MetMap specifications


Unique identifier OMICS_00618
Name MetMap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No


No version available


This tool is not available anymore.

Publication for MetMap

MetMap citations


EHR based Genetic Testing Knowledge Base (iGTKB) Development

BMC Med Inform Decis Mak
PMCID: 4660117
PMID: 26606281
DOI: 10.1186/1472-6947-15-S4-S3

[…] s from a local copy of the HPO for each genetic disorder. In order to facilitate further data integration, we mapped all collected clinical features to Unified Medical Language System (UMLS) via UMLS MetMap API. Then for each genetic test, we extracted mentions of the identified clinical features from clinical notes for each patient group by applying an existing NLP tool, MedTagger suite. [,] […]


Statistical Quantification of Methylation Levels by Next Generation Sequencing

PLoS One
PMCID: 3115964
PMID: 21698242
DOI: 10.1371/journal.pone.0021034

[…] rily focuses on the setting where paired-end HpaII fragment libraries without corresponding MspI libraries are sequenced, resembling the methylation sensitive cut counting approach . In addition, the MetMap program infers strongly unmethylated islands with a hidden markov model like structure.In this work, we study the statistical issues relating to the quantification of methylation levels by next […]

MetMap institution(s)
Computer Science Division, University of California at Berkeley, Berkeley, CA, USA; Children’s Hospital Oakland Research Institute, Oakland, CA, USA; Department of Mathematics, University of California at Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Illumina, Hayward, CA, USA
MetMap funding source(s)
Supported by the NIH grants HL084474, ES016581 and CA115768.

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