Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns

Journal of Biomedical Semantics
Zuoshuang XiangYongqun He

Abstract

It is time-consuming to build an ontology with many terms and axioms. Thus it is desired to automate the process of ontology development. Ontology Design Patterns (ODPs) provide a reusable solution to solve a recurrent modeling problem in the context of ontology engineering. Because ontology terms often follow specific ODPs, the Ontology for Biomedical Investigations (OBI) developers proposed a Quick Term Templates (QTTs) process targeted at generating new ontology classes following the same pattern, using term templates in a spreadsheet format. Inspired by the ODPs and QTTs, the Ontorat web application is developed to automatically generate new ontology terms, annotations of terms, and logical axioms based on a specific ODP(s). The inputs of an Ontorat execution include axiom expression settings, an input data file, ID generation settings, and a target ontology (optional). The axiom expression settings can be saved as a predesigned Ontorat setting format text file for reuse. The input data file is generated based on a template file created by a specific ODP (text or Excel format). Ontorat is an efficient tool for ontology expansion. Different use cases are described. For example, Ontorat was applied to automatically generate o...Continue Reading

References

Oct 23, 2004·Science·UNKNOWN ENCODE Project Consortium
May 9, 2008·BMC Bioinformatics·Mikel Egaña ArangurenRobert Stevens
Jun 24, 2010·BMC Research Notes·Zuoshuang XiangYongqun He
Jul 16, 2010·Journal of Biomedical Semantics·Ryan R BrinkmanUNKNOWN OBI consortium
Jun 1, 2011·Journal of Biomedical Semantics·Stefan SchulzMartin Boeker
Jun 1, 2011·Journal of Biomedical Semantics·Arzucan OzgürYongqun He
Nov 26, 2011·BMC Bioinformatics·Martin BoekerStefan Schulz
Dec 15, 2011·Journal of Biomedical Semantics·Robert HoehndorfDietrich Rebholz-Schuhmann
Mar 1, 2012·BMC Bioinformatics·Simon JuppRobert Stevens
Oct 11, 2012·Journal of Biomedical Semantics·Djamila Seddig-RaufieStefan Schulz
Feb 13, 2013·The British Journal of Nutrition·Miriam Bermudez-BritoAngel Gil
Nov 22, 2013·Nucleic Acids Research·Yongqun HeZuoshuang Xiang
Jan 1, 2014·Journal of Biomedical Semantics·Sirarat SarntivijaiYongqun He

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Citations

Mar 24, 2016·Drug Safety : an International Journal of Medical Toxicology and Drug Experience·Sirarat SarntivijaiDarrell R Abernethy
Oct 25, 2016·Journal of Biomedical Informatics·Julien SouvignetCédric Bousquet
Nov 27, 2018·Nucleic Acids Research·Sebastian KöhlerPeter N Robinson
Dec 7, 2018·Semantic Web·Agnieszka ŁawrynowiczTania Tudorache
Jul 31, 2019·BMC Bioinformatics·Rebecca C JacksonJames A Overton
Jan 1, 2020·Journal of Biomedical Semantics·Yongqun HeJihad S Obeid
Jan 15, 2020·Journal of Biomedical Semantics·Sara AlthubaitiRobert Hoehndorf
Jun 17, 2021·PLoS Computational Biology·Simon J D CoxMaria-Cristina Marinescu

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Methods Mentioned

BETA
immunoprecipitation
Assay

Software Mentioned

Ontorat Excel
Excel
Populous
Selinux
OntoFox
Protege
QTT
CLO
OWL editor
Ontorat

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