SR4GN specifications

Information


Unique identifier OMICS_09124
Name SR4GN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Zhiyong Lu <>

Publication for SR4GN

SR4GN in publications

 (5)
PMCID: 5691349
PMID: 29220476
DOI: 10.1093/database/bax081

[…] used for species (e.g. zm for maize and bra for brassica rapa, see in ()). the gene mentions are then associated with the species based on a set of rules which extends the rules developed for sr4gn (). context of the gene mention and information about the identifiers obtained from the uniprot are utilized to choose one of the candidate identifiers as the final gene normalization result. […]

PMCID: 5414807
PMID: 28529714
DOI: 10.12688/f1000research.10788.1

[…] identifiers to genes retrieved from biomedical text. in order to improve efficiency, gnormplus integrates other resources such as simconcept for identifying and simplifying composite names and sr4gn for species named entity identification in biomedical text. pubtator is another resource for biocuration that incorporates biomedical text search. a user may search for pubmed articles […]

PMCID: 5130168
PMID: 27902695
DOI: 10.1371/journal.pcbi.1005017

[…] gene/proteins from a given text in two steps. in the first step it recognizes the gene/protein entity mention using a novel crf++ [] based module in combination with the species recognition module sr4gn []. in the second step, the gene/protein mention is normalized using gennorm [] in combination with the composite mention simplification tool, simconcept [] and an abbreviation resolution tool […]

PMCID: 4074764
PMID: 24980129
DOI: 10.1093/database/bau053

[…] definitions and random analogs ()., a number of named entity recognition (ner) tools are available in the bioc format (). these include dnorm for disease names (, ), tmvar for mutations (), sr4gn for species (), tmchem for chemicals () and gennorm for gene normalization (). the results of these tools can be used directly or as features for even further entity recognition […]

PMCID: 3629104
PMID: 23613707
DOI: 10.1371/journal.pone.0055814

[…] set., for gene mentions where full resolution into an entrez gene identifier is not possible, gennorm still assigns the most likely organism of the mention, using its stand-alone open source module sr4gn . sr4gn was proven to achieve state of the art results, reporting 85.42% in accuracy., the three normalization algorithms described above exhibit different properties () and their complementary […]


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SR4GN institution(s)
National Center for Biotechnology Information (NCBI), National Library of Medicine, Bethesda, MD, USA; Department of Computer Science and Information Engineering, National Cheng Kung University, Taiwan, China

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