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THE NATIONAL CENTER FORBIOMEDICAL ONTOLOGY
BioPortal Updates and Planned Features
Trish WhetzelMay 3, 2012
New Functionality in Last Year
• Allow BioPortal configuration– My Bioportal, Slices
• Improved support for Notes– Provisional ids for new terms, archiving, email notification
• Allow private and licensed ontologies• Flag obsolete terms• “Productionized” Ontology Recommender• Automated handling of OWL2 ontologies• Created beta version of triple-store architecture
Systemic Improvements
• Solidified core system• Monthly release schedule• Many long-standing bugs fixed• Established regular VM release cycle (3x/year)• Reworked entire UI to be simpler and more consistent• Improved Annotator performance by 5-10x• Improved user-tracking with API Key mechanism
Home PageRecommender Tab
Browse Page
Custom display of selected ontologies
Search
Ontology Recommender
Annotator
Slice
Resource Index
ODiSSea – Elsevier SciVerse
Who is using our Web services?
Who is using our Web services?
Technical Aims
1. Develop, enhance, and deploy software services and tools that allow investigators to use ontologies.
2. Integrate ontology publishing and peer review with ontology authoring.
3. Create a comprehensive ontology-based index for publicly available biomedical resources.
4. Develop analytic methods to summarize and profile biomedical data sets.
Plans for Coming Year
• Move RDF triple-store from beta to production release*• Synchronize Annotator and Mappings to ontology submission
and update• Re-implement Annotator and Resource Index to be more
reliable, better performing, and more scalable• Add additional resources in Resource Index• Provide improved support for projects and views• Implement CTS2 API for BioPortal*• Replace FlexViz Ontology Visualization with BioMixer*
* Beta version of feature
BioPortal Architecture Updates
RDF LexEVSProtégé DB
Hibernate ORM
Spring Framework
Restlet
Tomcat
OWLRDFProtégé frames
Ruby on Rails
OBO format UMLS RRFLexGrid XML
Transform Server
CTS2
BioPortal SPARQL Endpoint
http://sparql.bioontology.org/
Concluded Driving Biological Projects
• Candidate Gene Discovery through Ontological Indexing– Medical College of Wisconsin; Simon Twigger
• Annotation of Biomedical Data in CVRG– Johns Hopkins; Rai Winslow
• Cancer Nanotechnology Knowledge Base– Stanford/PNNL; David Paik & Nathan Baker
New Driving Biological Projects
• Ontology-driven analysis of high-throughput data– European Bioinformatics Institute;
Helen Parkinson
• Using ontologies and data fusion approaches to understand organismal aging– Buck Institute for Research on Aging;
Sean Mooney
• Synapse: A precondition space for integrative genomics– Sage Bionetworks; Michael Kellen
Collaborative R01 Projects
• Active– Integrative Tools for Protozoan Parasite Research - Chris Stoeckert, UPenn
• Completed (2011-2012) – Reference Ontologies for the Semantic Web - Jim Brinkley, University of
Washington– Neuroscience Information Framework - Maryann Martone, UCSD – Ontologies and Biomedical Language Processing - Larry Hunter, University of
Colorado– Ontology Development Information Extraction - Rebecca Crowley, University
of Pittsburgh– Context-based Ontology Integration - Gil Alterovitz, Brigham and Women’s
Hospital– Semantics and Services Enabled Problem Solving Environment for T. cruzi -
Amit Sheth, Wright State
Other NCBO collaborations
• Informatics for Integrating Biology and the Bedside (i2b2)
• BioSitemaps• UCSF Clinical and Translational Sciences
Institute• BioSharing (including Minimal Information for
Biological and Biomedical Investigations)• BioDBCore initiative of the
International Society for Biocuration
Links of Interest• Web service documentation
http://www.bioontology.org/wiki/index.php/NCBO_REST_services
• Release Notes– http://www.bioontology.org/wiki/index.php/
BioPortal_Release_Notes • Software questions– Software support: [email protected]
• Social media– Twitter: @bioontology– Facebook: http://on.fb.me/bioontology – LinkedIn: http://linkd.in/ncbo-group
