BioPortal 2.3 Release Notes

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Revision as of 17:39, 2 February 2010 by Noy (talk | contribs) (Known issues)
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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 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: 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 to request a specific UMLS ontology to be added to BioPortal.
  • UMLS SAB is no longer valid as ontologyId. Please refer to 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  • UMLS CUIs are no longer valid as conceptId.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 ( type in the CUI and check "Include attributes in search". You can also use the search REST service ( 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)