203 lines
9.4 KiB
HTML
203 lines
9.4 KiB
HTML
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<meta http-equiv="content-type" content="text/html; charset=UTF-8">
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<meta charset="utf-8">
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<title>VIVO Release 1 V1.4 Announcement</title>
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<div id="branding" role="banner">
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<h1 class="vivo-logo"><a href="http://vivoweb.org"><span class="displace">VIVO</span></a></h1>
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</div>
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<div id="wrapper-content" role="main">
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<h1>VIVO Release 1 V1.4 Announcement</h1>
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<small>
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December 10, 2011
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</small>
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<toc>
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<ul> <!-- filled out by js --> </ul>
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</toc>
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<div class="wiki-content">
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<!-- last edited by Jon Corson-Rikert on Dec 11, 2011 -->
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<h4><a
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name="VIVORelease1.4AnnouncementDRAFT-Overview"></a>Overview</h4>
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<p>VIVO 1.4 introduces two significant new features as well as
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extending development begun in previous releases. Proxy
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editing allows any VIVO user to designate another user as his
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or her proxy for review or update, a much-requested feature,
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and VIVO 1.4 also includes the ability to annotate VIVO
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entries with terms from controlled vocabularies using external
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terminology services. </p>
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<h4><a
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name="VIVORelease1.4AnnouncementDRAFT-Proxyediting"></a>Proxy
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editing</h4> <p>VIVO now allows anyone with a VIVO profile to
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delegate editing privileges for his or her entry to another
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user, or proxy. Proxy-based editing facilitates adoption and
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updating of VIVO in settings where researchers do not have the
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time to maintain their own entries and wish to delegate
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editing to specific persons. Proxy editing also supports
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granting a VIVO user the rights to edit other entities such as
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specific organizations, furthering sustainability by
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controlled distribution of editing responsibility. Proxy
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privileges can be managed by VIVO administrators on behalf of
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multiple users or by an individual user on his or her own
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behalf.</p>
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<h4><a
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name="VIVORelease1.4AnnouncementDRAFT-Linkingtoexternalvocabularies"></a>Linking
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to external vocabularies</h4> <p>Many people have requested
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support for associating terms from established controlled
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vocabularies with people, publications, grants, organizations,
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and other types of data in VIVO. While small taxonomies or
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vocabularies may most easily be imported in their entirety
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into VIVO, a number of the more popular controlled
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vocabularies are very large in proportion to the number of
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terms likely to be referenced within a single VIVO
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instance. Incorporating terms by reference helps keep terms in
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sync as these vocabularies continue to evolve and is more
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consistent with linked data principles.
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</p>
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<p>
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Stony Brook University's Department of Medical
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Bioinformatics, led by Dr. Moisés Eisenberg, hosts an RDF
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version of the National Library of Medicine's Unified
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Medical Language System or UMLS
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(<a href="http://www.nlm.nih.gov/research/umls/"
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class="external-link"
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rel="nofollow">http://www.nlm.nih.gov/research/umls/</a>). Through
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a 2011 VIVO mini-grant, Stony Brook has developed a web
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service that accepts incoming term requests from VIVO and
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returns one or more matching UMLS concepts with stable
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URIs. VIVO displays the label associated with the UMLS
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concept but the concept's URI ensures that references remain
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unambiguous, even across multiple VIVO instances at
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different institutions.</p>
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<p>
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The interface from VIVO to the UMLS service has been
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implemented to allow linking to additional vocabulary services such as
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GEMET (<a href="http://www.eionet.europa.eu/gemet"
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class="external-link"
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rel="nofollow">http://www.eionet.europa.eu/gemet</a>), and we will
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offer additional choices in upcoming releases. </p>
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<h4><a name="VIVORelease1.4AnnouncementDRAFT-Visualizations"></a>Visualizations</h4>
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<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>
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<p>All science map visualizations also now feature the updated
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basemap of science that uses 10 years of publication data
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(2001-2010) from Elsevier's Scopus and Thomson Reuters' Web of
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Science. The UCSD map was originally created by the Regents
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of the University of California and SciTech Strategies in
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2008. It was updated by SciTech Strategies, L'Observatoire des
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sciences et des technologies, and Indiana University's
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Cyberinfrastructure for Network Science Center (CNS) in
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2011.</p>
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<h4><a name="VIVORelease1.4AnnouncementDRAFT-Ontologychanges"></a>Ontology changes</h4>
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<p>Ontology changes from 1.3 to 1.4 were relatively minor,
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including an update to the Geopolitical Ontology and changes
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to support linking to external vocabulary references as
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described above. Changes for each release are documented on
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the VIVO wiki on Sourceforge
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at <a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology"
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class="external-link"
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rel="nofollow">http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology</a>.</p>
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<p>With version 1.4, the VIVO ontology will be submitted to
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the Bioportal (<a href="http://www.bioontology.org/bioportal"
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class="external-link"
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rel="nofollow">http://www.bioontology.org/bioportal</a>), an
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open repository of ontologies hosted by the National Center
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for Biomedical Ontology, to facilitate access and
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dissemination.</p>
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<h4><a name="VIVORelease1.4AnnouncementDRAFT-Freemarkerconversion"></a>Freemarker conversion</h4>
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<p>VIVO 1.4 continues the major effort begun with version 1.2
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and continued in 1.3 to convert VIVO's entire user-facing code
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base from Java Server Pages (JSPs) to FreeMarker, the Java
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template engine library
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(<a href="http://freemarker.sourceforge.net/"
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class="external-link"
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rel="nofollow">http://freemarker.sourceforge.net/</a>). FreeMarker
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more cleanly separates internal application programming logic
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from page display, making the VIVO application more
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understandable and extensible, especially for developers new
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to VIVO. The entire user-facing editing system has been
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refactored for VIVO 1.4 to simplify the configuration of
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custom forms and allow more rigorous code testing and data
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verification.</p>
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<h4><a name="VIVORelease1.4AnnouncementDRAFT-Improveddiagnostics"></a>Improved diagnostics</h4>
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<p>VIVO 1.4 features improved diagnostic messages to help with
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configuration issues. As VIVO starts up, it runs a series of
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tests looking for common configuration errors. If VIVO finds a
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problem it will display an error or warning message in the
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browser, instead of the VIVO home page. These start-time
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diagnostics and prominent display make it even easier to
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install VIVO.</p>
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<h4><a name="VIVORelease1.4AnnouncementDRAFT-Vitroasastandaloneapplication"></a>Vitro as a standalone application</h4>
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<p>VIVO extends the underlying Vitro open-source semantic web
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application with the VIVO ontology, software customizations
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specific to the VIVO ontology, and visual theming. With
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version 1.4 of VIVO, the underlying Vitro software has been
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packaged for use independently of the VIVO ontology. Vitro
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supports ontology creation and editing as well as importing
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existing ontologies, and is an excellent tool for populating
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ontologies with instance data, for publishing RDF as linked
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data, and for hands-on teaching about ontologies and semantic
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web concepts.</p>
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