Difference between revisions of "Lexicon Builder"
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== Usage == | == Usage == | ||
| − | Ontologies To Expand [default: all] | + | '''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. | (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) | You can find the list of localOntologyIDs available here: /obs/ontologies) | ||
| − | Concepts Under Parent Concept [default: all] | + | '''Concepts Under Parent Concept''' [default: all] |
(i.e. localConceptID of the concept to retrieve children concepts. | (i.e. localConceptID of the concept to retrieve children concepts. | ||
You can retrieve the list of concepts here :/obs/localConceptIDs) | You can retrieve the list of concepts here :/obs/localConceptIDs) | ||
| − | Synonyms true false [default: true] | + | '''Synonyms''' true false [default: true] |
(i.e., do you want the synonyms of the concept too?) | (i.e., do you want the synonyms of the concept too?) | ||
| − | Semantic Types For Concepts [default: all] | + | '''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. | (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) | You can find the list of localSemanticTypeIDs available here: /obs/semanticTypes) | ||
| − | Mapping Types For Mapped Concepts [default: all] | + | '''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. | (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. | 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] | + | '''Pubmed Counts''' [default: all] |
(i.e., PUBMED count of the concepts retrieved is greater than given count e.g. 10000 | (i.e., PUBMED count of the concepts retrieved is greater than given count e.g. 10000 | ||
| − | Result Offset [default: None] | + | '''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) | (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] | Result Count [default: None] | ||
| Line 41: | Line 41: | ||
Exclusion Criteria | Exclusion Criteria | ||
| − | stopWords [default: empty] | + | '''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. | (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] | withDefaultStopWords true false [default: false] | ||
| Line 47: | Line 47: | ||
Output Criteria | Output Criteria | ||
| − | Output Columns (i.e., the columns you want in the results.) [default: all] | + | '''Output Columns''' (i.e., the columns you want in the results.) [default: all] |
LocalConceptID | LocalConceptID | ||
LocalOntologyID | LocalOntologyID | ||
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MappingType | MappingType | ||
| − | Output Format (i.e., the format of the results.) [default: asXml] | + | '''Output Format''' (i.e., the format of the results.) [default: asXml] |
asXML | asXML | ||
asText | asText | ||
asTabDelimited | asTabDelimited | ||
Revision as of 07:54, 7 December 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