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NIHVIVO-3846 Pasted the release announcement from https://confluence.cornell.edu/display/ennsrd/VIVO+Release+1.5+Announcement

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<title>VIVO Release 1 V1.4 Announcement</title> <title>VIVO Release 1 V1.5 Announcement</title>
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<h1 class="vivo-logo"><a href="http://vivoweb.org"><span class="displace">VIVO</span></a></h1> <h1 class="vivo-logo">
</div> <a href="http://vivoweb.org"><span class="displace">VIVO</span></a>
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<h1>VIVO Release 1 V1.4 Announcement</h1> <h1>VIVO Release 1 V1.5 Announcement</h1>
<small> <small> July 11, 2012 </small>
December 10, 2011 <toc>
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<!-- last edited by Jon Corson-Rikert on Dec 11, 2011 --> <h4>
<h4><a <a name="VIVORelease1.5Announcement-Overview"></a>Overview
name="VIVORelease1.4AnnouncementDRAFT-Overview"></a>Overview</h4> </h4>
<p>VIVO 1.4 introduces two significant new features as well as <p>VIVO 1.5 introduces a number of new features addressing
extending development begun in previous releases. Proxy extensibility and interoperability, reasoning, page customization,
editing allows any VIVO user to designate another user as his and a first step toward internationalization. VIVO's profile
or her proxy for review or update, a much-requested feature, management has been improved with a number of new custom forms, and
and VIVO 1.4 also includes the ability to annotate VIVO there are significant improvements to ontology browsing and editing.</p>
entries with terms from controlled vocabularies using external
terminology services. </p>
<h4><a <p>The VIVO 1.5 development cycle has also included extensive
name="VIVORelease1.4AnnouncementDRAFT-Proxyediting"></a>Proxy design work on features anticipated for implementation beginning
editing</h4> <p>VIVO now allows anyone with a VIVO profile to with version 1.6, including increased modularity, the introduction
delegate editing privileges for his or her entry to another of a separate ontology for display and editing controls, and the
user, or proxy. Proxy-based editing facilitates adoption and addition of a graphical ontology class expression editor.</p>
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.</p>
<h4><a <h4>
name="VIVORelease1.4AnnouncementDRAFT-Linkingtoexternalvocabularies"></a>Linking <a name="VIVORelease1.5Announcement-Extensibility"></a>Extensibility
to external vocabularies</h4> <p>Many people have requested </h4>
support for associating terms from established controlled <p>Since version 1.2, VIVO’s use of the Jena Semantic Web
vocabularies with people, publications, grants, organizations, framework (1) has allowed implementation sites to use any database
and other types of data in VIVO. While small taxonomies or supported by Jena, including MySQL, PostgreSQL, and Oracle. VIVO
vocabularies may most easily be imported in their entirety Release 1.5 extends this flexibility a major step further by making
into VIVO, a number of the more popular controlled it much easier to extend VIVO to use any triple store, and include
vocabularies are very large in proportion to the number of an experimental feature that supports connecting to any triple store
terms likely to be referenced within a single VIVO that exposes a SPARQL endpoint that supports SPARQL update. Initial
instance. Incorporating terms by reference helps keep terms in tests with Sesame are quite promising.</p>
sync as these vocabularies continue to evolve and is more
consistent with linked data principles.
</p>
<p> <h4>
Stony Brook University's Department of Medical <a name="VIVORelease1.5Announcement-VIVOisnowanOpenSocialcontainer"></a>VIVO
Bioinformatics, led by Dr. Moisés Eisenberg, hosts an RDF is now an OpenSocial container
version of the National Library of Medicine's Unified </h4>
Medical Language System or UMLS <p>The OpenSocial standard (2) defines a web-based container
(<a href="http://www.nlm.nih.gov/research/umls/" environment for hosting third-party components in a web application
class="external-link" and provides a set of common application programming interfaces for
rel="nofollow">http://www.nlm.nih.gov/research/umls/</a>). Through developing these components by leveraging the Google Gadgets (3)
a 2011 VIVO mini-grant, Stony Brook has developed a web framework. Eric Meeks and colleagues at the University of
service that accepts incoming term requests from VIVO and California–San Francisco and other institutions have developed
returns one or more matching UMLS concepts with stable OpenSocial gadgets designed to work with RDF expressed using the
URIs. VIVO displays the label associated with the UMLS VIVO ontology. For VIVO 1.5, Eric has adapted the Apache Shindig (4)
concept but the concept's URI ensures that references remain OpenSocial reference implementation to communicate with VIVO and
unambiguous, even across multiple VIVO instances at collaborated with the VIVO development team in extending VIVO itself
different institutions.</p> to support OpenSocial gadgets referencing data in VIVO or bringing
additional data to VIVO based on page being viewed.</p>
<p> <h4>
The interface from VIVO to the UMLS service has been <a name="VIVORelease1.5Announcement-Reasoning"></a>Reasoning
implemented to allow linking to additional vocabulary services such as </h4>
GEMET (<a href="http://www.eionet.europa.eu/gemet" <p>The simple reasoner built into VIVO now has support for sameAs
class="external-link" reasoning to allow joint display of statements associated with two
rel="nofollow">http://www.eionet.europa.eu/gemet</a>), and we will URIs that have been asserted or inferred to be sameAs each other.
offer additional choices in upcoming releases. </p> 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.</p>
<h4><a name="VIVORelease1.4AnnouncementDRAFT-Visualizations"></a>Visualizations</h4> <h4>
<p>The VIVO 1.4 release features a novel science maps visualization that supports the comparison of publication profiles of up to three organizations.</p> <a name="VIVORelease1.5Announcement-Newpagetypes"></a>New page types
</h4>
<p>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).</p>
<p>All science map visualizations also now feature the updated <h4>
basemap of science that uses 10 years of publication data <a name="VIVORelease1.5Announcement-Customizedshortviews"></a>Customized
(2001-2010) from Elsevier's Scopus and Thomson Reuters' Web of short views
Science. The UCSD map was originally created by the Regents </h4>
of the University of California and SciTech Strategies in <p>Site maintainers may also customize the way that individuals
2008. It was updated by SciTech Strategies, L'Observatoire des are displayed on VIVO index pages, browse pages, or search results -
sciences et des technologies, and Indiana University's all without modifying the basic VIVO code. Custom templates,
Cyberinfrastructure for Network Science Center (CNS) in populated by custom queries, can be assigned to classes of
2011.</p> individuals in any of these contexts.</p>
<h4><a name="VIVORelease1.4AnnouncementDRAFT-Ontologychanges"></a>Ontology changes</h4> <h4>
<p>Ontology changes from 1.3 to 1.4 were relatively minor, <a name="VIVORelease1.5Announcement-Languagefilter"></a>Language
including an update to the Geopolitical Ontology and changes filter
to support linking to external vocabulary references as </h4>
described above. Changes for each release are documented on
the VIVO wiki on Sourceforge
at <a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology"
class="external-link"
rel="nofollow">http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology</a>.</p>
<p>With version 1.4, the VIVO ontology will be submitted to <p>VIVO 1.5 will respect a user's browser language preference
the Bioportal (<a href="http://www.bioontology.org/bioportal" setting and filter labels and data property text strings to only
class="external-link" display values matching that language setting whenever versions in
rel="nofollow">http://www.bioontology.org/bioportal</a>), an multiple languages are available. This is an important first step
open repository of ontologies hosted by the National Center toward internationalization of the VIVO application, an effort we
for Biomedical Ontology, to facilitate access and expect to continue in future releases.</p>
dissemination.</p>
<h4><a name="VIVORelease1.4AnnouncementDRAFT-Freemarkerconversion"></a>Freemarker conversion</h4> <h4>
<p>VIVO 1.4 continues the major effort begun with version 1.2 <a name="VIVORelease1.5Announcement-Improvedediting"></a>Improved
and continued in 1.3 to convert VIVO's entire user-facing code editing
base from Java Server Pages (JSPs) to FreeMarker, the Java </h4>
template engine library <p>VIVO 1.5 includes new forms to simplify entry and editing of
(<a href="http://freemarker.sourceforge.net/" awards, advising relationships, and additional types of
class="external-link" publications. Forms make greater use of autocomplete functionality,
rel="nofollow">http://freemarker.sourceforge.net/</a>). FreeMarker and very large pick lists are converted to autocomplete
more cleanly separates internal application programming logic functionality by the application on the fly.</p>
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.</p>
<h4><a name="VIVORelease1.4AnnouncementDRAFT-Improveddiagnostics"></a>Improved diagnostics</h4> <h4>
<p>VIVO 1.4 features improved diagnostic messages to help with <a
configuration issues. As VIVO starts up, it runs a series of name="VIVORelease1.5Announcement-ImprovedMapofSciencevisualization"></a>Improved
tests looking for common configuration errors. If VIVO finds a Map of Science visualization
problem it will display an error or warning message in the </h4>
browser, instead of the VIVO home page. These start-time <p>VIVO's Map of Science visualizations benefit from improved
diagnostics and prominent display make it even easier to labeling and color coding as well as additional explanation; the
install VIVO.</p> maps also now support dynamic interchange between discipline and
sub-discipline sliders.</p>
<h4><a name="VIVORelease1.4AnnouncementDRAFT-Vitroasastandaloneapplication"></a>Vitro as a standalone application</h4> <h4>
<p>VIVO extends the underlying Vitro open-source semantic web <a name="VIVORelease1.5Announcement-Ontologychanges"></a>Ontology
application with the VIVO ontology, software customizations changes
specific to the VIVO ontology, and visual theming. With </h4>
version 1.4 of VIVO, the underlying Vitro software has been <p>
packaged for use independently of the VIVO ontology. Vitro Ontology changes from 1.4 to 1.5 include identifying primary job
supports ontology creation and editing as well as importing appointments, modeling citation information for publications, and
existing ontologies, and is an excellent tool for populating adding new types of publications to better align with PubMed.
ontologies with instance data, for publishing RDF as linked Changes for each release are documented on the VIVO wiki on
data, and for hands-on teaching about ontologies and semantic Sourceforge at <a
web concepts.</p> href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology"
</div> <!-- wiki content --> class="external-link" rel="nofollow">http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology</a>.
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<script> <p>
The VIVO ontology is now available via the Bioportal (<a
function init(){ href="http://www.bioontology.org/bioportal" class="external-link"
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//fill out TOC <h4>
var tocList = document.querySelector('toc>ul'); <a name="VIVORelease1.5Announcement-Acknowledgements"></a>Acknowledgements
var h4Anchors = document.querySelectorAll('a[name]'); </h4>
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</body> <p>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.</p>
<p>The VIVO project is funded by the National Institutes of
Health, U24 RR029822, "VIVO: Enabling National Networking of
Scientists".</p>
<h4>
<a name="VIVORelease1.5Announcement-References"></a>References
</h4>
<ol>
<li><a href="http://jena.apache.org/" class="external-link"
rel="nofollow">http://jena.apache.org/</a></li>
<li><a href="http://docs.opensocial.org/display/OS/Home"
class="external-link" rel="nofollow">http://docs.opensocial.org/display/OS/Home</a></li>
<li><a href="https://developers.google.com/gadgets/"
class="external-link" rel="nofollow">https://developers.google.com/gadgets/</a></li>
<li><a href="http://shindig.apache.org/" class="external-link"
rel="nofollow">http://shindig.apache.org/</a></li>
<li><a
href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=SPARQL_Resources"
class="external-link" rel="nofollow">http://sourceforge.net/apps/mediawiki/vivo/index.php?title=SPARQL_Resources</a></li>
</ol>
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