The primary goal of MetaMapLite is to provide a near real-time named-entity recognizer which is not as 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:
Example of invocation on Linux or MINGW using script:
./metamaplite.sh [options] [<input file>|--]
Example of invocation on Windows using batch file:
metamaplite.bat [options] [<input file>|--]
Example of invocation using Java VM directly when running from the public_mm_lite directory:
$ java -cp target/metamaplite-3.6.2rc5-standalone.jar \
gov.nih.nlm.nls.ner.MetaMapLite \
--indexdir=data/ivf/2019AB/USAbase \
--modelsdir=data/models \
--specialtermsfile=data/specialterms.txt [options] [<input file>|--]
echo "asymptomatic patient populations" | ./metamaplite.sh --pipe
or
cat file | ./metamaplite.sh --pipe
Output will be sent to standard output.
The list of concepts returned can be restricted to a only those that refer to a subset of the UMLS semantic types by semantic type abbreviations:
./metamaplite.sh --restrict_to_sts=abbrev,abbrev ...
The following option restricts to concepts that have the semantic types disease or syndrome (dsyn) and hazardous or poisonous substance (hops):
./metamaplite.sh --restrict_to_sts=dsyn,hops
A full list of semantic types and their abbreviations is at:
https://metamap.nlm.nih.gov/Docs/SemanticTypes_2018AB.txt
The follows option specifies that only concepts that appear in the MeSH (MSH), and NCBI Taxonomy (NCBI) vocabularies will be returned:
./metamaplite.sh --restrict_to_sources=MSH,NCBI ...
A full list of the current source vocabularies and their abbreviations can be found at:
https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html
To create annotation files (.ann) in a directory from the associated text files (.txt)
./metamaplite.sh --brat directory/*.txt
The option –uda allows a user to supply a list of user defined acronyms or abbreviations with associated long forms. When MetaMapLite encounters a user defined acronym, it will attach the information associated with the acronym’s long form.
./metamaplite.sh --uda=acronymfile ...
The acronym file is the form „acronym|long form“, for example:
LAD|Left anterior descending coronary artery
SVG|Saphenous Vein Graft
PLB|Posterior lateral branch
PDA|Patent Ductus Arteriosus
IM|Intramuscular
The option –cuitermlistfile allows a user to add a list of concepts not present in MetaMapLite’s dataset at invocation:
./metamaplite.sh --cuitermlistfile=conceptfile ...
The concepts file is the form „cui|term“, for example:
C5203670|COVID-19
C5203671|Suspected COVID-19
C5203672|SARS-CoV-2 vaccination
C5203673|Antigen of SARS-CoV-2
C5203674|Antibody to SARS-CoV-2
C5203675|Exposure to SARS-CoV-2
C5203676|severe acute respiratory syndrome coronavirus 2
input options:
-- Read from standard input
--pipe Read from standard input
Configuration Options:
--configfile=<filename> Use configuration file
--set_property=name=value set property "name" to value
--filelistfn=<filename> file containing a list of files to processed, one line per file
--filelist=<file0,file1,...> list of files to processed separated by commas
--uda=<filename> user defined acronyms file.
--cuitermlistfile=<filename> user defined concepts 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. (default)
--inputformat=<loadername> Use input format specified by loader name.
--inputformat=pubmed PubMed XML format
--inputformat=medline Medline format
--inputformat=ncbicorpus NCBI Disease Corpus: tab separated fields: id \t title \t abstract
--inputformat=chemdner CHEMDNER document: tab separated fields: id \t title \t abstract
--inputformat=chemdnersldi CHEMDNER document: id with pipe followed by tab separated fields: id |t title \t abstract
output options:
--mmilike|mmi similar to MetaMap Fielded MMI output (default)
--bioc|cdi|bc|bc-evaluate output compatible with evaluation program bc-evaluate
--brat BRAT annotation format
--outputformat=<format>
--outputformat=json JSON output format
processing options:
--restrict_to_sts=<semtype>[,<semtype>,<semtype>...]
Restrict output to concepts that have at least one member
in the list of user-specified semantic-types. The list of
supported semantic type short forms used by this program is
available at https://metamap.nlm.nih.gov/Docs/SemanticTypes_2018AB.txt
--restrict_to_sources=<source>[,<source>...]
Restrict output to concepts that belong to the list of specified vocabularies.
A full list of the current source vocabularies and their abbreviations
can be found at https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html
--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.
--postaglist=tag,tag,...
List of part-of-speech tags to use for term lookup (each Penn Treebank
part-of-speech tag is separated by commas.)
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
These properties can be set using a System property (-D{propertyname}={value}).
| metamaplite.property.file | load configuration from file (default: ./config/metamaplite.properties)
These properties can be set using a System property (-D{propertyname}={value}) or in configuration file.
| metamaplite.document.inputtype | document input type (default: freetext)
| metamaplite.outputextension | result output file extension (default: .mmi)
| metamaplite.outputformat | result output format (default: mmi)
| 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.normalized.string.cache.size | set maximum size of string -> normalized string cache
| metamaplite.normalized.string.cache.enable | if true enable string -> normalized string cache
| metamaplite.entitylookup4.term.concept.cache.enable | if true enable term -> concept info cache
| metamaplite.entitylookup4.term.concept.cache.size | set maximum size of term -> concept info cache
| metamaplite.entitylookup4.cui.preferredname.cache.enable | if true enable cui -> preferred name cache
| metamaplite.entitylookup4.cui.preferredname.cache.size | set maximum size cui -> preferred name cache
| metamaplite.excluded.termsfile | cui/terms pairs that are exclude from results (default: data/specialterms.txt)
| metamaplite.index.directory | the directory the indexes reside
| opennlp.models.directory | the directory the models reside (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.postaglist | List of part-of-speech tags to use for term lookup
| (each Penn Treebank part-of-speech tag is separated by commas.)
| metamaplite.enable.scoring | turn on chunker (currently OpenNLP's chunker) and score concepts.
| metamaplite.uda.filename | user defined acronyms file.
| metamaplite.cuitermlistfile.filename | user defined concepts file.
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/2019AB/USAbase");
myProperties.setProperty("metamaplite.excluded.termsfile",
"/home/piro/Projects/public_mm_lite/data/specialterms.txt");
Loading properties file in „config“:
myProperties.load(new FileReader("config/metamaplite.properties"));
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);
From public_mm_lite directory install Context, BioC, and NLS NLP libraries
$ mvn install:install-file \
-Dfile=lib/context-2012.jar \
-DgroupId=context \
-DartifactId=context \
-Dversion=2012 \
-Dpackaging=jar
$ mvn install:install-file \
-Dfile=lib/bioc-1.0.1.jar \
-DgroupId=bioc \
-DartifactId=bioc \
-Dversion=1.0.1 \
-Dpackaging=jar
$ mvn install:install-file \
-Dfile=lib/nlp-2.4.C.jar \
-DgroupId=gov.nih.nlm.nls \
-DartifactId=nlp \
-Dversion=2.4.C \
-Dpackaging=jar
$ mvn install:install-file \
-Dfile=lib/lvgdist-2020.0.jar \
-DgroupId=gov.nih.nlm.nls.lvg \
-DartifactId=lvgdist \
-Dversion=2020.0 \
-Dpackaging=jar
Then install metamaplite into your local Maven repository:
$ mvn install
Add the following dependency to your webapps pom.xml:
<dependency>
<groupId>gov.nih.nlm.nls</groupId>
<artifactId>metamaplite</artifactId>
<version>3.0-SNAPSHOT</version>
</dependency>
Currently, five tables are used:
Two new indexes have been introduced to support scoring similar to the original MetaMap and MMI ranking of which MetaMap scoring is a component.
NOTE: Currently, the only mechanism for generating the treecodes and vars (variants) tables from a UMLS subset (generated by Metamorphosys) is by installing the original MetaMap and the Data File Builder using the Data Builder to generate the necessary Treecodes and Vars table files. See the next section for information on adding these indices to a custom dataset.
The CreateIndexes class generates the tables needed by MetaMapLite for a particular UMLS release. The tables cuiconcept, cuisourceinfo, cuist, meshtcrelaxed, and vars are derived from the UMLS tables MRCONSO.RRF, MRSAT.RRF, and MRSTY.RRF and then CreateIndexes produces the associated indexes for derived tables. To produce the vars table you will need to install the Lexical Variant Generator (LVG) which is available from the Lexical Tools Page: https://lexsrv3.nlm.nih.gov/LexSysGroup/Projects/lvg/current/web/index.html . LVG is used when generating the vars table from MRCONSO.RRF.
Usage:
java -Xmx15g -cp target/metamaplite-<version>-standalone.jar \
gov.nih.nlm.nls.metamap.dfbuilder.CreateIndexes \
<mrconsofile> <mrstyfile> <mrsatfile> <ivfdir>
When running CreateIndexes must be provided the location of LVG configuration file by one of two mechanisms: Setting an environment variable LVG_DIR or LVG_CONFIG or setting a system property when invoking java. The simplest way of doing this by setting LVG_DIR to the location of LVG and CreateIndexes program will infer the location of the properties file:
on windows:
set LVG_DIR=<location of lvg2020>
in bash on MacOS or Linux:
export LVG_DIR=<location of lvg2020>
If you have a modified lvg.property file in an custom location you can set the variable LVG_CONFIG to the location of your custom lvg property file.
Alternatively, you can set system property gv.lvg.dirname to the location of LVG or setting the property gv.lvg.config.file to the location of lvg.properties, usually lvg2020/data/config/lvg.properties:
-Dgv.lvg.dirname={location of lvg}
or:
-Dgv.lvg.config.file={location of lvg.properties}
The resulting indices are in
You can use the class irutils.MappedMultiKeyIndexLookup to check the new indexes:
java -Xmx20g -cp target/metamaplite-<version>-standalone.jar \
irutils.MappedMultiKeyIndexLookup lookup workingdir indexname column query
For example:
java -Xmx20g -cp target/metamaplite-<version>-standalone.jar \
irutils.MappedMultiKeyIndexLookup lookup data/ivf/2016AB/USAbase/strict cuisourceinfo 3 heart
To use the new indexes do one of the following:
Use the –indexdir=
java -cp target/metamaplite-<version>-standalone.jar \
gov.nih.nlm.nls.ner.MetaMapLite --indexdir=<ivfdir> <other-options> <other-args>
Or modify the configuration file config/metamap.properties:
metamaplite.index.directory: <ivfdir>
New document loader class must conform to BioCDocumentLoader interface.
Example implementations of BioCDocumentLoader are available in public_mm_lite/src/main/java/gov/nih/nlm/nls/metamap/document and on Github: https://github.com/lhncbc/metamaplite/tree/master/src/main/java/gov/nih/nlm/nls/metamap/document.
One can add a document loader class in MetaMapLite’s classpath to MetaMapLite’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
An example of using the new custom document format through a properties:
-Dmetamaplite.document.inputtype=<name>
For example:
-Dmetamaplite.document.inputtype=qadocument
On the command line use the ‘inputformat=
--inputformat=qadocument
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 „bratsemtype“:
-Dmetamaplite.result.formatter.brat=examples.BratSemType
Or add it to config/metamaplite.properties:
metamaplite.result.formatter.brat: examples.BratSemType
Source code for the BratSemType result formatter is provided in the directory public_mm_lite/src/main/java/examples/BratSemType.java.
A extensive example of providing a servlet complete with data and configuration files in the war (web archive) file is available on the MetaMap website on the MetaMapLite web page (https://metamap.nlm.nih.gov/MetaMapLite.shtml).
Below is an alternate configuration for users who don’t want to place the configuration and data in webapp deployment archive file (war).
Place the „metamaplite.properties“ file in the tomcat „conf/“ directory and specify that in servlet:
public class SampleWebApp extends HttpServlet {
/** location of metamaplite.properties configuration file */
static String configPropertyFilename =
System.getProperty("metamaplite.property.file", "conf/metamaplite.properties");
Properties properties;
MetaMapLite metaMapLiteInst;
public SampleWebApp() {
try {
this.properties = new Properties();
// default properties that can be overriden
this.properties.setProperty("metamaplite.index.directory","data/ivf/2019AB/USAbase");
...
// load user properties
this.properties.load(new FileReader(configPropertyFilename));
this.metaMapLiteInst = new MetaMapLite(this.properties);
...
} catch (Exception e) {
throw new RuntimeException(e);
}
}
...
}
The absolute locations of indexes and model files can be specified in „metamaplite.properties“.
The file biocprocess.sh is a wrapper for the BioC to BioC pipeline.
./biocprocess.sh <bioc-xml-input-file> <bioc-xml-output-file>
Note that the class is missing the command line options handler that is present in the gov.nih.nlm.nls.ner.MetaMapLite class, use the config/metamaplite.properties file to set any custom properties or place the properties in another custom file and use the system property „metamaplite.propertyfile“ to refer to the custom file.
The following java archive files have sources available from NLM but the sources are not provided by this distribution.
The sources are available at the following locations: