<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear NCBO Users,<div><br></div><div>We are planning a BioPortal 2.3 release tomorrow, February 3d, 2010. These release includes some changes to the Annotator Service and Hierarchy Services. Specifically, there are changes in the content the services access, the way UMLS terminologies are addressed, and minor changes in the Annotator service XML output. Please, see the release notes below for the details. </div><div><br></div><div>If these upcoming changes present a serious problem for you, please let us know at <a href="mailto:support@bioontology.org">support@bioontology.org</a> as soon as possible.</div><div><div><div><div><br></div> <div>Natasha</div> <br></div> </div><div><b><span class="Apple-style-span" style="font-size: large; ">BioPortal 2.3</span></b></div><div><br></div><div><b>New features:</b></div><div><ul><li>BioPortal will process SKOS labels for preferred names and synonyms</li><li>Ontologies used by Annotator & Hierarchy services will now be updated on a regular basis (around every week).</li><li>The filtering of annotation by semantic types is available only for the ontologies which provide that information</li><li>The Annotator scoring function has changed a bit. </li><li>Users can now exclude the annotations created with synonym terms. </li><li>Users can now exclude the annotations less than a certain length. </li><li>There is a change in the XML returned by the Annotator service. The <sematicTypeBean> information is presented differently. The Get all terms REST service is also affected.</li></ul></div><div>Please refer to <a href="http://www.bioontology.org/wiki/index.php/Annotator_User_Guide">http://www.bioontology.org/wiki/index.php/Annotator_User_Guide</a> for details on Annotator enhancements</div><div><br></div><div><b>New way to address UMLS ontologies:</b></div><div><br></div><div>We have harmonized the ontologies in the Annotator and BioPortal. The full list is available at: <a href="http://rest.bioontology.org/obs/ontologies">http://rest.bioontology.org/obs/ontologies</a>. This change has implications when using the Annotator with UMLS ontologies.</div><div><ul><li>Currently, BioPortal (and, therefore, Annotator and Hierarchy services) can use 16 ontologies from UMLS. We will add UMLS ontologies to BioPortal on demand. Please send email to <a href="mailto:support@bioontology.org">support@bioontology.org</a> to request a specific UMLS ontology to be added to BioPortal. </li><li>UMLS SAB is no longer valid as ontologyId. Please refer to <a href="http://bioportal.bioontology.org/ontologies/?filter=UMLS">http://bioportal.bioontology.org/ontologies/?filter=UMLS</a> to map your SAB to the corresponding ontology version id. </li><li>UMLS CUIs are no longer valid as conceptId. You can look up the conceptId corresponding to a CUI by using the NCBO search interface (<a href="http://bioportal.bioontology.org/search">http://bioportal.bioontology.org/search</a>): type in the CUI and check "Include attributes in search". You can also use the search REST service (<a href="http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Search_services">http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Search_services</a>) to search for the concept by CUI. We are working on a new concept service that will accept CUI as conceptId in the near future.</li></ul></div><div><b>Known issues:</b></div><div><ul><li>ISA closure in the Annotator and Hierarchy services do not work properly for NCIT and Galen. This will be fixed in an upcoming release.</li><li>Some mappings present in BioPortal are not yet available for use with the Annotator.</li><div><br></div></ul></div></div></body></html>