BioPortal 2.3 Release Notes

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New features

  • BioPortal will process SKOS labels for preferred names and synonyms:
  • 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.
  • Users can now define target terminologies for RRF ontologies via the BioPortal UI.
  • Referencing the tabs on ontology visualization pages in the BioPortal UI is now done using the tab name:

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  • UMLS SAB is no longer valid as ontologyId.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  • UMLS CUIs are no longer valid as conceptId.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)