ontoCAT statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ontoCAT

Tool usage distribution map

This map represents all the scientific publications referring to ontoCAT per scientific context
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ontoCAT specifications


Unique identifier OMICS_26394
Name ontoCAT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Apache License version 2.0
Computer skills Advanced
Version 1.29
Stability Stable
Maintained Yes


No version available


  • person_outline Natalja Kurbatova

Additional information

http://master.bioconductor.org/packages/release/bioc/html/ontoCAT.html https://sourceforge.net/projects/ontocat/

Publication for ontoCAT

ontoCAT citations


Knowledge base and mini expert platform for the diagnosis of inborn errors of metabolism

Genet Med
PMCID: 5763153
PMID: 28726811
DOI: 10.1038/gim.2017.108

[…] from IEMbase (version 1.0.0) and the four vocabularies. For SNOMED CT, extraction was restricted to only the terms categorized under “Clinical finding” and “Substance,” to minimize false mapping. The OntoCAT R package was used to parse HPO terms. The standard string library and Nokogiri gem in Ruby programming language were used to parse all others. Second, all extracted terms were normalized usin […]


Genome wide identification of splicing QTLs in the human brain and their enrichment among schizophrenia associated loci

Nat Commun
PMCID: 5333373
PMID: 28240266
DOI: 10.1038/ncomms14519

[…] file). We considered SNPs associated with any of the child terms of ‘EFO_0000408: disease' as disease-associated SNPs. Information of child terms of ‘EFO_0000408: disease' was collected by using the ontoCAT package of R. We evaluate whether there is enrichment of sQTL SNPs among associated loci by one-tailed Fisher's exact test with the following 2 × 2 table: columns; sQTL SNPs and non-sQTL SNPs, […]


KneeTex: an ontology–driven system for information extraction from MRI reports

J Biomed Semantics
PMCID: 4561435
PMID: 26347806
DOI: 10.1186/s13326-015-0033-1

[…] affected must be soft tissue such as ligament or tendon. Similarly, if the affected anatomical entity is cartilage, then its qualifier must be related to bone or joint. We originally considered using OntoCAT for this purpose, as it provides a programming interface to query ontologies shared on BioPortal or user–specified local OBO files []. However, this would separate ontology querying from query […]


BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing

PMCID: 4433361
PMID: 25361575
DOI: 10.1136/amiajnl-2013-002577

[…] cation System, because ATC codes are commonly used to store information regarding medication usage. Users can use any or all of these ontologies. The ontology terms are retrieved from BioPortal using OntoCAT software and stored in a local Lucene index. Use of this local index solves the problem of slow response when many requests are made over slow internet connections. […]


The ontology based answers (OBA) service: a connector for embedded usage of ontologies in applications

Front Genet
PMCID: 3464866
PMID: 23060901
DOI: 10.3389/fgene.2012.00197

[…] , the OBA service can load and process any ontology in the OBO or OWL format, giving access to their fundamental information to developers who otherwise would probably not use ontologies.Portals like OntoCAT (), the OLS (), or the NCBO BioPortal () aim to provide access to huge collections of ontologies in a standardized manner. This is the preferred way if the unique definitions of terms in ontol […]


LibKiSAO: a Java library for Querying KiSAO

BMC Res Notes
PMCID: 3532180
PMID: 23006857
DOI: 10.1186/1756-0500-5-520

[…] interfaces for manipulating ontologies, such as OWL API [], and ontology reasoners, such as HermiT []. Richer programming interfaces for interacting with ontology resources are also available, e.g., OntoCAT [], an application suite enabling the querying of several resources simultaneously, looking for synonyms and definitions (which is not supported directly by OWL API). Nevertheless, due to the […]

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ontoCAT institution(s)
EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK; Genomics Coordination Center, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
ontoCAT funding source(s)
Supported by the European Community’s Seventh Framework Programme projects GEN2PHEN (grant number 200754); SYBARIS (grant number 242220); and NWO/Rubicon (grant number 825.09.008).

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