BioPortal 2.3 Release Notes
- 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 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 firstname.lastname@example.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- UMLS SAB is no longer valid as ontologyId.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- UMLS CUIs are no longer valid as conceptId.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.
- 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)