NCBO User Profiles

Mining the Gene Wiki for Structured Gene Annotations Using the NCBO Annotator  

“The NCBO Annotator made it exceptionally easy to mine biomedical concepts out of free text" More >
   Andrew Su, PhD
Associate Professor
Department of Molecular and Experimental Medicine
    The Scripps Research Institute




Jessica Turner, PhD, Angela R. Laird, PhD
Georgia State University, Florida International University


A Novel Knowledge Representation Framework for the Statistical Validation of Quantitative Imaging Biomarkers 


Andrew_Buckler“Specify, a web-based tool that helps a researcher to traverse concepts in the ontology according to their relationships to create statements represented as Resource Description Framework (RDF) triples, uses NCBO’s BioPortal as its repository of ontologies, including the QIBO and approximately 200 others. BioPortal encapsulates disparate ontologies and related annotated data in one common interface available via Representational State Transfer (REST) Web service More >


  Andrew J. Buckler, MS, David Paik, PhD, Matt Ouellette, BS, Jovanna Danagoulian, PhD, Gary Wernsing, BS, Baris E. Suzek, PhD
  BBMSC, Stanford University, Georgetown University


OntoFinder/OntoFactory: ontology production based on BioPortal 

Jin-Dong Kim“Ontology engineering can be greatly synergized by the spirit of sharing" More >
  Jin-Dong Kim, Ph.D
  Project Associate Professor
Database Center for Life Science



Semantic Technologies in the Earth and Climate Systems Sciences 

Line Pouchard“The NCBO Virtual Machine installed at ORNL has been invaluable to demonstrate the potential of ontologies and semantics. Scientists apply them for interoperability, and developers have gained a better appreciation for the complexity of interdisciplinary research" More >
  Line Pouchard (lead), Robert Cook, Jim Green, Michaels Huhns, Natasha Noy, Giri Palanisamy
  Oak Ridge National Laboratory, University of South Carolina, Stanford University



Sujatha Mohan“Developing and establishing a web-based integrated RAPID phenotype ontology resource - PhenomeR” More >
  Dr. Sujatha Mohan
  Research Center for Allergy and Immunology (RCAI)
  The Institute of Physical and Chemical Research (RIKEN)




Domeo Annotation Toolkit

“The NCBO BioPortal is an important resource in my work and the REST services made my life as a software developer much easier." More >
Dr. Paolo Ciccarese
Biomedical Informatics Research & Development
Instructor of Neurology at Harvard Medical School
Assistant in Neuroscience at Mass General Hospital



ISA Software and ISA Commons - Standards-Driven Biocuration in Action 

“Our job is to contribute to the realization of the data sharing vision, by empowering scientists to take data management and sharing into their own hands and minimizing the curation effort. The NCBO BioPortal helps us to serve actionable ontologies to our users, shielding them from the underlying complexities." More >
   Dr. Susanna-Assunta Sansone, Eamonn Maguire and Dr. Philippe Rocca-Serra
Infrastructure and Standards for Data Sharing Team
   University of Oxford, UK 


Data Management and Integration in the Biological Sciences 

   Simon Twigger, PhD
Assistant Professor
   Medical College of Wisconsin 



Cross-domain data integration for decision support in life sciences and healthcare 

“Being able to directly import and merge ontologies via NCBO's web services, rather than building them from scratch, has been invaluable in semantically integrating research, public, and clinical data to formal concepts." More >
   Dr. Erich A. Gombocz
Vice President, Chief Scientific Officer
   IO Informatics, Inc. 




Understanding the Molecular Causes of Genetic Diseases and Cancer 

“The NCBO Web services have proven to be invaluable for enabling modern bioinformatics research in our group. We use the Annotator service to identify and study concepts present in our datasets and generate new hypotheses, it is very useful." More >
   Sean Mooney, Ph.D. 
Associate Professor and Director of Bioinformatics
   Buck Institute for Age Research




Building Models to Help Translational Researchers Test Hypotheses 

Gary An picture“Through Interactions with the NCBO I have realized that the development of agent-based modeling is intimately tied to the advances in the ontologies and tools provided by the NCBO via BioPortal.” 

More > 




  Gary An, MD
  Associate Professor of Surgery
Section of General Surgery
Department of Surgery
The University of Chicago


Using NCBO Technology to Help Integrate the Diverse Data, Systems, People, and Organizations Needed for Marine Research   

Duane Edgington“Thanks to its open-source nature, well written code, easy extensibility, and excellent support, BioPortal helped us set up our own deployment, called the MMI Ontology Registry and Repository successfully and in a very short period of time.” More >
  Duane Edgington, Ph.D.
  MMI Principal Investigator
  Software Engineering Group Leader
  Monterey Bay Aquarium Research Institute



Using NCBO Technology to Improve Global Health Outcomes  at the World Health Organization (WHO) 

“NCBO services made it very simple for our developers to import entries from other terminologies directly into the ICD…NCBO technology has changed completely the way that we are thinking about the revision.” More >


   Dr. T.B.  Üstün
Team Coordinator, Classification, Terminologies and Standards
Department of Health Statistics and Informatics
World Health Organization