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tmChem specifications


Unique identifier OMICS_11807
Name tmChem
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Java, Perl
Computer skills Advanced
Stability Stable
Maintained Yes




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  • person_outline Robert Leaman

Publication for tmChem

tmChem citations


Distant Supervision with Transductive Learning for Adverse Drug Reaction Identification from Electronic Medical Records

PMCID: 5635478
PMID: 29090077
DOI: 10.1155/2017/7575280

[…] normalization by developing computational tools such as ctakes (, freeling-med, metamap (, medlee (, tmchem (, dnorm (, gate (, or stanford […]


A neural network multi task learning approach to biomedical named entity recognition

BMC Bioinformatics
PMCID: 5558737
PMID: 28810903
DOI: 10.1186/s12859-017-1776-8

[…] with recent systems reporting similar results (see e.g. [])., in the original biocreative iv chemical entity mention recognition task [], the highest performance, 87.39% f-score, was achieved by the tmchem system of leaman et al. []. the task required exact matching of gold entities, i.e. the same criterion applied in our primary evaluation., the recent biocreative v chemical disease relation […]


Deep learning with word embeddings improves biomedical named entity recognition

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

[…] described in section 2.4., for each of the five entity classes considered in our evaluation, we chose the presumably best performing and publicly available current ner tool: chemicals: we employed tmchem ( () model i, considered as the state-of-the-art chemical ner tool also in other recent studies (; ;). tmchem model i trains […]


Recent advances in predicting gene–disease associations

PMCID: 5414807
PMID: 28529714
DOI: 10.12688/f1000research.10788.1

[…] of their results is evaluated, the idea being that a result that is supported by many workers is most likely to be correct. like in burger et al. , li et al. also incorporated text mining tools tmchem and dnorm in addition to the wisdom of the crowd to identify associations between chemical substances and diseases from text., the review articles and together with provide […]


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

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

[…] 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. first, two […]


Improving chemical disease relation extraction with rich features and weakly labeled data

J Cheminform
PMCID: 5054544
PMID: 28316651
DOI: 10.1186/s13321-016-0165-z

[…] as some asserted relations are only in the full text. moreover, the raw data contains no mention-level chemical and disease annotations. thus, we applied two state-of-the-art bio-entity taggers tmchem [] and dnorm [] to recognize and normalize chemicals and diseases respectively. to maximize recall, we also applied a dictionary look-up method with a controlled vocabulary (mesh). […]

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tmChem institution(s)
National Center for Biotechnology Information, Bethesda, MD, USA
tmChem funding source(s)
The Intramural Research Program of the NIH, National Library of Medicine

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