Annotator Client Examples

Annotator Web service Validation

• Note: All NCBO REST Web services will be required to contain the parameter "apikey=YourApiKey" starting June 2011. The parameter will be added to all Web service calls for the April 27, 2011 release but will not be required until June 2011. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.

• Note for Application Developers: Application developers will also need to include the apikey parameter on all NCBO Web service calls. This allows us to track usage of our system at the level of an application. To obtain an API key, login to BioPortal and go to "Account" where your API key will be displayed. The addition of the API key replaces the use of the email parameter.

* Warning on Examples *

We strongly encourage that all users of the NCBO Annotator Web service use only the virtual ontology identifier. To do so, set the "isVirtualOntolgyId" parameter to "true". This will ensure that you access the version of the ontology that is actually in the database. Failure to do this will result in your code breaking every time we update the database (as often as weekly!).

NCBO Sample Code

• Sample code is available for the Annotator and for use of other NCBO Web services, the code is located here

• For instructions on how to perform a SVN checkout of the sample code, see:

https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=AccessInfo

• ALERT - Setting the parameter 'longestOnly' to true will result in a 500 internal server error. We have an update to handle this more gracefully that will be pushed to production next week (July 5, 2011).

Excel Addin

• NOTE: We are no longer supporting the Excel Addin. If you have use cases for the Addin please email support@bioontology.org so that we can catalog user requests for this tool.
• Use the Annotator directly from within Excel. This Addin provides access to all parameters available for the Annotator and can be used to annotate multiple rows of text data.
• Get the Addin from here.

HTML client example

• HTML Client http://rest.bioontology.org/test_oba.html

NOTE: The list of ontologies that are available via the Annotator Web service are those listed with <status>28</status> from this Web service call: http://rest.bioontology.org/obs/ontologies

Ruby client example

• NCBO Community contributed Annotator client. See http://oba-client.rubyforge.org/index.html

NOTE: The list of ontologies that are available via the Annotator Web service are those listed with <status>28</status> from this Web service call: http://rest.bioontology.org/obs/ontologies

Java client example

• The Java sample client is located in the NCBO Gforge server at:

https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2FJava%2FAnnotator%2F

NOTE: The Apache HttpClient is needed and can be downloaded at: http://hc.apache.org/downloads.cgi Please include a method to set the user agent. See example below. For documentation, see:
http://hc.apache.org/httpclient-3.x/apidocs/org/apache/commons/httpclient/params/HttpMethodParams.html#USER_AGENT
http://en.wikipedia.org/wiki/User_agent

NOTE: The list of ontologies that are available via the Annotator Web service are those listed with <status>28</status> from this Web service call: http://rest.bioontology.org/obs/ontologies

Perl client example

• The Perl client example is located at:

https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2FPerl%2FAnnotator-Perl%2F

For instructions on how to perform a SVN checkout of the code, see: https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=AccessInfo

NOTE: The list of ontologies that are available via the Annotator Web service are those listed with <status>28</status> from this Web service call: http://rest.bioontology.org/obs/ontologies

Python client example

• The Python client is located here

• NCBO Community contributed Annotator client. A Python client has been developed by Nolan Nichols at NLM : [1] Many thanks to him.

NOTE: The list of ontologies that are available via the Annotator Web service are those listed with <status>28</status> from this Web service call: http://rest.bioontology.org/obs/ontologies

R client example

• NCBO Community contributed Annotator client in R donated by Andrew Su is located here. Many thanks to him.

NOTE: The list of ontologies that are available via the Annotator Web service are those listed with <status>28</status> from this Web service call: http://rest.bioontology.org/obs/ontologies