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[protege-discussion] BioPortal 2.2 Release

Trish Whetzel plwhetzel at
Wed Oct 28 23:16:13 PDT 2009

The BioPortal team is pleased to announce the release of BioPortal 2.2 ( Release notes and known issues are
listed below.

New Features

   - Ontology Views

   - 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.
      - A view can also serve as a mechanism to define value sets, which are
      quite useful in combination with the BioPortal ontology-term selection
      - View generation and storage in BioPortal is the result of
      collaboration with Dr. Jim Brinkley’s group at the University of
   - NCBO Resource Index
      - 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:  Array Express, Biositemaps,
      caNanoLab, Conserved Domain Database,, DrugBank, Gene
      Expression Omnibus, Online Mendelian Inheritance in Man,
PharmGKB, Reactome,
      ResearchCrossroads (Grant funding database), Stanford Microarray
      UniProt KB, and WikiPathways.  The resulting annotations are
      accessible for browsing via the Resources tab corresponding to
any ontology
      concept. The annotations can also be accessed programmatically:
      - If you have recommendations on additional publicly accessible
      resources to index, let us know at support at
   - Search filter for Ontology Groups and Categories
      - 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.,

New REST Web Services

   - Services to access ontologies and ontology versions
      - List all Categories
      - List all Groups
      - Download by virtual ontology identifier
   - Services to access ontology views and ontology view versions
      - List all Views of all Ontologies (lists the latest version)
      - List all versions for a given View
   - Concept services
      - Get all concepts
   - Search service – parameter added to enable search within an ontology
   - Service to access the NCBO Resource Index

See for
the full list of BioPortal REST Web services.

New Data:

   - Mapping data generated by the LOOM algorithm are now in BioPortal
   (close to 1 million new lexical-based mappings). See for more details about
   this tool.
   - Selected UMLS ontologies are now available in BioPortal. Email
   support at to request loading of additional UMLS ontologies.

Known Issues:

   - The tree navigation shows ‘Too many children’ in cases where the number
   of siblings is greater than 500.

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at

bioportal-announce mailing list
bioportal-announce at
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