MetaMap ================================= MetaMap, from the National Library of Medicine (NLM), maps biomedical text to the UMLS Metathesaurus and allows Metathesaurus concepts to be discovered in a text corpus. The MetaMap plugin for GATE wraps the MetaMap Java API client to allow GATE to communicate with a remote (or local) MetaMap PrologBeans mmserver and MetaMap distribution. This allows the content of specified annotations (or the entire document content) to be processed by MetaMap and the results converted to GATE annotations and features. To use this plugin, you will need access to a remote MetaMap server, or install one locally by downloading and installing the complete distribution: http://metamap.nlm.nih.gov/ and Java PrologBeans mmserver http://metamap.nlm.nih.gov/README_javaapi.html Parameters ========== - Initialisation-time --------------------------- excludeSemanticTypes: list of MetaMap semantic types that should be excluded from the final output annotation set. Useful for reducing the number of generic annotations output (e.g. for qualitative and temporal concepts). restrictSemanticTypes: list of MetaMap semantic types that should be the only types from which output annotations are created. E.g. if bpoc (Body Part Organ or Organ Component) is specified here, only MetaMap matches of these concepts will result in GATE annotations being created for these matches, and no others. Overrides the excludeSemanticTypes parameter. mmServerHost: name or IP address of the server on which the MetaMap terminology server (skrmedpostctl), disambiguation server (wsdserverctl) and API PrologServer (mmserver09) are running. Default is localhost. NB: all three need to be on the same server, unless you wish to recompile mmserver09 from source and add functionality to point to different terminology and word-sense disambiguation server locations. mmServerPort: port number of the mmserver09 PrologServer running on mmServerHost. Default is 8066 mmServerTimeout: milliseconds to wait for PrologServer. Default is 150000 outputASType: output annotation name to be used for all MetaMap annotations - Run-time ---------------- annotatePhrases: set to true to output MetaMap phrase-level annotations (generally noun-phrase chunks). Only phrases containing a MetaMap mapping will be annotated. Can be useful for post-coordination of phrase-level terms that do not exist in a pre-coordinated form in UMLS. inputASName: input Annotation Set name. Use in conjunction with inputASTypes (see below). Unless specified, the entire document content will be sent to MetaMap. inputASTypes: only send the content of the named annotations listed here, within inputASName, to MetaMap. Unless specified, the entire document content will be sent to MetaMap. metaMapOptions: set parameter-less MetaMap options here. Default is -Xt (truncate Candidates mappings and do not use full text parsing). See http://metamap.nlm.nih.gov/README_javaapi.html for more details. NB: only set the -y parameter (word-sense disambiguation) if wsdserverctl is running. Running the Java MetaMap API with a large corpus with word-sense disambiguation can cause a 'too many open files' error - this appears to be a PrologServer bug. outputASName: output Annotation Set name. outputMode: determines which mappings are output as annotations in the GATE document: - MappingsOnly: only annotate the final MetaMap Mappings. This will result in fewer annotations with higher precision (e.g. for 'lung cancer' only the complete phrase will be annotated as neop) - CandidatesOnly: annotate only Candidate mappings and not the final Mappings. This will result in more annotations with less precision (e.g. for 'lung cancer' both 'lung' (bpoc) and 'lung cancer' (neop) will be annotated). - CandidatesAndMappings: annotate both Candidate and final mappings. This will usually result in multiple, overlapping annotations for each term/phrase scoreThreshold: set from 0 to 1000. The lower the threshold, the greater the number of annotations but the lower precision. Default is 500. useNegEx: set this to true to add NegEx features to annotations (NegExType and NegExTrigger). See http://www.dbmi.pitt.edu/chapman/NegEx.html for more information on NegEx
