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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 citations


Translational Biomedical Informatics and Pharmacometrics Approaches in the Drug Interactions Research

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 […]


Deep learning with word embeddings improves biomedical named entity recognition

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 […]


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

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. […]


A corpus for plant chemical relationships in the biomedical domain

BMC Bioinformatics
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 […]


Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning

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 […]


Developing a hybrid dictionary based bio entity recognition technique

BMC Med Inform Decis Mak
PMCID: 4460617
PMID: 26043907
DOI: 10.1186/1472-6947-15-S1-S9

[…] and obtained better results than those of the one-phase model over the genia corpus annotated with 23 categories. the ner technique has also been applied to extract chemical components from text. chemspot is the ner algorithm that extracts mentions of chemicals such as trivial names, drugs, abbreviations, and molecular formulas [] whereas [] focuses on the identification of international […]

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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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