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 REST Web Service Usage

All to NCBO REST web services MUST append a search query parameter with the pattern of "emai=ENCODEDEMAIL" where ENCODEDEMAIL is your user URL encoded email address. For example, benjamin.dai@stanford.edu would look like benjamin.dai%40stanford.edu. This is critical to ensure we can maintain the quality of service expected for you as our customers. Later in 2009, we will likely begin rejecting REST service calls that do not have this paramter. In the meantime, please start adding this URL parameter to all your REST calls.

NCBO Products

Below are developer links associated with the various NCBO products and solutions.

BioPortal

Focus: Browsing, searching and exploring Biomedical Ontologies. In addition, BioPortal contains mappings between ontologies and a list of ontology-based projects.

BioPortal 2.0 REST web service API documentation and examples.

Previous documentation:

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 - 11/13/2008

BioPortal 2.0.3 (Label 1012) Release Notes - 11/21/2008

BioPortal 2.0.4 (Label 1016) Release Notes - 1/13/2009

Open Biomedical Resources

Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here: http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: OBR Stand-Alone User Interface.

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 prototype 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

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

BioPortal Repository Plugin for Protege 4

Focus: Leveraging BioPortal Ontologies in Protege 4

BioPortal Repository Plugin for Protege 4 - Documentation Under Construction

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).

OOR

The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

• Establishing a host registry-repository
• Enabling and facilitating open, federated, collaborative ontology repositories
• Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the NCBO-OOR Development page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

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/