The primary goal of MetaMapLite to provide a near real-time named-entity recognizer which is not a rigorous as MetaMap but much faster while allowing users to customize and augment its behavior for specific purposes.
It uses some of the tables used by MetaMap but all lexical variants used in the table are pre-processed. Named Entities are found using longest match. Restriction by UMLS source and Semantic type is optional. Part-of-speech tagging which improves precision by a small amount (at the cost of speed) is also optional. Negation detection is available using either Wendy Chapman’s context or a native negation detection algorithm based on Wendy Chapman’s NegEx which is somewhat less effective, but faster.
It has:
What is missing:
./metamaplite.sh [options] [<input file>|--]
Example of use:
$ java -cp public_mm_lite/target/metamaplite-2.0-SNAPSHOT.jar \
gov.nih.nlm.nls.ner.MetaMapLite \
--indexdir=public_mm_lite/data/ivf/strict \
--modelsdir=public_mm_lite/data/models \
--specialtermsfile=public_mm_lite/data/specialterms.txt <arguments>
Current options are:
input options:
-- Read from standard input
--pipe Read from standard input
Configuration Options:
--configfile=<filename> Use configuration file
Options that can be used to override configuration file or when configuration file is not present:
--indexdir=<directory> location of program's index directory
--modelsdir=<directory> location of models for sentence breaker and part-of-speech tagger
--specialtermsfile=<filename> location of file of terms to be excluded
document processing options:
--freetext Text with no markup.
--ncbicorpus NCBI Disease Corpus: tab separated fields: id \t title \t abstract
--chemdner CHEMDNER document: tab separated fields: id \t title \t abstract
--chemdnersldi CHEMDNER document: id with pipe followed by tab separated fields: id |t title \t abstract
--inputformat=<loadername>
Use input format specified by loader name.
output options:
--bioc|cdi|bc|bc-evaluate output compatible with evaluation program bc-evaluate
--mmilike|mmi similar to MetaMap Fielded MMI output
--brat BRAT annotation format
processing options:
--restrict_to_sts=<semtype>[,<semtype>,<semtype>...]
--restrict_to_sources=<source>[,<source>...]
--segmentation_method=SENTENCES|BLANKLINES|LINES
Set method for text segmentation
--segment_sentences Segment text by sentence
--segment_blanklines Segment text by blankline
--segment_lines Segment text by line
--usecontext Use ConText Negation Detector instead of NLM's implementation of NegEx
--negationDetectorClass=className
Use a user-defined class for negation detector, class must implement to
gov.nih.nlm.nls.metamap.lite.NegationDetector interface.
alternate output options:
--list_sentences list sentences in input
--list_acronyms list acronyms in input if present.
--list_sentences_postags list sentences in input with part-of-speech tags
| metamaplite.segmentation.method | Set method for text segmentation (values: SENTENCES, BLANKLINES, LINES; default: SENTENCES)
| metamaplite.sourceset | use only concepts from listed sources (default: all)
| metamaplite.semanticgroup | use only concepts belonging to listed semantic types (default: all)
| metamaplite.negation.detector | negation detector class: default: gov.nih.nlm.nls.metamap.lite.NegEx
Alternate:
| metamaplite.excluded.termsfile | cui/terms pairs that are exclude from results (default: data/specialterms.txt)
| metamaplite.index.directory | the directory the indexes resides (sets the following properties)
| metamaplite.ivf.cuiconceptindex | cui/concept/preferredname index
| metamaplite.ivf.cuisourceinfoindex | cui/sourceinfo index
| metamaplite.ivf.cuisemantictypeindex | cui/semantictype index
| opennlp.models.directory | the directory the models resides (sets the following properties. default: data/models)
| opennlp.en-pos.bin.path | (default: data/models/en-pos-maxent.bin)
| opennlp.en-token.bin.path | (default: data/models/en-token.bin)
| opennlp.en-sent.bin.path | (default: data/models/en-sent.bin)
| metamaplite.enable.postagging | Enable part of speech tagging (default: "true" [on])
| metamaplite.document.inputtype | document input type (default: freetext)
| metamaplite.outputextension | result output file extension (default: .mmi)
| metamaplite.property.file | load configuration from file (default: ./config/metamaplite.properties)
| metamaplite.outputformat | result output format (default: mmi)
Creating properties for configuring MetaMapLite Instance:
Properties myProperties = new Properties();
MetaMapLite.expandModelsDir(myProperties,
"/home/piro/public_mm_lite/data/models");
MetaMapLite.expandIndexDir(myProperties,
"/home/piro/Projects/public_mm_lite/data/ivf/strict");
myProperties.setProperty("metamaplite.excluded.termsfile",
"/home/piro/Projects/public_mm_lite/data/specialterms.txt");
Creating a metamap lite instance:
MetaMapLite metaMapLiteInst = new MetaMapLite(myProperties);
Creating a document list with one or more documents:
BioCDocument document = FreeText.instantiateBioCDocument("diabetes");
document.setID("1");
List<BioCDocument> documentList = new ArrayList<BioCDocument>();
documentList.add(document);
Getting a list of entities for the document list:
List<Entity> entityList = metaMapLiteInst.processDocumentList(documentList);
Traversing the entity list displaying cui and matching text:
List<Entity> entityList = metaMapLiteInst.processDocumentList(documentList);
for (Entity entity: entityList) {
for (Ev ev: entity.getEvSet()) {
System.out.print(ev.getConceptInfo().getCUI() + "|" + entity.getMatchedText());
System.out.println();
}
}
Disable the Part of Speech Tagger using the following property: “metamaplite.enable.postagging=false”. Add the following line right before instantiating the MetaMapLite instance.
myProperties.setProperty("metamaplite.enable.postagging", "false");
MetaMapLite metaMapLiteInst = new MetaMapLite(myProperties);
Add each term as a single document:
BioCDocument document = FreeText.instantiateBioCDocument(term);
Currently, three tables are used:
The CreateIndexes class generates tables cuiconcept, cuisourceinfo, and cuist from MRCONSO.RRF and MRSTY.RRF and then produces corresponding indexes for tables.
Usage:
java -cp target/metamaplite-2.0-SNAPSHOT.jar \
gov.nih.nlm.nls.metamap.dfbuilder.CreateIndexes <mrconsofile> <mrstyfile> <ivfdir>
The resulting indices are in
To use the new indexes do one of the following:
Use the –indexdir=
java -cp target/metamaplite-2.0-SNAPSHOT-standalone.jar \
gov.nih.nlm.nls.ner.MetaMapLite --indexdir=<ivfdir> <other-options> <other-args>
Or modify the configuration file config/metamap.properties:
metamaplite.ivf.cuiconceptindex: <ivfdir>/indices/cuiconcept
mmetamaplite.ivf.cuisourceinfoindex: <ivfdir>/indices/cuisourceinfo
metamaplite.ivf.cuisemantictypeindex: <ivfdir>/indices/cuist
New document loader class must conform to BioCDocumentLoader interface. One can add a document loader class in MetaMapLite’s classpath to MetaLite’s list of document loaders by adding it to the properties using System properties or modifying MetaMapLite’s configuration file:
Set as system property:
-Dbioc.document.loader.<name>=<fully-specified class name>
For example creating a loader with the name “qadocument”:
-Dbioc.document.loader.qadocument=gov.nih.nlm.nls.metamap.document.QAKeyValueDocument
Or add it to config/metamaplite.properties:
bioc.document.loader.qadocument: gov.nih.nlm.nls.metamap.document.QAKeyValueDocument
New result formatter class must conform to ResultFormatter interface. One can add the result formatter to MetaMapLite by adding its class file to MetaMapLite’s classpath and then adding a reference to it as a property:
Set as system property:
-Dmetamaplite.result.formatter.<name>=<fully-specified class name>
For example creating a formatter with the name “brat”:
-Dmetamaplite.result.formatter.brat=gov.nih.nlm.nls.metamap.lite.resultformats.Brat
Or add it to config/metamaplite.properties:
metamaplite.result.formatter.brat: gov.nih.nlm.nls.metamap.lite.resultformats.Brat
Added mechanism to use custom user-supplied segmenters.