Peregrine protocols

View Peregrine computational protocol

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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 in pipeline

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

[…] a common approach to increase precision as used by many systems in the biocreative competitions. our list contains 23 generic concepts (eg, ‘disease’, ‘abnormality’) that were wrongly annotated by peregrine in the training set., the rules in the nlp module were developed on the basis of an error analysis of the peregrine annotations of the training set. the annotations of metamap were not used […]


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Peregrine in publications

 (4)
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 (https://trac.nbic.nl/data-mining/) as the basis of our concept identification system. peregrine is a dictionary-based concept recognition and normalization tool, developed […]

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 […]

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 […]

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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