Difference between revisions of "NCBO Developer Documentation"
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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. | 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 | + | =NCBO Virtual Appliance= |
| − | + | If you would like to install your own local instance of BioPortal, please review the documentation for the [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance Virtual Appliance] and contact [mailto:support@bioontology.org Support] to request the virtual appliance. | |
| − | =NCBO | + | =NCBO Software= |
| − | Below are developer links | + | Below are developer links for NCBO software items. |
| − | ==BioPortal | + | ==BioPortal== |
| − | Focus: | + | Focus: Browsing and searching biomedical ontologies. |
| − | The | + | BioPortal provides access via both Web browsers and Web services to biomedical ontologies. Features include browsing, searching and exploring biomedical ontologies. BioPortal also contains mappings between ontologies and facilitates point-to-point mappings to be added as well as bulk upload of mappings. The Notes feature allows comments to be added to individual ontology terms for discussion with the ontology curators. The Project section of BioPortal contains a list of ontology-based projects. Login and add your ontology-based project to the list! |
| − | + | Additional features include a text annotation tool where the user can select any or all ontologies in BioPortal to use for the annotation. One can also search ontology-indexed resources such as GEO (Gene Expression Omnibus), ClinicalTrials.gov, and Reactome through BioPortal. | |
| − | + | ===NCBO Web Services === | |
| + | All BioPortal REST web service calls '''MUST append a search query parameter''' with the pattern of "email=YourEmail". Note that some clients may need to use a URL encoded email address, for example ''user@example.edu'' would look like ''user%40example.edu''. This is critical to ensure we can maintain the quality of service expected for you as our customer. Later in 2009, we may start challenging REST service calls that do not have this parameter. In the meantime, please start adding this URL parameter to all your web service invocations. | ||
| − | + | - See [[NCBO_REST_services|NCBO Web services]] for API documentation and examples. | |
| − | |||
| − | |||
| − | + | Previous documentation: | |
| + | [[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]] | ||
| − | [ | + | [[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]] |
| − | [[ | + | ===Widgets=== |
| + | See [[NCBO_Widgets|Widgets]] for information on how to add BioPortal widgets to your web site. | ||
| − | === | + | ===Local Installation=== |
| − | [ | + | If you would like to install your own local instance of BioPortal, please review the documentation for the [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance Virtual Appliance] and contact [mailto:support@bioontology.org Support] to request the virtual appliance. |
| − | == | + | ==NCBO Resource Index== |
Focus: Using Ontologies to Access Public Data | Focus: Using Ontologies to Access Public Data | ||
| + | Formerly named Open Biomedical Resources. | ||
| + | Technical documentation, prototypes and products will be available here: [[Resource_Index|NCBO Resource Index]] | ||
| − | + | ==NCBO Annotator== | |
| − | + | Focus: Using Ontologies to Annotate Your Data. | |
| − | + | Formerly the Open Biomedical Annotator. | |
| − | == | ||
| − | Focus: Using Ontologies to Annotate Your Data | ||
| − | Technical documentation, prototypes and products will be available here: | + | Technical documentation, prototypes and products will be available here: [[Annotator_Web_service|NCBO Annotator]]. |
| − | |||
| − | ==UMLS Services== | + | ==UMLS Web Services== |
| − | + | Web services to access UMLS terminologies are now available as one of the [[BioPortal_REST_services|NCBO Web services]]. | |
==Developer Documentation Under Development== | ==Developer Documentation Under Development== | ||
| Line 51: | Line 51: | ||
===NCBO PURL Server=== | ===NCBO PURL Server=== | ||
Focus: Providing URIs for Biomedical Concepts | Focus: Providing URIs for Biomedical Concepts | ||
| + | |||
| + | The NCBO PURL server is accessible at http://purl.bioontology.org. | ||
| + | |||
| + | ===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= | =NCBO Partner Development= | ||
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base. | 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/ | *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]] | *Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]] | ||
| − | *The MMI Ontology Repository is | + | *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== | ==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/ | 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/ | ||
Latest revision as of 18:44, 26 October 2012
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 Virtual Appliance
If you would like to install your own local instance of BioPortal, please review the documentation for the Virtual Appliance and contact Support to request the virtual appliance.
NCBO Software
Below are developer links for NCBO software items.
BioPortal
Focus: Browsing and searching biomedical ontologies.
BioPortal provides access via both Web browsers and Web services to biomedical ontologies. Features include browsing, searching and exploring biomedical ontologies. BioPortal also contains mappings between ontologies and facilitates point-to-point mappings to be added as well as bulk upload of mappings. The Notes feature allows comments to be added to individual ontology terms for discussion with the ontology curators. The Project section of BioPortal contains a list of ontology-based projects. Login and add your ontology-based project to the list!
Additional features include a text annotation tool where the user can select any or all ontologies in BioPortal to use for the annotation. One can also search ontology-indexed resources such as GEO (Gene Expression Omnibus), ClinicalTrials.gov, and Reactome through BioPortal.
NCBO Web Services
All BioPortal REST web service calls MUST append a search query parameter with the pattern of "email=YourEmail". Note that some clients may need to use a URL encoded email address, for example user@example.edu would look like user%40example.edu. This is critical to ensure we can maintain the quality of service expected for you as our customer. Later in 2009, we may start challenging REST service calls that do not have this parameter. In the meantime, please start adding this URL parameter to all your web service invocations.
- See NCBO Web services for 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)
Widgets
See Widgets for information on how to add BioPortal widgets to your web site.
Local Installation
If you would like to install your own local instance of BioPortal, please review the documentation for the Virtual Appliance and contact Support to request the virtual appliance.
NCBO Resource Index
Focus: Using Ontologies to Access Public Data Formerly named Open Biomedical Resources. Technical documentation, prototypes and products will be available here: NCBO Resource Index
NCBO Annotator
Focus: Using Ontologies to Annotate Your Data. Formerly the Open Biomedical Annotator.
Technical documentation, prototypes and products will be available here: NCBO Annotator.
UMLS Web Services
Web services to access UMLS terminologies are now available as one of the NCBO Web services.
Developer Documentation Under Development
NCBO PURL Server
Focus: Providing URIs for Biomedical Concepts
The NCBO PURL server is accessible at http://purl.bioontology.org.
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/