https://github.com/lhncbc/metamaplite

A near real-time named-entity recognizer
https://github.com/lhncbc/metamaplite

metamap named-entity-recognition umls

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A near real-time named-entity recognizer

• Host: GitHub
• URL: https://github.com/lhncbc/metamaplite
• Owner: LHNCBC
• License: other
• Created: 2018-02-08T19:17:44.000Z (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2024-01-16T14:17:39.000Z (12 months ago)
• Last Synced: 2024-05-20T02:20:39.186Z (8 months ago)
• Topics: metamap, named-entity-recognition, umls
• Language: Java
• Homepage: https://metamap.nlm.nih.gov/MetaMapLite.shtml
• Size: 1010 KB
• Stars: 54
• Watchers: 8
• Forks: 14
• Open Issues: 16
• Metadata Files:
  • Readme: README.bioc
  • License: LICENSE.md

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README

        
## A BioC XML to A BioC XML implementation of MetaMapLite

The class gov.nih.nlm.nls.metamap.lite.BioCProcess allows MetaMapLite

to process BioC XML input and write the results in BioC XML.

### Using from Java

Below is an example using BioC Processing with MetaMapLite

    // Initialize MetaMapLite

    Properties defaultConfiguration = getDefaultConfiguration();

	String configPropertiesFilename =

		System.getProperty("metamaplite.propertyfile",

		                   "config/metamaplite.properties");

    Properties configProperties = new Properties();

    // set any in-line properties here.

    FileReader fr = new FileReader(configPropertiesFilename);

    configProperties.load(fr);

    fr.close();

    configProperties.setProperty("metamaplite.semanticgroup",

    "acab,anab,bact,cgab,dsyn,emod,inpo,mobd,neop,patf,sosy");

    Properties properties =

        Configuration.mergeConfiguration(configProperties,

					   defaultConfiguration);

    BioCProcess process = new BioCProcess(properties);

    // read BioC XML collection

    Reader inputReader = new FileReader(inputFile);

    BioCFactory bioCFactory = BioCFactory.newFactory("STANDARD");

    BioCCollectionReader collectionReader =

    bioCFactory.createBioCCollectionReader(inputReader);

    BioCCollection collection = collectionReader.readCollection();

    // Run named entity recognition on collection

    BioCCollection newCollection = process.processCollection(collection);

    // write out the annotated collection

    File outputFile = new File(outputFilename);

    Writer outputWriter = new PrintWriter(outputFile, "UTF-8");

    BioCCollectionWriter collectionWriter = bioCFactory.createBioCCollectionWriter(outputWriter);

    collectionWriter.writeCollection(newCollection);

    outputWriter.close();

This process attempts to preserve any annotation present in the

original BioC XML input.    Some annotations applied to BioC

structures before entity lookup, including `tokenization and

part-of-speech-tagging, are discarded before the writing out the final

annotated collection.   This occurs in the entity lookup class

BioCEntityLookup (java package: gov.nih.nlm.nls.metamap.lite).

### Omissions in BioC version

The current version of the BioCProcess class does not call the

abbreviation detector or the negation detector.   This should be

relatively simple to add (particularly the abbreviation detector) and

will probably be added in the next release.