Lexicon Builder

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. You can find the list of localOntologyIDs available here: /obs/ontologies)

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

Compressed Output (Yes: Dictionary as a compressed ZIP file. No: Dictionary displayed on browser. ) [default: No] Yes No