NCBO Developer Documentation
With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.
NCBO Source Code Repository
NCBO source code for all products and solutions can be found on our [NCBO GForge site|https://bmir-gforge.stanford.edu/gf/project/ncbo/].
NCBO Products
Below are developer links associated with the various NCBO products and solutions.
BioPortal 2.0
Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.
The following two document describe the BioPortal 2.0 REST web service APIs.
BioPortal 2.0 REST Web Service URL Documentation
BioPortal 2.0 REST Web Service URL Documentation (with Admin role)
Local Installation
Please contact BioPortal Support for information on how to request or contribute features.
Release Notes
BioPortal 2.0.1 (Label 1005) Release Notes - 9/19/2008
BioPortal 2.0.2 (Label 1006) Release Notes - Under Construction
Open Biomedical Resources
Focus: Using Ontologies to Access Public Data
Technical documentation, prototypes and products will be available here: http://obs.bioontology.org/
Open Biomedical Annotator
Focus: Using Ontologies to Annotate Your Data
Technical documentation, prototypes and products will be available here: http://obs.bioontology.org/
UMLS Services
The UMLS Services pertain to a number of internally reusable services and APIs. Our UMLS REST Services are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.
Developer Documentation Under Development
NCBO PURL Server
Focus: Providing URIs for Biomedical Concepts
NCBO Partner Development
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.
Marine Metadata Interoperability
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.
- For more information about MMI, please peruse their web site: http://marinemetadata.org/
- Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: MMI Development
- The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).
National Cancer Institute
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/