing editing system has been - refactored for VIVO 1.4 to simplify the configuration of - custom forms and allow more rigorous code testing and data - verification.
++ Improved + editing +
+VIVO 1.5 includes new forms to simplify entry and editing of + awards, advising relationships, and additional types of + publications. Forms make greater use of autocomplete functionality, + and very large pick lists are converted to autocomplete + functionality by the application on the fly.
-Improved diagnostics
-VIVO 1.4 features improved diagnostic messages to help with - configuration issues. As VIVO starts up, it runs a series of - tests looking for common configuration errors. If VIVO finds a - problem it will display an error or warning message in the - browser, instead of the VIVO home page. These start-time - diagnostics and prominent display make it even easier to - install VIVO.
++ Improved + Map of Science visualization +
+VIVO's Map of Science visualizations benefit from improved + labeling and color coding as well as additional explanation; the + maps also now support dynamic interchange between discipline and + sub-discipline sliders.
-Vitro as a standalone application
-VIVO extends the underlying Vitro open-source semantic web - application with the VIVO ontology, software customizations - specific to the VIVO ontology, and visual theming. With - version 1.4 of VIVO, the underlying Vitro software has been - packaged for use independently of the VIVO ontology. Vitro - supports ontology creation and editing as well as importing - existing ontologies, and is an excellent tool for populating - ontologies with instance data, for publishing RDF as linked - data, and for hands-on teaching about ontologies and semantic - web concepts.
-+ Ontology + changes +
++ Ontology changes from 1.4 to 1.5 include identifying primary job + appointments, modeling citation information for publications, and + adding new types of publications to better align with PubMed. + Changes for each release are documented on the VIVO wiki on + Sourceforge at http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology. +
- ++ Acknowledgements +
- +This release represents the work of the entire VIVO team and + contributions of feature requests, requirements development and + design, ontology design reviews, software development, and testing + from the larger VIVO open source community.
+ +The VIVO project is funded by the National Institutes of + Health, U24 RR029822, "VIVO: Enabling National Networking of + Scientists".
+ +