MutationFinder protocols

View MutationFinder computational protocol

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MutationFinder specifications


Unique identifier OMICS_09111
Name MutationFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Perl, Python
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for MutationFinder

MutationFinder in pipeline

PMCID: 3662864
PMID: 23707966
DOI: 10.1093/database/bat033

[…] not repeat the existing evaluations performed in biocontext () for anatomy, negation and speculation contexts. similarly, mutation detection and normalization had also been previously evaluated for mutationfinder (). however, to evaluate the mutation to protein linking method, we selected 100 event chains that matched at least one mutation in the original sentence used to extract the data. […]

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MutationFinder in publications

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

[…] confine their scope 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 […]

PMCID: 4176422
PMID: 25285203
DOI: 10.5256/f1000research.3422.r3233

[…] from the literature., text mining of mutations in the scientific literature has been addressed by several tools, including mutationminer , markerinfofinder , emu (extractor of mutations) , mutationfinder , tmvar , and seth . a summary of previous work can be found in naderi and witte (2012) . these tools have been shown to achieve a performance over 0.90 in f1 measure, […]

PMCID: 4168744
PMID: 25254099
DOI: 10.5256/f1000research.3456.r4561

[…] corpus contains annotations for metabolites and enzymes names in almost 300 abstracts and was used for the evaluation of dictionary-based approaches for the recognition of these entity types., mutationfinder. the mutationfinder corpus is composed of 508 medline abstracts annotated with mutations and it was used for the evaluation of the homonymous tool based on regular expression […]

PMCID: 3939821
PMID: 24568600
DOI: 10.1186/2041-1480-5-11

[…] subsets., we retrieved 201 documents annotated with singular amino acid substitutions grounded to proteins, from the kinmutbase [] database. we additionally curated the selection by running mutationfinder [], which is a reliable tool for this purpose due to its very high recall, and comparing the results with the annotations in the database. based on this comparison, we discarded […]

PMCID: 3662864
PMID: 23707966
DOI: 10.1093/database/bat033

[…] gene2go mapping of entrez gene ids to go ids available on the national center for biotechnology information ftp service ()., point mutation context was added to proteins in event chains by using mutationfinder to match and normalize mutation instances in the text (). mutationfinder was run only on sentences that were the source of each event chain in our pain set. however, […]

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MutationFinder institution(s)
University of Colorado Health Sciences Center, Aurora, CO; Motorola Mobile Devices, Libertyville, IL; Department of Computer Science; Department of Linguistics, University of Colorado at Boulder, Boulder, CO, USA

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