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ChemSpot specifications


Unique identifier OMICS_11325
Name ChemSpot
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License Common Public License Version 1.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes




No version available



  • person_outline Ulf Leser

Publication for ChemSpot

ChemSpot citations


Translational Biomedical Informatics and Pharmacometrics Approaches in the Drug Interactions Research

PMCID: 5824109
PMID: 29193890
DOI: 10.1002/psp4.12267

[…] nition (NER) of pharmacological substances, the best results were achieved by WBI_NER. This NER approach is formulated as a sequence labeling task (IOB format). Using domain‐independent features from ChemSpot, Jochem, and ChEBI ontology, linear‐chain conditional random field model was implemented to predict the sequences of name entities. The second best method (NLM LHC) utilized dictionaries from […]


A method for named entity normalization in biomedical articles: application to diseases and plants

BMC Bioinformatics
PMCID: 5640957
PMID: 29029598
DOI: 10.1186/s12859-017-1857-8

[…] ions. This program maps biological entities to concept identifiers in the Unified Medical Language System (UMLS) Metathesaurus. GenNorm [] and GNAT [], which are used for gene name normalization, and ChemSpot [], which is used for chemical name normalization, also normalize entities that were extracted by their own dictionary components. Gimli [] is an NER tool designed to recognize the names of v […]


Deep learning with word embeddings improves biomedical named entity recognition

PMCID: 5870729
PMID: 28881963
DOI: 10.1093/bioinformatics/btx228
call_split See protocol

[…] I trains a first-order CRF using features from BANNER () plus further ones obtained through a trial-and-error procedure, including character n-grams, chemical specific identifiers, and the output of ChemSpot () (another high-quality chemical NER tool). The output of the model is filtered by several type-specific post-processing steps for abbreviation resolution, enforcing of tagging consistency a […]


Recognizing chemicals in patents: a comparative analysis

J Cheminform
PMCID: 5086069
PMID: 27843493
DOI: 10.1186/s13321-016-0172-0
call_split See protocol

[…] Over the last years, many tools have been presented for chemical NER, including tmChem [], ChER [], ChemSpot [], becas [], OSCAR [] or ChemXSeer-tagger []. We chose two of them based on their good overall performance in a number of evaluations: (1) tmChem developed by Leaman et al. [], as the best s […]


Disease named entity recognition by combining conditional random fields and bidirectional recurrent neural networks

PMCID: 5088735
PMID: 27777244
DOI: 10.1093/database/baw140

[…] ed on biomedical dictionaries. For example, the Jochem dictionary () employed a lexical approach to recognize the diverse representation of chemical information in literatures; a hybrid system called ChemSpot () also used the lexical-based approach to locate chemical named entities. Systems based on machine learning and large training corpora were also developed. Klinger et al. () employed conditi […]


A corpus for plant chemical relationships in the biomedical domain

BMC Bioinformatics
PMCID: 5029005
PMID: 27650402
DOI: 10.1186/s12859-016-1249-5
call_split See protocol

[…] web site. After constructing the dictionary, LingPipe [], a dictionary-based exact-matching NER tool, was applied to all collected abstracts to locate plant names. Chemical names were annotated using ChemSpot [], which is a specialized tool for locating chemical names that covers trivial names, drugs, abbreviations, and molecular formulas in texts. For the annotation of chemical identifiers (IDs), […]


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ChemSpot institution(s)
Department of Computer Science, Humboldt-Universität zu Berlin, Berlin, Germany
ChemSpot funding source(s)
This work was undertaken as part of the Virtual Liver Network, funded by the German Ministry for Education and Research (BMBF) [0315746].

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