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Peregrine specifications

Information


Unique identifier OMICS_07944
Name Peregrine
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

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Publication for Peregrine

Peregrine citations

 (12)
library_books

CodeMapper: semiautomatic coding of case definitions. A contribution from the ADVANCE project

2017
PMCID: 5575526
PMID: 28657162
DOI: 10.1002/pds.4245

[…] adings (MeSH), Medical Dictionary for Regulatory Activities (MedDRA), Systematized Nomenclature of Medicine—Clinical Terms (SNOMED‐CT), ICD‐9 CM, ICD‐10 CM, ICPC‐2, and CTv3. Our text‐indexing engine Peregrine uses this dictionary to identify medical concepts in the case definition. CodeMapper provides two operations to improve the sensitivity of the mapping by expanding a concept to more general […]

call_split

Recognition of chemical entities: combining dictionary based and grammar based approaches

2015
J Cheminform
PMCID: 4331686
PMID: 25810767
DOI: 10.1186/1758-2946-7-S1-S10
call_split See protocol

[…] We employed the Peregrine tagger [,] to analyze the performance of the individual terminological resources. Tokenization of text that contains chemical terms can be complicated as compound names may include punctuati […]

library_books

Knowledge based extraction of adverse drug events from biomedical text

2014
BMC Bioinformatics
PMCID: 3973995
PMID: 24593054
DOI: 10.1186/1471-2105-15-64

[…] tion system), in a ratio of 1.26:1. To create a corpus with the same ratio to train and test our system and allow comparison of results, we took all true relations in which the concepts were found by Peregrine and the NLP module, and randomly added false co-occurrence relations generated by Peregrine and the NLP module, until the ratio of 1.26:1 was reached.Table  shows the performance of our know […]

library_books

Generic Information Can Retrieve Known Biological Associations: Implications for Biomedical Knowledge Discovery

2013
PLoS One
PMCID: 3834066
PMID: 24260124
DOI: 10.1371/journal.pone.0078665

[…] The Open Source concept recognition software Peregrine scans free-text and resolves homonyms and maps ambiguous terminology and spellings to unique biomedical concepts – (software available at https://trac.nbic.nl/data-mining/). Peregrine uses a […]

call_split

Using rule based natural language processing to improve disease normalization in biomedical text

2012
PMCID: 3756254
PMID: 23043124
DOI: 10.1136/amiajnl-2012-001173
call_split See protocol

[…] We evaluated two concept normalization systems, MetaMap and Peregrine. Both systems were downloaded from their official websites with default configurations and parameters, and no attempt was made to optimize their performance.MetaMap (http://metamap.nlm.nih.g […]

library_books

Integrating Various Resources for Gene Name Normalization

2012
PLoS One
PMCID: 3440407
PMID: 22984434
DOI: 10.1371/journal.pone.0043558

[…] lexicon, as the identifiers and symbols from different databases are not in accordance with each other, and there is not always a direct one-to-one mapping between different database identifiers. The Peregrine system analyzes the terms of the lexicon and prunes it by removing highly ambiguous terms and the terms that cause false positives.Disambiguation and filtering: determining which meaning of […]

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Peregrine institution(s)
Biosemantics Group, Medical Informatics Department, ErasmusMC University Medical Center Rotterdam, Rotterdam, Netherlands

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