[Po-dev] [bioportal-announce] BioPortal 2.2 Release

[Trish Whetzel]

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 support at 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 support at 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
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at stanford.edu
http://www.bioontology.org




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