Difference between revisions of "BioPortal REST services"
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(Updated service descriptions for Bioportal release 2.0.4) |
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This page documents the signatures for NCBO (and, more specifically, BioPortal) REST services. This list may not be exhaustive. | This page documents the signatures for NCBO (and, more specifically, BioPortal) REST services. This list may not be exhaustive. | ||
| − | '''Note''': ''Signatures for BioPoral services | + | '''Note''': ''Signatures for BioPoral services have changed in Bioportal 2.0.4 release on January 13th, 2009. This page has the new service URLs. If you have any questions, please contact [mailto:bioontology-support@lists.stanford.edu BioPortal Support].'' |
The '''prefix''' for all service URLs in the table below is http://rest.bioontology.org/bioportal/rest | The '''prefix''' for all service URLs in the table below is http://rest.bioontology.org/bioportal/rest | ||
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* '''Signature''': ./ontologies | * '''Signature''': ./ontologies | ||
| − | * '''Example''': http://rest.bioontology.org/bioportal | + | * '''Example''': http://rest.bioontology.org/bioportal/ontologies |
== Find a specific ontology based on a version id == | == Find a specific ontology based on a version id == | ||
* '''Signature''': ./ontologies/{ontology version id} | * '''Signature''': ./ontologies/{ontology version id} | ||
| − | * '''Example''': http://rest.bioontology.org/bioportal | + | * '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002 |
== Find all versions of an ontology form a virtual ontology id == | == Find all versions of an ontology form a virtual ontology id == | ||
* '''Signature''':./virtual/{virtual ontology id} | * '''Signature''':./virtual/{virtual ontology id} | ||
| − | * '''Example''': http://rest.bioontology.org/bioportal | + | * '''Example''': http://rest.bioontology.org/bioportal/virtual/1104 |
== Download an ontology file == | == Download an ontology file == | ||
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version ID. | * '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version ID. | ||
* '''Signature''': ./ontologies/download/{ontology version id} | * '''Signature''': ./ontologies/download/{ontology version id} | ||
| − | * '''Example''': http://rest.bioontology.org/bioportal | + | * '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002 |
| − | == Get | + | == Get version ids based on a virtual ontology id == |
| − | * '''Signature''': ./ontologies/ | + | * '''Signature''': ./ontologies/versions/{ontology id} |
| − | * '''Example''': http://rest.bioontology.org/bioportal | + | * '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104 |
== Get latest version of an ontology id == | == Get latest version of an ontology id == | ||
* '''Signature''': ./virtual/{ontology_id} | * '''Signature''': ./virtual/{ontology_id} | ||
| − | * '''Example''': http://rest.bioontology.org/bioportal | + | * '''Example''': http://rest.bioontology.org/bioportal/virtual/1104 |
== Get concept id == | == Get concept id == | ||
* '''Signature''': ./concepts/{ontology version id}/{concept id} | * '''Signature''': ./concepts/{ontology version id}/{concept id} | ||
| − | * '''Example''': http://rest.bioontology.org/bioportal | + | * '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource |
== Get all root concepts for an ontology id == | == Get all root concepts for an ontology id == | ||
* '''Signature''': ./concepts/{ontology version id}/root | * '''Signature''': ./concepts/{ontology version id}/root | ||
| − | * '''Example''': http://rest.bioontology.org/bioportal | + | * '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root |
== Search for concepts id == | == Search for concepts id == | ||
* '''Signature''': ./search/concepts/{query>?ontologies={ids} | * '''Signature''': ./search/concepts/{query>?ontologies={ids} | ||
| − | * '''Example''': http://rest.bioontology.org/bioportal | + | * '''Example''': http://rest.bioontology.org/bioportal/search/concepts/cancer?ontologies=13578,38312 |
== Get concept for latest ontology version id == | == Get concept for latest ontology version id == | ||
* '''Signature''': ./virtual/{ontology id}/{concept id} | * '''Signature''': ./virtual/{ontology id}/{concept id} | ||
| − | * '''Example''': http://rest.bioontology.org/bioportal | + | * '''Example''': http://rest.bioontology.org/bioportal/virtual/1104/BRO:Resource |
| + | |||
| + | == Search BioPortal == | ||
| + | * '''Signature''': ./search/{query}[?{optional args}] | ||
| + | * '''Example''': http://rest.bioontology.org/bioportal/search/Gene | ||
| + | * You can use multiple query terms, separated by a space, for example: [http://rest.bioontology.org/bioportal/search/lung%20disease http://rest.bioontology.org/bioportal/search/lung disease] | ||
| + | * '''Optional arguments:''' | ||
| + | ** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies) | ||
| + | ** isexactmatch=[1/0] – match the entire concept name (default: 0) | ||
| + | ** includeproperties=[1/0] – include attributes in the search (default: 0) | ||
| + | ** pagesize=<pagesize> - the number of results to display in a single request (default: all) | ||
| + | ** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1) | ||
| + | ** '''Example''': http://rest.bioontology.org/bioportal/search/software/?ontologyid=39002&isexactmatch=1 | ||
== List all ontology categories id == | == List all ontology categories id == | ||
* '''Signature''': ./categories | * '''Signature''': ./categories | ||
| − | * '''Example''': http://rest.bioontology.org/bioportal | + | * '''Example''': http://rest.bioontology.org/bioportal/categories |
Revision as of 15:30, 13 January 2009
This page documents the signatures for NCBO (and, more specifically, BioPortal) REST services. This list may not be exhaustive.
Note: Signatures for BioPoral services have changed in Bioportal 2.0.4 release on January 13th, 2009. This page has the new service URLs. If you have any questions, please contact BioPortal Support.
The prefix for all service URLs in the table below is http://rest.bioontology.org/bioportal/rest
List all the latest version of ontologies
- Signature: ./ontologies
- Example: http://rest.bioontology.org/bioportal/ontologies
Find a specific ontology based on a version id
- Signature: ./ontologies/{ontology version id}
- Example: http://rest.bioontology.org/bioportal/ontologies/39002
Find all versions of an ontology form a virtual ontology id
- Signature:./virtual/{virtual ontology id}
- Example: http://rest.bioontology.org/bioportal/virtual/1104
Download an ontology file
- Description: Download the file (.obo, .owl) corresponding to the given ontology version ID.
- Signature: ./ontologies/download/{ontology version id}
- Example: http://rest.bioontology.org/bioportal/ontologies/download/39002
Get version ids based on a virtual ontology id
- Signature: ./ontologies/versions/{ontology id}
- Example: http://rest.bioontology.org/bioportal/ontologies/versions/1104
Get latest version of an ontology id
- Signature: ./virtual/{ontology_id}
- Example: http://rest.bioontology.org/bioportal/virtual/1104
Get concept id
- Signature: ./concepts/{ontology version id}/{concept id}
- Example: http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource
Get all root concepts for an ontology id
- Signature: ./concepts/{ontology version id}/root
- Example: http://rest.bioontology.org/bioportal/concepts/39002/root
Search for concepts id
- Signature: ./search/concepts/{query>?ontologies={ids}
- Example: http://rest.bioontology.org/bioportal/search/concepts/cancer?ontologies=13578,38312
Get concept for latest ontology version id
- Signature: ./virtual/{ontology id}/{concept id}
- Example: http://rest.bioontology.org/bioportal/virtual/1104/BRO:Resource
Search BioPortal
- Signature: ./search/{query}[?{optional args}]
- Example: http://rest.bioontology.org/bioportal/search/Gene
- You can use multiple query terms, separated by a space, for example: http://rest.bioontology.org/bioportal/search/lung disease
- Optional arguments:
- ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)
- isexactmatch=[1/0] – match the entire concept name (default: 0)
- includeproperties=[1/0] – include attributes in the search (default: 0)
- pagesize=<pagesize> - the number of results to display in a single request (default: all)
- pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)
- Example: http://rest.bioontology.org/bioportal/search/software/?ontologyid=39002&isexactmatch=1
List all ontology categories id
- Signature: ./categories
- Example: http://rest.bioontology.org/bioportal/categories