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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



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  • person_outline Ulf Leser <>

Publication for ChemSpot

ChemSpot in publications

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

[…] (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 […]

PMCID: 5870729
PMID: 28881963
DOI: 10.1093/bioinformatics/btx228

[…] 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 […]

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

[…] the recognition of named entities of diseases is rather tougher than those of chemical names. although there are some remarkable chemical named entity recognition systems available online such as chemspot and tmchem, the publicly available recognition systems of disease named entities are rare. this article presents a system for disease named entity recognition (dner) and normalization. […]

PMCID: 5029005
PMID: 27650402
DOI: 10.1186/s12859-016-1249-5

[…] 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 […]

PMCID: 4834204
PMID: 27087307
DOI: 10.1093/database/baw049

[…] ner systems for scientific literature, by providing a large-scale standard corpus (). typical approaches applied to chemical ner in representative systems such as whatizit (), oscar3/4 (, ), chemspot () and tmchem () included dictionary lookup (), machine learning-based models (, , ) and hybrid methods that combined a dictionary with a machine learning-based classifier (). in addition […]

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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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