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Associated diseases

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NLProt specifications

Information


Unique identifier OMICS_20064
Name NLProt
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Information


Unique identifier OMICS_20064
Name NLProt
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publications for NLProt

NLProt in publications

 (5)
PMCID: 4674139
PMID: 26650466
DOI: 10.1371/journal.pcbi.1004630

[…] quickly become available online (e.g. through pubmed, http://www.ncbi.nlm.nih.gov/pubmed), and are a growing resource for automated mining of the pp binding mode. many applications (pubmed entrez, nlprot, medminer, etc.) utilizing tm techniques have been developed to improve access to the published knowledge []. tm converts textual information into database content and complex networks, […]

PMCID: 4391036
PMID: 25914674
DOI: 10.3389/fmicb.2015.00235

[…] a host and pathogen protein, features that make use of the negation signaling keywords were also designed. the protein and gene names, as well as the corresponding organisms were tagged by using the nlprot software (). a set of dictionaries for interaction keywords, experimental keywords, negation keywords, phi-keywords, host names, pathogen names, and uncertainty keywords was manually compiled. […]

PMCID: 3596348
PMID: 23516571
DOI: 10.1371/journal.pone.0058895

[…] for afld, and 868 papers and 2217 co-occurrences for nafld. the query involves retrieving extensible markup language (xml) pubmed abstracts for pmid list, passing xml pubmed abstracts for nlprot analysis (a tool for finding protein names in natural language text), and tagging protein names and performing co-occurrences analyses. after carrying out terms' tagging, a total of 228 […]

PMCID: 3269935
PMID: 22151823
DOI: 10.1186/1471-2105-12-S8-S12

[…] correlation coefficient, and f-score. we observe that the most useful named entity recognition and dictionary tools for classification of articles relevant to protein-protein interaction are: abner, nlprot, oscar 3 and the psi-mi ontology. for the imt, our results are comparable to those of other systems, which took very different approaches. while the performance is not very high, we focus […]

PMCID: 1175978
PMID: 15998455
DOI: 10.1186/gb-2005-6-7-224

[…] a list of the words observed in the document and a statistical quality score that indicates how probable it is that the each word represents a gene or protein name. another online protein tagger is nlprot, developed at columbia university [,]. nlprot is based on a machine learning technique called support vector machines (svms) and allows protein identification either in a submitted text […]


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NLProt institution(s)
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; Columbia University Center for Computational Biology and Bioinformatics (C2B2), Russ Berrie Pavilion, New York, NY, USA; Institute of Physical Biochemistry, University Witten/Herdecke, Witten, Germany
NLProt funding source(s)
Supported by the grants RO1-GM63029-01 from the National Institutes of Health (NIH), R01-LM07329-01 from the National Library of Medicine (NLM) and DBI-0131168 from the National Science Foundation (NSF).

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