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SimConcept specifications


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




No version available

Publication for SimConcept

SimConcept citations


Recent advances in predicting gene–disease associations

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 biome […]


Text Mining Genotype Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine

PLoS Comput Biol
PMCID: 5130168
PMID: 27902695
DOI: 10.1371/journal.pcbi.1005017
call_split See protocol

[…] 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 Ab3P [].tmVar. tmVar uses a conditional random field (CRF) model to detect mutation mentions in text []. The CRF model identifies the mutation type, r […]


NERChem: adapting NERBio to chemical patents via full token features and named entity feature with chemical sub class composition

PMCID: 5091336
DOI: 10.1093/database/baw135

[…] rticipants and the average performance of 21 teams in and . We found that some composite names such as (C1–C4) alkoxy methyl, C4–C8 alcohol and C6–C9 aroyl were misidentified in our system. However, SimConcept () focused on decomposing these mentions and was able to successfully recognize them. These cases were overlooked in our previous work, and we will seek to improve our system based on the a […]


A knowledge poor approach to chemical disease relation extraction

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. […]


Mining chemical patents with an ensemble of open systems

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

[…] es, 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 from […]


A method of searching for related literature on protein structure analysis by considering a user's intention

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

[…] milar 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 belo […]


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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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