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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>
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<h1 class="vivo-logo"><a href="http://vivoweb.org"><span class="displace">VIVO</span></a></h1>
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<h1>VIVO Release 1 V1.4 Announcement</h1>
<small>
December 10, 2011
</small>
<h1>VIVO Release 1 V1.5 Announcement</h1>
<small> July 11, 2012 </small>
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<h4><a
name="VIVORelease1.4AnnouncementDRAFT-Overview"></a>Overview</h4>
<p>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. </p>
<h4>
<a name="VIVORelease1.5Announcement-Overview"></a>Overview
</h4>
<p>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.</p>
<h4><a
name="VIVORelease1.4AnnouncementDRAFT-Proxyediting"></a>Proxy
editing</h4> <p>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.</p>
<p>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.</p>
<h4><a
name="VIVORelease1.4AnnouncementDRAFT-Linkingtoexternalvocabularies"></a>Linking
to external vocabularies</h4> <p>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.
<h4>
<a name="VIVORelease1.5Announcement-Extensibility"></a>Extensibility
</h4>
<p>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.</p>
<h4>
<a name="VIVORelease1.5Announcement-VIVOisnowanOpenSocialcontainer"></a>VIVO
is now an OpenSocial container
</h4>
<p>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.</p>
<h4>
<a name="VIVORelease1.5Announcement-Reasoning"></a>Reasoning
</h4>
<p>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.</p>
<h4>
<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>
<h4>
<a name="VIVORelease1.5Announcement-Customizedshortviews"></a>Customized
short views
</h4>
<p>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.</p>
<h4>
<a name="VIVORelease1.5Announcement-Languagefilter"></a>Language
filter
</h4>
<p>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.</p>
<h4>
<a name="VIVORelease1.5Announcement-Improvedediting"></a>Improved
editing
</h4>
<p>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.</p>
<h4>
<a
name="VIVORelease1.5Announcement-ImprovedMapofSciencevisualization"></a>Improved
Map of Science visualization
</h4>
<p>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.</p>
<h4>
<a name="VIVORelease1.5Announcement-Ontologychanges"></a>Ontology
changes
</h4>
<p>
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 <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>
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
(<a href="http://www.nlm.nih.gov/research/umls/"
class="external-link"
rel="nofollow">http://www.nlm.nih.gov/research/umls/</a>). 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.</p>
The VIVO ontology is now available via the Bioportal (<a
href="http://www.bioontology.org/bioportal" class="external-link"
rel="nofollow">http://www.bioontology.org/bioportal</a>), an open
repository of ontologies hosted by the National Center for
Biomedical Ontology.
</p>
<p>
The interface from VIVO to the UMLS service has been
implemented to allow linking to additional vocabulary services such as
GEMET (<a href="http://www.eionet.europa.eu/gemet"
class="external-link"
rel="nofollow">http://www.eionet.europa.eu/gemet</a>), and we will
offer additional choices in upcoming releases. </p>
<h4>
<a name="VIVORelease1.5Announcement-Acknowledgements"></a>Acknowledgements
</h4>
<h4><a name="VIVORelease1.4AnnouncementDRAFT-Visualizations"></a>Visualizations</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>
<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>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.</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="VIVORelease1.4AnnouncementDRAFT-Ontologychanges"></a>Ontology changes</h4>
<p>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 <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>
<h4>
<a name="VIVORelease1.5Announcement-References"></a>References
</h4>
<p>With version 1.4, the VIVO ontology will be submitted to
the Bioportal (<a href="http://www.bioontology.org/bioportal"
class="external-link"
rel="nofollow">http://www.bioontology.org/bioportal</a>), an
open repository of ontologies hosted by the National Center
for Biomedical Ontology, to facilitate access and
dissemination.</p>
<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>
<h4><a name="VIVORelease1.4AnnouncementDRAFT-Freemarkerconversion"></a>Freemarker conversion</h4>
<p>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
(<a href="http://freemarker.sourceforge.net/"
class="external-link"
rel="nofollow">http://freemarker.sourceforge.net/</a>). 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.</p>
<h4><a name="VIVORelease1.4AnnouncementDRAFT-Improveddiagnostics"></a>Improved diagnostics</h4>
<p>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.</p>
<h4><a name="VIVORelease1.4AnnouncementDRAFT-Vitroasastandaloneapplication"></a>Vitro as a standalone application</h4>
<p>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.</p>
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