<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><p class="MsoNormal"><span style="font-family: Arial; ">The BioPortal team is pleased to announce the release of BioPortal 2.2 (<a href="http://bioportal.bioontology.org/">http://bioportal.bioontology.org/</a>). Release notes and known issues are listed below.<o:p></o:p></span></p><p class="MsoNormal">New Features</p><ul class="MailOutline"><li>Ontology Views</li></ul><ul type="disc" style="margin-top: 0in; "><ul type="circle" style="margin-top: 0in; "><li class="MsoNormal"><span style="font-family: Arial; ">Views in BioPortal are subsets or other derivatives of ontologies in the repository that you can share with the community. You can upload views for any ontology, and review them, add notes, create mappings, and use REST Web services to access them programmatically.<o:p></o:p></span></li><li class="MsoNormal"><span style="font-family: Arial; ">A view can also serve as a mechanism to define value sets, which are quite useful in combination with the BioPortal ontology-term selection widget.<o:p></o:p></span></li><li class="MsoNormal"><span style="font-family: Arial; ">View generation and storage in BioPortal is the result of collaboration with Dr. Jim Brinkley’s group at the University of Washington.<o:p></o:p></span></li></ul><li class="MsoNormal"><span style="font-family: Arial; ">NCBO Resource Index</span><span style="font-family: ArialMT; "><o:p></o:p></span></li><ul type="circle" style="margin-top: 0in; "><li class="MsoNormal"><span style="font-family: Arial; ">We have initiated automated indexing of the contents of public databases using ontology terms. The indexing is done using the same workflow that drives the previously released Annotator web service. Currently we index the following public databases:<span> </span>Array Express, Biositemaps, caNanoLab, Conserved Domain Database, ClinicalTrials.gov, DrugBank, Gene Expression Omnibus, Online Mendelian Inheritance in Man, PharmGKB, Reactome, ResearchCrossroads (Grant funding database), Stanford Microarray Database, UniProt KB, and WikiPathways.<span> </span>The resulting annotations are accessible for browsing via the Resources tab corresponding to any ontology concept. The annotations can also be accessed programmatically: <a href="http://www.bioontology.org/wiki/index.php/Resource_Index"><span style="color: rgb(21, 77, 175); ">http://www.bioontology.org/wiki/index.php/Resource_Index</span></a>. <o:p></o:p></span></li><li class="MsoNormal"><span style="font-family: Arial; ">If you have recommendations on additional publicly accessible resources to index, let us know at <a href="mailto:support@bioontology.org"><span style="color: rgb(21, 77, 175); ">support@bioontology.org</span></a>. <o:p></o:p></span></li></ul><li class="MsoNormal"><span style="font-family: Arial; ">Search filter for Ontology Groups and Categories<o:p></o:p></span></li><ul type="circle" style="margin-top: 0in; "><li class="MsoNormal"><span style="font-family: Arial; ">You can now limit your search to ontologies from a certain group (e.g., OBO Foundry, caBIG) or ontologies in a certain category (e.g., anatomy). </span></li></ul></ul><p class="MsoNormal"><br></p><p class="MsoNormal"><span style="font-family: Arial; ">New REST Web Services<o:p></o:p></span></p><ul type="disc" style="margin-top: 0in; "><li class="MsoNormal"><span style="font-family: Arial; ">Services to access ontologies and ontology versions<o:p></o:p></span></li><ul type="circle" style="margin-top: 0in; "><li class="MsoNormal"><span style="font-family: Arial; ">List all Categories<o:p></o:p></span></li><li class="MsoNormal"><span style="font-family: Arial; ">List all Groups<o:p></o:p></span></li><li class="MsoNormal"><span style="font-family: Arial; ">Download by virtual ontology identifier<o:p></o:p></span></li></ul><li class="MsoNormal"><span style="font-family: Arial; ">Services to access ontology views and ontology view versions<o:p></o:p></span></li><ul type="circle" style="margin-top: 0in; "><li class="MsoNormal"><span style="font-family: Arial; ">List all Views of all Ontologies (lists the latest version)<o:p></o:p></span></li><li class="MsoNormal"><span style="font-family: Arial; ">List all versions for a given View<o:p></o:p></span></li></ul><li class="MsoNormal"><span style="font-family: Arial; ">Concept services<o:p></o:p></span></li><ul type="circle" style="margin-top: 0in; "><li class="MsoNormal"><span style="font-family: Arial; ">Get all concepts<o:p></o:p></span></li></ul><li class="MsoNormal"><span style="font-family: Arial; ">Search service – parameter added to enable search within an ontology branch<o:p></o:p></span></li><li class="MsoNormal"><span style="font-family: Arial; ">Service to access the NCBO Resource Index<o:p></o:p></span></li></ul><p class="MsoNormal" style="margin-left: 0.25in; "><span style="font-family: Arial; ">See <a href="http://www.bioontology.org/wiki/index.php/BioPortal_REST_services">http://www.bioontology.org/wiki/index.php/BioPortal_REST_services</a> for the full list of BioPortal REST Web services.<o:p></o:p></span></p><div><span style="font-family: Arial; "> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal"><span style="font-family: Arial; ">New Data:<o:p></o:p></span></p><ul type="disc" style="margin-top: 0in; "><li class="MsoNormal"><span style="font-family: Arial; ">Mapping data generated by the LOOM algorithm are now in BioPortal (close to 1 million new lexical-based mappings). See <a href="http://www.bioontology.org/wiki/index.php/LOOM">http://www.bioontology.org/wiki/index.php/LOOM</a> for more details about this tool.<o:p></o:p></span></li><li class="MsoNormal"><span style="font-family: Arial; ">Selected UMLS ontologies are now available in BioPortal. Email <a href="mailto:support@bioontology.org">support@bioontology.org</a> to request loading of additional UMLS ontologies.<o:p></o:p></span></li></ul><p class="MsoNormal"><span style="font-family: Arial; "> <o:p></o:p></span></p><p class="MsoNormal"><span style="font-family: Arial; ">Known Issues:<o:p></o:p></span></p><ul type="disc" style="margin-top: 0in; "><li class="MsoNormal"><span style="font-family: Arial; ">The tree navigation shows ‘Too many children’ in cases where the number of siblings is greater than 500.<o:p></o:p></span></li></ul><p class="MsoNormal"><span style="font-family: Arial; "> <o:p></o:p></span></p><p class="MsoNormal"><span style="font-family: Arial; "> <o:p></o:p></span></p><div class="MsoNormal"><span class="Apple-style-span" style="font-family: Helvetica; font-size: 12px; ">Trish Whetzel, PhD</span></div></div><div apple-content-edited="true"><span class="Apple-style-span" style="font-family: Helvetica; font-size: 12px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Outreach Coordinator</div><div>The National Center for Biomedical Ontology</div><div>Ph: 650-721-2378</div><div><a href="mailto:whetzel@stanford.edu">whetzel@stanford.edu</a></div><div><a href="http://www.bioontology.org/">http://www.bioontology.org</a></div><div><br></div><div> </div><div><br></div></div></div></span></div></div><br></body></html>