[bioportal-announce] BioPortal 2.2 Release
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Trish Whetzel
Oct 28, 2009, 10:34:52 PM10/28/09
to bioportal...@lists.stanford.edu
The BioPortal team is pleased to announce the release of BioPortal 2.2 (http://bioportal.bioontology.org/). 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 widget.
- View generation and storage in BioPortal is the result of collaboration with Dr. Jim Brinkley’s group at the University of Washington.
- 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, ClinicalTrials.gov, DrugBank, Gene Expression Omnibus, Online Mendelian Inheritance in Man, PharmGKB, Reactome, ResearchCrossroads (Grant funding database), Stanford Microarray Database, 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: http://www.bioontology.org/wiki/index.php/Resource_Index.
- If you have recommendations on additional publicly accessible resources to index, let us know at sup...@bioontology.org.
- 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., anatomy).
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 branch
- Service to access the NCBO Resource Index
See http://www.bioontology.org/wiki/index.php/BioPortal_REST_services 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 http://www.bioontology.org/wiki/index.php/LOOM for more details about this tool.
- Selected UMLS ontologies are now available in BioPortal. Email sup...@bioontology.org 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
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