BioPortal 2.3 Release Notes

New features

• BioPortal will process SKOS labels for preferred names, synonyms, etc.
• Ontologies used by Annotator & Hierarchy services will now be updated on a regular basis (around every week).
• The filtering of annotation by semantic types is available only for the ontologies which provide that information
• The Annotator scoring function has changed a bit.
• Users can now exclude the annotations created with synonym terms.
• Users can now exclude the annotations less than a certain length.
• 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.

Please refer to http://www.bioontology.org/wiki/index.php/Annotator_User_Guide for details on Annotator enhancements

New way to address UMLS ontologies

We have harmonized the ontologies in the Annotator and BioPortal. The full list is available at: http://rest.bioontology.org/obs/ontologies. This change has implications when using the Annotator with UMLS ontologies.

• 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 support@bioontology.org to request a specific UMLS ontology to be added to BioPortal.
• UMLS SAB is no longer valid as ontologyId. Please refer to http://bioportal.bioontology.org/ontologies/?filter=UMLS to map your SAB to the corresponding ontology version id.
• UMLS CUIs are no longer valid as conceptId. You can look up the conceptId corresponding to a CUI by using the NCBO search interface (http://bioportal.bioontology.org/search): type in the CUI and check "Include attributes in search". You can also use the search REST service (http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Search_services) 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.

Known issues

• ISA closure in the Annotator and Hierarchy services do not work properly for NCIT and Galen. This will be fixed in an upcoming release.
• Some mappings present in BioPortal are not yet available for use with the Annotator.

Other features and bug fixes

• Implemented updates to Hierarchy (OBS Wrapper) Services to conform to the new OBS output XML structure
• Added case sensitivity check for the root concept (per #1793)
• Upgraded the deprecated Acegi Security to Spring Security
• Implemented support for OpenID Authentication
• New lexbig JAR intended to fix the problem with the graph not focused properly when there are 2 ontologies with the same uri.(Bioportal bug #1783)