THE NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY BioPortal Updates and Planned Features Trish Whetzel May 3, 2012.

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Presentation transcript:

THE NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY BioPortal Updates and Planned Features Trish Whetzel May 3, 2012

New Functionality in Last Year Allow BioPortal configuration – My Bioportal, Slices Improved support for Notes – Provisional ids for new terms, archiving, 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 Page Recommender Tab

Browse Page Custom display of selected ontologies Custom display of selected ontologies

Search

Ontology Recommender

Annotator

Slice

Resource Index

ODiSSea – Elsevier SciVerse

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 OWL RDF Protégé frames Ruby on Rails OBO format UMLS RRF LexGrid XML Transform Server CTS2

BioPortal SPARQL Endpoint

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 ( ) – 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 EST_services Release Notes – ease_Notes ease_Notes Software questions – Software support: Social media – – Facebook: – LinkedIn: