Difference between revisions of "Lexicon Builder"
(→Usage) |
|||
| Line 18: | Line 18: | ||
'''Ontologies''' [default: all] | '''Ontologies''' [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. | ||
| − | |||
'''Parent Concept''' [default: all] | '''Parent Concept''' [default: all] | ||
(i.e. localConceptID of the concept to retrieve children concepts. | (i.e. localConceptID of the concept to retrieve children concepts. | ||
| − | |||
'''Synonyms''' true false [default: true] | '''Synonyms''' true false [default: true] | ||
| Line 28: | Line 26: | ||
'''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 | + | (i.e., list of UMLS semantic types you want to use separated with comma (without spaces) e.g., T000,T047,T048. |
| − | |||
| − | '''Mapping Types For Mapped Concepts''' [default: | + | '''Mapping Types For Mapped Concepts''' [default: none] |
| − | (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.) |
| − | |||
'''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] | ||
| Line 50: | Line 46: | ||
Output Criteria | Output Criteria | ||
| − | '''Output Columns''' (i.e., the columns you want in the results.) | + | '''Output Columns''' (i.e., the columns you want in the results.) |
LocalConceptID | LocalConceptID | ||
LocalOntologyID | LocalOntologyID | ||
Revision as of 09:53, 15 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/
Note: The prototype is currently in the development phase and constantly undergoing changes.
Usage
Ontologies [default: all] (i.e., list of ontologies you want to use to expand separated with comma (without spaces) e.g., SNOMEDCT,NCI,MSH.
Parent Concept [default: all] (i.e. localConceptID of the concept to retrieve children concepts.
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., T000,T047,T048.
Mapping Types For Mapped Concepts [default: none] (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.)
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.) LocalConceptID LocalOntologyID OntologyName OntologyVersion OntologyDescription TermName LocalSemanticTypeID LocalSemanticTypeName MappedLocalConceptID MappingType
Output Format (i.e., the format of the results.) [default: asXml] asXML asText asTabDelimited
Compressed Output (Yes: Dictionary as a compressed ZIP file. No: Dictionary displayed on browser. ) [default: No] Yes No