Humboldt-Universität zu Berlin - Mathematisch-Naturwissenschaftliche Fakultät - Wissensmanagement in der Bioinformatik

ChemSpot

ChemSpot 2.0 is a set of tools for named entity recognition and classification of chemicals in natural language texts, including trivial names, abbreviations, molecular formulas and IUPAC entities. Since the different classes of relevant entities have rather different naming characteristics, ChemSpot uses a combined approach of employing a Conditional Random Field and a dictionary, as well as pattern-based recognition, a classifier model and several methods for consolidating all annotations. ChemSpot also performs named entity normalization by assigning identifiers from numerous chemical databases. It achieves an F1 measure of 79.0% on the SCAI corpus.

ChemSpot is released under the Common Public License 1.0.

The warning message "Couldn't open cc.mallet.util.MalletLogger resources/logging.properties file." can be ignored.

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Changelog

Version 2.0
  • Updated dictionary file and ids list (ChEBI version 2014-01-02)
  • New multi-class label tagger and classifier model
  • Support for classification of chemicals into: SYSTEMATIC, IDENTIFIER, FORMULA, TRIVIAL, ABBREVIATION, FAMILY and MULTIPLE
  • New automated dictionary and id file updater
Version 1.6
  • Updated dictionary file and ids list (ChEBI version 2013-12-03)
  • Some improvements in annotation merger component
  • Fixed bug where ChemSpot would not process some sentences if they weren't annotated properly
  • Various minor improvements and bugfixes
Older versions ▲

Running ChemSpot from the Command-Line

  1. Extract chemspot.zip into a directory

    unzip chemspot.zip

  2. To tag a sample text file, run

    java -Xmx16G -jar chemspot.jar -t sample.txt -o predict.txt

Dictionary Update
  • To update the dictionary, run

    java -Xmx5G -jar chemspot.jar -u

Memory Usage
  • If you would like to reduce memory consumption and do not need ChemSpot to assign identifiers to chemicals, you can run it without the ids file. Note however that this will completely disable named entity normalization.

    java -Xmx12G -jar chemspot.jar -t sample.txt -o predict.txt -i ""

  • If you would like to further reduce the memory footprint, you can run ChemSpot without the dictionary or multi-class model as well. Note however that this will result in worse NER performance.

    java -Xmx7G -jar chemspot.jar -t sample.txt -o predict.txt -i "" -d ""

    java -Xmx9G -jar chemspot.jar -t sample.txt -o predict.txt -i "" -M ""

Parameters

  • arguments:
    • -m path to a CRF model file (internal default model file will be used if not provided)
    • -s path to a OpenNLP sentence model file (internal default model file will be used if not provided)
    • -d path to a zipped set of brics dictionary automata (parameter defaults to 'dict.zip' if not provided)
    • -i path to a zipped tab-separated text file representing a map of terms to ids (parameter defaults to 'ids.zip' if not provided)
    • -M path to a multi-class model file (parameter defaults to 'multiclass.bin' if not provided)
  • flags:
    • -e if this flag is set, the performance of ChemSpot on an IOB gold-standard corpus (cf. -c) is evaluated
    • -u if this flag is set, ChemSpot will update the dictionary and ids file
    • -T number of threads to create when processing a document collection
  • input control:
    • -c path to a directory containing corpora in IOB format
    • -g path to a directory containing gzipped text files
    • -t path to a text file
    • -f path to a directory of text files
  • output control:
    • -o path to output file
    • -I if this flag is set, the output will be converted into the IOB format

Using ChemSpot in your Code


ChemSpot tagger = ChemSpotFactory.createChemSpot("./dict.zip", "./ids.zip", "./multiclass.bin.gz");
String text = "The abilities of LHRH and a potent LHRH agonist ([D-Ser-(But),6, " +
  "des-Gly-NH210]LHRH ethylamide) inhibit FSH responses by rat " +
  "granulosa cells and Sertoli cells in vitro have been compared.";
for (Mention mention : tagger.tag(text)) {
  System.out.printf("%d\t%d\t%s\t%s\t%s,\t%s%n", 
  mention.getStart(), mention.getEnd(), mention.getText(), 
  mention.getCHID(), mention.getSource(), mention.getType().toString());
}

Database identifiers as provided by Jochem and OPSIN

Method (in class Mention) Database
getCHID()ChemIDplus
getCHEB()ChEBI
getCAS()CAS registry number
getPUBC()PubChem compound
getPUBS()PubChem substance
getINCH()InChI
getDRUG()DrugBank
getHMBD()Human Metabolome Database
getKEGG()KEGG compound
getKEGD()KEGG drug
getMESH()MeSH

Reproducing our Results

  1. Download the SCAI corpus (chemicals-test-corpus-27-04-2009-v3.iob.gz) and put it in the same directory
  2. To reproduce our results, run

    java -Xmx16G -jar chemspot.jar -c chemicals-test-corpus-27-04-2009-v3.iob.gz -o predict.txt -e

Evaluation on the SCAI corpus

For a more detailed evaluation on the SCAI corpus and 5 other corpora, see the detailed evaluation.

Tool Precision Recall F1 Measure
ChemSpot 2.0 74.6 83.9 79.0
ChemSpot 1.6 77.0 73.5 75.2
OSCAR4.1 * 66.0 75.3 70.3
ChemSpot (as published) 67.3 68.9 68.1
OSCAR3 (Kolárik et al.) 52 72 60
OSCAR3 (Hettne et al.) 45 82 58
OSCAR4 45.7 76.5 57.3
OSCAR3 41.4 81.6 54.9

* This evaluation of OSCAR differs from former evaluations in that the better-performing PubMed recognizer model was used.

Links

ChemSpot largely builds upon the work of

Citing

Rocktäschel, T., Weidlich, M., and Leser, U. (2012).  ChemSpot: A Hybrid System for Chemical Named Entity Recognition. Bioinformatics 28 (12): 1633-1640.

Acknowledgements

We would like to thank Daniel Lowe and Philippe Thomas for many valuable suggestions.

Development

ChemSpot was developed by Tim Rocktäschel, Torsten Huber and Michael Weidlich.

Contact

For further questions, remarks or bug-reports please contact:

thuber [at] informatik [dot] hu-berlin [dot] de