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Peregrine specifications


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


Knowledge based extraction of adverse drug events from biomedical text

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

[…] an adverse effect relation can be established between the entities that are found. all modules were integrated in the unstructured information management architecture framework []., we used the peregrine system ( as the basis of our concept identification system. peregrine is a dictionary-based concept recognition and normalization tool, developed […]


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

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

[…] the usefulness of natural language processing (nlp) as an adjunct to dictionary-based concept normalization., we compared the performance of two biomedical concept normalization systems, metamap and peregrine, on the arizona disease corpus, with and without the use of a rule-based nlp module. performance was assessed for exact and inexact boundary matching of the system annotations […]


Automatic Filtering and Substantiation of Drug Safety Signals

PMCID: 3320573
PMID: 22496632
DOI: 10.1371/journal.pcbi.1002457

[…] in the eu-adr project were captured and stored in a database. briefly, all abstracts in the medline database were split into sentences, and all sentences were indexed by the concept-recognition tool peregrine to find drugs and adverse events. a chi-square test was performed to check if the probability of the drug and the adverse event co-occurring together in a sentence was significantly […]


Overview of BioCreative II gene normalization

PMCID: 2559987
PMID: 18834494
DOI: 10.1186/gb-2008-9-s2-s3

[…] was fast and efficient, avoiding the traditional string matching techniques, which were replaced by simple matrix manipulations. the system achieved an f-measure of 0.76 for the gn task., the peregrine system [] was tested in two separate runs: with the lexicon provided by the biocreative ii organizers, and with a lexicon constructed by combining five different gene databases []. four […]

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

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