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SimConcept specifications

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Unique identifier OMICS_13816
Name SimConcept
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format PubTator
Operating system Unix/Linux, Windows
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SimConcept

SimConcept in publications

 (5)
PMCID: 5414807
PMID: 28529714
DOI: 10.12688/f1000research.10788.1

[…] in , is the process of identifying and assigning biomedical database 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 […]

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

[…] 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 ab3p []., tmvar. tmvar uses a conditional random field (crf) model to detect mutation mentions in text []. the crf model identifies the mutation […]

PMCID: 4869795
PMID: 27189609
DOI: 10.1093/database/baw071

[…] neurological and cardiovascular toxicity). in this regard, only 1% of disease and chemical mentions are composite mentions in the provided data set, and so we do not use any specific resource (e.g. simconcept tool) to deal with such cases., as mentioned above, it is not straightforward to apply standard re approaches in the cid re task due to the specific characteristics of the task. in nlp, […]

PMCID: 4865327
PMID: 27173521
DOI: 10.1093/database/baw065

[…] digits, tokens, and binary features of common gene/protein (e.g. ‘alpha’) or family (e.g. ‘proteins’) suffixes., we also filtered composite mentions (‘multiple’ type) by applying our previous study simconcept () to recognize these mentions rather than simplify them. the mentions are recognized as mention with coordination ellipsis or range mention are definitely type 2 and should be removed […]

PMCID: 4423583
PMID: 25952498
DOI: 10.1186/1471-2105-16-S7-S4

[…] the fewer the concepts that are located on the path pair. therefore, from the concepts that constitute the shortest-related path pair between concepts, the degree of similarity between concepts simconcept(t1, t2) is defined as follows., definition 3 degree of similarity between concepts. the degree of similarity between two concepts t1 and t2, simconcept(t1, t2) is defined by the equation […]

SimConcept institution(s)
National Center for Biotechnology Information, Bethesda, MA, USA
SimConcept funding source(s)
This research was supported by the NIH Intramural Research Program, National Library of Medicine.

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