Lexicon Builder - Revision history

Fergerson: /* Code location */

2014-03-18T21:56:47Z

Code location

Nigam: /* Publication */

2011-02-01T22:53:20Z

Publication

Nigam: /* Code location */

2011-02-01T22:52:44Z

Code location

Alexskr at 00:41, 26 January 2011

2011-01-26T00:41:33Z

Whetzel: /* Introduction */

2010-07-11T22:50:42Z

Introduction

Whetzel: /* Introduction */

2010-07-11T22:49:26Z

Introduction

Nigam at 00:51, 20 February 2010

2010-02-20T00:51:27Z

Gkparai: /* Usage */

2010-01-19T20:07:16Z

Usage

Gkparai: /* Usage */

2010-01-19T20:04:53Z

Usage

Gkparai: /* Usage */

2010-01-19T20:03:59Z

Usage

@@ Line 9: / Line 9: @@
 == Code location ==
-https://bmir-gforge.stanford.edu/gf/project/lexicon_builder/
+The prototype Lexicon Builder code and REST services are no longer available. We plan to reimplement the Lexicon Builder in 2014-2015.
 == Publication ==

@@ Line 22: / Line 22: @@
 The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies
 Gautam Kumar Parai, Clement Jonquet, Rong Xu, Mark A. Musen and Nigam H. Shah
-AMIA Annu Symp Proc. 2010 [[Media:LexiconBuilder.pdf]]
+AMIA Annu Symp Proc. 2010
 == Usage ==

← Older revision		Revision as of 22:52, 1 February 2011
Line 17:		Line 17:

	'''Note: The prototype is currently in the development phase and constantly undergoing changes.'''		'''Note: The prototype is currently in the development phase and constantly undergoing changes.'''
		+
		+	== Publication ==
		+
		+	The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies
		+	Gautam Kumar Parai, Clement Jonquet, Rong Xu, Mark A. Musen and Nigam H. Shah
		+	AMIA Annu Symp Proc. 2010 [[Media:LexiconBuilder.pdf]]

	== Usage ==		== Usage ==

@@ Line 11: / Line 11: @@
 https://bmir-gforge.stanford.edu/gf/project/lexicon_builder/
-Home page: http://ncbolabs-dev1.stanford.edu:8080/LexiconBuilder/
+Home page: http://labs.bioontology.org/LexiconBuilder/
-The Service end point:    http://ncbolabs-dev1.stanford.edu:8080/LexiconBuilderService/
+The Service end point:    http://labs.bioontology.org/LexiconBuilderService/

@@ Line 3: / Line 3: @@
 The LexiconBuilder project has been undertaken for creating a Web service that allows building of custom lexicons from BioPortal ontologies. The custom lexicons built by our system can be used for a variety of natural language processing and other ontology related tasks.
-While generating the custom lexicons, several features of our system can be utilized for ease of creation, integration and maintainence of such lexicons. The users can specify ontology mappings in order to identify and retrieve relevant concepts in other ontologies which they might not even know about, in order to assist in enriching the custom lexicons. It also facilitates the interpretation of datasets using the concept mappings between particular datasets. They can also make use of the visualization services provided by NCBO to view and understand the ontology structure retrieved, which otherwise can be a daunting task. Additionally, users can also retrieve identifiers for concepts etc using the lexicon builder and can then utilize the hierarchy services using those ids to identify and visualize the hierarchies(using the visualization service) in the lexicon and can then subsequently make changes to their lexicon building parameters, until they narrow down to their exact requirements. Our system also simplifies the task of performing version management of the custom lexicons. When changes occur to the underlying data, new data is added to the ontologies or old data is changed/deleted, the users can simply retrieve a newer version of their lexicon using our services.
+While generating the custom lexicons, several features of our system can be utilized for ease of creation, integration and maintainence of such lexicons. The users can specify ontology mappings in order to identify and retrieve relevant concepts in other ontologies which they might not otherwise know about, in order to assist in enriching the custom lexicons. It also facilitates the interpretation of datasets using the concept mappings between particular datasets. They can also make use of the visualization services provided by NCBO to view and understand the ontology structure retrieved, which otherwise can be a daunting task. Additionally, users can also retrieve identifiers for concepts etc using the lexicon builder and can then utilize the hierarchy services using those ids to identify and visualize the hierarchies(using the visualization service) in the lexicon and can then subsequently make changes to their lexicon building parameters, until they narrow down to their exact requirements. Our system also simplifies the task of performing version management of the custom lexicons. When changes occur to the underlying data, new data is added to the ontologies or old data is changed/deleted, the users can simply retrieve a newer version of their lexicon using our services.
 The custom lexicons generated by using our system can help users in a variety of tasks, some exemplified by the users of our system. These lexicons can be used for domain or requirement specific text annotation tasks. e.g. annotation of protein mutations with disease terms. They can also be very useful for ontology related tasks such as ontology learning especially information extraction and also for the task of ontology enrichment. One of our users want to use our service for compiling a disease dictionary, which has actually served as our driving use case. They can also be employed for the purpose of tagging elements for enhancing the user browsing experience for domain specific information e.g. For the task of assisting the user when they are browsing the Web especially for documents related to the biomedical domain we could possible tag elements related to say Tumors and add more context specific information using a Tumor lexicon generated using our system. Another example comes from our user who are using our system to create workflow specific lexicons for concept recognition tasks.

@@ Line 1: / Line 1: @@
 == Introduction ==
-The LexiconBuilder project has been undertaken for creating a service that allows building of custom lexicons from bioportal ontologies. The custom lexicons built by our system can be potentially used for a variety of natural language processing and other ontology related tasks.
+The LexiconBuilder project has been undertaken for creating a Web service that allows building of custom lexicons from BioPortal ontologies. The custom lexicons built by our system can be used for a variety of natural language processing and other ontology related tasks.
 While generating the custom lexicons, several features of our system can be utilized for ease of creation, integration and maintainence of such lexicons. The users can specify ontology mappings in order to identify and retrieve relevant concepts in other ontologies which they might not even know about, in order to assist in enriching the custom lexicons. It also facilitates the interpretation of datasets using the concept mappings between particular datasets. They can also make use of the visualization services provided by NCBO to view and understand the ontology structure retrieved, which otherwise can be a daunting task. Additionally, users can also retrieve identifiers for concepts etc using the lexicon builder and can then utilize the hierarchy services using those ids to identify and visualize the hierarchies(using the visualization service) in the lexicon and can then subsequently make changes to their lexicon building parameters, until they narrow down to their exact requirements. Our system also simplifies the task of performing version management of the custom lexicons. When changes occur to the underlying data, new data is added to the ontologies or old data is changed/deleted, the users can simply retrieve a newer version of their lexicon using our services.

@@ Line 19: / Line 19: @@
 == Usage ==
-'''Inclusion Criteria'''
+===Inclusion Criteria===
 '''Ontologies'''   [default: all]
@@ Line 45: / Line 45: @@
 e.g. 'Result Offset' = 0 'Result Count' = 100 For retrieving the top 100 results.
-'''Exclusion Criteria'''
+===Exclusion Criteria===
 '''stopWords''' [default: empty]
@@ Line 53: / Line 53: @@
 (i.e., do you want to use our default stop word list available here: /obs/stopwords . This cancel the above one.)
-'''Output Criteria'''
+===Output Criteria===
 '''Output Columns''' (i.e., the columns you want in the results.)

@@ Line 70: / Line 70: @@
 LocalConceptID
 TermName
 '''Output Format''' (i.e., the format of the results.) [default: asXml]

@@ Line 66: / Line 66: @@
 MappedLocalConceptID
 MappingType
 '''Output Format''' (i.e., the format of the results.) [default: asXml]