tmVar protocols

View tmVar computational protocol

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tmVar specifications

Information


Unique identifier OMICS_04860
Name tmVar
Alternative name tmVar 2.0
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Zhiyong Lu <>

Publications for tmVar

tmVar in pipeline

2016
PMCID: 5130168
PMID: 27902695
DOI: 10.1371/journal.pcbi.1005017

[…] of annotated relationships between genes, variants, drugs, and cell lines from the full text of 108 articles []. finally, this proposed framework directly uses several state-of-the-art tools (like tmvar, dnorm and gnormplus). future advances in the respective domains of these tools would enable increased performance of the proposed approach. this study has been helpful to excavate several […]


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tmVar in publications

 (8)
PMCID: 5414807
PMID: 28529714
DOI: 10.12688/f1000research.10788.1

[…] biotechnology information (ncbi) maintains a set of high-quality text mining software in its tool set. some examples of tools that are relevant for processing genome variation information include tmvar , for extracting sequence variants at the levels of both genes and proteins from biomedical literature; dnorm , which is a resource that is used to automatically identify disease names […]

PMCID: 5215527
PMID: 28054646
DOI: 10.1038/srep40154

[…] with its reverse reaction (e.g., phosphorylation-dephosphorylation) into a single event type, since reaction directionality does not affect disease-related gene ranking. in addition, it utilizes tmvar to locate mutation events. in total, digsee all-disease version locates 15 types of biological events. the turku event extraction system was reported to achieve a precision of 53.98%, a recall […]

PMCID: 5130168
PMID: 27902695
DOI: 10.1371/journal.pcbi.1005017

[…] to mutation entity extraction without exploring the relationships of those mutations to other entities, such as diseases or genes. examples of mutation recognition tools include mutationfinder [], tmvar [], and several others []., several groups, however, have addressed variant relationship mining in text. one early, notable method developed by kuipers et al [] introduced an automatic method […]

PMCID: 4852402
PMID: 27141091
DOI: 10.1093/database/baw061

[…] challenge (). the tmchem system is an ensemble system that combines the output of two crf-based systems. the first system is a modified version of the banner system (), the second is based on the tmvar system (), which employs crf ++ libraries (https://taku910.github.io/crfpp/). previous results of tmchem showed that the second system outperformed the first as well as the ensemble system (). […]

PMCID: 4460711
PMID: 26043747
DOI: 10.1186/1472-6947-15-S1-S6

[…] as keywords. then, we found all related genes for each abstract and sentence containing the relevant genes using gene2pubmed []. next, we tagged the mutations and their locations using tmvar, which is a previously published software, to extract mutation information from the literature : substitutions, insertions, deletions, and snp and frameshift mutations of dna and protein […]


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tmVar institution(s)
National Center for Biotechnology Information (NCBI), National Library of Medecine (NLM), Bethesda, MD, USA
tmVar funding source(s)
NIH Intramural Research Program, National Library of Medicine; NLM Associate Fellowship Program sponsored by the National Library of Medicine and administered by the Oak Ridge Institute for Science and Education

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