Sample Code Cookbook - Revision history

Dan Bolser: Fixing a link

2012-09-18T11:31:38Z

Fixing a link

Whetzel at 03:55, 13 March 2012

2012-03-13T03:55:13Z

Whetzel at 03:54, 13 March 2012

2012-03-13T03:54:37Z

Whetzel at 03:54, 13 March 2012

2012-03-13T03:54:03Z

Whetzel at 03:53, 13 March 2012

2012-03-13T03:53:25Z

Whetzel at 09:13, 22 August 2011

2011-08-22T09:13:09Z

Whetzel at 19:27, 3 November 2010

2010-11-03T19:27:44Z

Whetzel: /* Use Cases */

2010-11-03T19:27:16Z

Use Cases

Whetzel at 18:40, 3 November 2010

2010-11-03T18:40:51Z

Whetzel: SampleCodeCookbook moved to Sample Code Cookbook: Add spaces to page name for readability and searchability.

2010-11-03T06:30:34Z

SampleCodeCookbook moved to Sample Code Cookbook: Add spaces to page name for readability and searchability.

← Older revision		Revision as of 11:31, 18 September 2012
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	'''I have a web form with text fields I would like to populate with ontology terms, e.g. to select relevant Gene Ontology terms.'''		'''I have a web form with text fields I would like to populate with ontology terms, e.g. to select relevant Gene Ontology terms.'''
−	* Use the Autocomplete widget (~~example for the Gene Ontology,~~ http://bioportal.bioontology.org/ontologies/44532#widgets). Select the "Get Code" button for the code and instructions on how to add this Javascript to your web form. If you would like to limit the terms to a subset of the Gene Ontology, create this subset and then load this ontology subset as a View of the Gene Ontology (http://bioportal.bioontology.org/ontologies/44532#views).	+	* Use the Autocomplete widget ([http://bioportal.bioontology.org/ontologies/44532?p=widgets example for the Gene Ontology]). Select the "Get Code" button for the code and instructions on how to add this Javascript to your web form. If you would like to limit the terms to a subset of the Gene Ontology, create this subset and then load this ontology subset as a View of the Gene Ontology (http://bioportal.bioontology.org/ontologies/44532#views).

@@ Line 2: / Line 2: @@
 <hr>
-'''Email us your Sample Code Cookbook request at bioontology-support _at_ lists.stanford.edu'''
+''Email us your Sample Code Cookbook request at bioontology-support _at_ lists.stanford.edu''
 <hr>

@@ Line 2: / Line 2: @@
 <hr>
-Email us your Sample Code Cookbook request to bioontology-support _at_ lists.stanford.edu
+'''Email us your Sample Code Cookbook request at bioontology-support _at_ lists.stanford.edu'''
 <hr>

@@ Line 2: / Line 2: @@
 <hr>
-* Email us your Sample Code Cookbook request to bioontology-support@lists.stanford.edu
+Email us your Sample Code Cookbook request to bioontology-support _at_ lists.stanford.edu
 '''I have a list of terms that were used to annotate a data set, how can I see if any of these terms exist in standard ontologies?'''

@@ Line 1: / Line 1: @@
 This page lists use cases and provides examples of how these questions can be answered using NCBO software (web services and widgets), and includes links to code samples and documentation.
 <hr>
 '''I have a list of terms that were used to annotate a data set, how can I see if any of these terms exist in standard ontologies?'''

← Older revision		Revision as of 09:13, 22 August 2011
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	* Use the Get All Terms Web service to get all terms and properties for your ontology of interest.		* Use the Get All Terms Web service to get all terms and properties for your ontology of interest.
	** Get All Terms Web service documentation: http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_all_terms_using_the_specific_ontology_version_id and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_all_terms_using_the_virtual_ontology_id) to get a list of all of the terms and all details about each term, e.g. synonyms, definition, subclass, etc.		** Get All Terms Web service documentation: http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_all_terms_using_the_specific_ontology_version_id and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_all_terms_using_the_virtual_ontology_id) to get a list of all of the terms and all details about each term, e.g. synonyms, definition, subclass, etc.
		+
		+	'''I need to navigate through an ontology and traverse the ontology hierarchy for my software application, how can I use the Web services to do this?'''
		+	* Use the Get All terms Web service.
		+	** Example coming soon...
		+
		+	'''How can I limit the selection of ontologies used with the NCBO Annotator to a certain Category or Domain?'''
		+	* Use the List all ontologies and Get Groups/Domains Web service to identify the group/domain of interest.
		+	** Example coming soon...

← Older revision		Revision as of 19:27, 3 November 2010
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	This page lists use cases and provides examples of how these questions can be answered using NCBO software (web services and widgets), and includes links to code samples and documentation.		This page lists use cases and provides examples of how these questions can be answered using NCBO software (web services and widgets), and includes links to code samples and documentation.
		+	<hr>

	'''I have a list of terms that were used to annotate a data set, how can I see if any of these terms exist in standard ontologies?'''		'''I have a list of terms that were used to annotate a data set, how can I see if any of these terms exist in standard ontologies?'''

@@ Line 2: / Line 2: @@
 == Use Cases ==
-* I have a list of terms that were used to annotate a data set, how can I see if any of these terms exist in standard ontologies?
+'''I have a list of terms that were used to annotate a data set, how can I see if any of these terms exist in standard ontologies?'''
-** Use the Search Web service to search for your term in all ontologies in BioPortal. If you have a small list of terms, searching each term individually via the [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services BioPortal Search UI] may be sufficient. Otherwise, for a long list of terms, use the Search Web service directly.
+* Use the Search Web service to search for your term in all ontologies in BioPortal. If you have a small list of terms, searching each term individually via the [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services BioPortal Search UI] may be sufficient. Otherwise, for a long list of terms, use the Search Web service directly.
-*** Search Web service documentation: http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services
+** Search Web service documentation: http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services
-*** Example code: https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F
+** Example code: https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F
-* I am the curator for a database and need to triage papers to identify which papers from PubMed are most related to my database and a good source of new information to add to my database
+'''I would like to find all terms mapped from my ontology to other ontologies in BioPortal'''
-** Use the Annotator Web service to identify ontology terms in textual data.
+* Use the Mapping web service to find terms in other BioPortal ontologies similar to terms in your ontology. These mappings include mapping generated manually (DbXrefs) and programatically (LOOM).
-*** Annotator Web service documentation: http://www.bioontology.org/wiki/index.php/Annotator_Web_service
+** Mapping Web service documentation: http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Mapping_Service
-*** Example code: https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2FJava%2FAnnotator%2F (Java), https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2FPython%2FAnnotator%2F (Python)
+** Example code: https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2FPerl%2FExtractMappings%2F
-* I have a web form with text fields I would like to populate with ontology terms, e.g. to select relevant Gene Ontology terms.
+'''I am the curator for a database and need to triage papers to identify which papers from PubMed are most related to my database and a good source of new information to add to my database'''
-** Use the Autocomplete widget (example for the Gene Ontology, http://bioportal.bioontology.org/ontologies/44532#widgets). Select the "Get Code" button for the code and instructions on how to add this Javascript to your web form.  If you would like to limit the terms to a subset of the Gene Ontology, create this subset and then load this ontology subset as a View of the Gene Ontology (http://bioportal.bioontology.org/ontologies/44532#views).
+* Use the Annotator Web service to identify ontology terms in textual data.
-* I would like to get all terms from an ontology and re-format the data to use in my own system.
+'''I have PubMed abstracts and want to link information in the abstracts to my database of interest.'''
-** Use the Get All Terms Web service to get all terms and properties for your ontology of interest.
+* Use the Annotator Web service. If your database of interest is included in the NCBO Resource Index you can search the database(s) for records that contain these terms. See http://www.bioontology.org/wiki/index.php/Resource_Index for more details on the Resource Index web service.
-*** Get All Terms Web service documentation: http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_all_terms_using_the_specific_ontology_version_id and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_all_terms_using_the_virtual_ontology_id) to get a list of all of the terms and all details about each term, e.g. synonyms, definition, subclass, etc.