Difference between revisions of "Lexicon Builder"

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== Usage ==
 
== Usage ==
 +
 +
Ontologies To Expand  [default: all]
 +
(i.e., list of ontologies you want to use to expand separated with comma (without spaces) e.g., SNOMEDCT,NCI,MSH.
 +
You can find the list of localOntologyIDs available here: /obs/ontologies)
 +
 +
Concepts Under Parent Concept [default: all]
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(i.e. localConceptID of the concept to retrieve children concepts.
 +
You can retrieve the list of concepts here :/obs/localConceptIDs)
 +
 +
Synonyms true false [default: true]
 +
(i.e., do you want the synonyms of the concept too?)
 +
 +
Semantic Types For Concepts [default: all]
 +
(i.e., list of UMLS semantic types you want to use separated with comma (without spaces) e.g., T047,T048,T191.
 +
You can find the list of localSemanticTypeIDs available here: /obs/semanticTypes)
 +
 +
Mapping Types For Mapped Concepts [default: all]
 +
(i.e., list of mapping types you want to use for the mapping expansion component separated with comma (without spaces) e.g., inter-cui,from-mrrel.
 +
You can find the list of mapping types available here: /obs/mappingTypes). Note if you use the keyword null in your list, it will disable the mapping expansion component.
 +
 +
Pubmed Counts [default: all]
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(i.e., PUBMED count of the concepts retrieved is greater than given count e.g. 10000
 +
 +
Result Offset [default: None]
 +
(i.e., Retrieve results starting from this result. If Result Offset and NO Result Count then returns the top 'Result Offset' results)
 +
Result Count [default: None]
 +
(i.e., Number of results you want to retrieve starting from the offset.)
 +
Exclusion Criteria
 +
 +
stopWords [default: empty]
 +
(i.e., list of stop words to use (i.e., not to use for annotation) separated with comma (without spaces) e.g., in,am,be,is.
 +
withDefaultStopWords true false [default: false]
 +
(i.e., do you want to use our default stop word list available here: /obs/stopwords . This cancel the above one.)
 +
Output Criteria
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 +
Output Columns (i.e., the columns you want in the results.) [default: all]
 +
LocalConceptID
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LocalOntologyID
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OntologyName
 +
OntologyVersion
 +
OntologyDescription
 +
TermName
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LocalSemanticTypeID
 +
LocalSemanticTypeName
 +
MappedLocalConceptID
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MappingType
 +
 +
Output Format (i.e., the format of the results.) [default: asXml]
 +
asXML
 +
asText
 +
asTabDelimited

Revision as of 00:18, 22 November 2009

Introduction

Build lexicons for text annotation according to user requirements.

Code location

https://bmir-gforge.stanford.edu/gf/project/lexicon_builder/

Home page: http://ncbolabs-dev1.stanford.edu:8080/LexiconBuilder/

The Service end point: http://ncbolabs-dev1.stanford.edu:8080/LexiconBuilderService/

Usage

Ontologies To Expand [default: all] (i.e., list of ontologies you want to use to expand separated with comma (without spaces) e.g., SNOMEDCT,NCI,MSH. You can find the list of localOntologyIDs available here: /obs/ontologies)

Concepts Under Parent Concept [default: all] (i.e. localConceptID of the concept to retrieve children concepts. You can retrieve the list of concepts here :/obs/localConceptIDs)

Synonyms true false [default: true] (i.e., do you want the synonyms of the concept too?)

Semantic Types For Concepts [default: all] (i.e., list of UMLS semantic types you want to use separated with comma (without spaces) e.g., T047,T048,T191. You can find the list of localSemanticTypeIDs available here: /obs/semanticTypes)

Mapping Types For Mapped Concepts [default: all] (i.e., list of mapping types you want to use for the mapping expansion component separated with comma (without spaces) e.g., inter-cui,from-mrrel. You can find the list of mapping types available here: /obs/mappingTypes). Note if you use the keyword null in your list, it will disable the mapping expansion component.

Pubmed Counts [default: all] (i.e., PUBMED count of the concepts retrieved is greater than given count e.g. 10000

Result Offset [default: None] (i.e., Retrieve results starting from this result. If Result Offset and NO Result Count then returns the top 'Result Offset' results) Result Count [default: None] (i.e., Number of results you want to retrieve starting from the offset.) Exclusion Criteria

stopWords [default: empty] (i.e., list of stop words to use (i.e., not to use for annotation) separated with comma (without spaces) e.g., in,am,be,is. withDefaultStopWords true false [default: false] (i.e., do you want to use our default stop word list available here: /obs/stopwords . This cancel the above one.) Output Criteria

Output Columns (i.e., the columns you want in the results.) [default: all] LocalConceptID LocalOntologyID OntologyName OntologyVersion OntologyDescription TermName LocalSemanticTypeID LocalSemanticTypeName MappedLocalConceptID MappingType

Output Format (i.e., the format of the results.) [default: asXml] asXML asText asTabDelimited