Literature DB >> 30505251

Discovery of Emerging Design Patterns in Ontologies Using Tree Mining.

Agnieszka Ławrynowicz1, Jedrzej Potoniec1, Michał Robaczyk1, Tania Tudorache2.   

Abstract

The research goal of this work is to investigate modeling patterns that recur in ontologies. Such patterns may originate from certain design solutions, and they may possibly indicate emerging ontology design patterns. We describe our tree-mining method for identifying the emerging design patterns. The method works in two steps: (1) we transform the ontology axioms in a tree shape in order to find axiom patterns; and then, (2) we use association analysis to mine co-occuring axiom patterns in order to extract emerging design patterns. We conduct an experimental study on a set of 331 ontologies from the BioPortal repository. We show that recurring axiom patterns appear across all individual ontologies, as well as across the whole set. In individual ontologies, we find frequent and non-trivial patterns with and without variables. Some of the former patterns have more than 300,000 occurrences. The longest pattern without a variable discovered from the whole ontology set has size 12, and it appears in 14 ontologies. To the best of our knowledge, this is the first method for automatic discovery of emerging design patterns in ontologies. Finally, we demonstrate that we are able to automatically detect patterns, for which we have manually confirmed that they are fragments of ontology design patterns described in the literature. Since our method is not specific to particular ontologies, we conclude that we should be able to discover new, emerging design patterns for arbitrary ontology sets.

Entities:  

Keywords:  BioPortal; ODP; emerging design pattern; ontology; ontology fragment; ontology reuse; pattern mining; tree mining

Year:  2018        PMID: 30505251      PMCID: PMC6261490          DOI: 10.3233/SW-170280

Source DB:  PubMed          Journal:  Semant Web        ISSN: 1570-0844            Impact factor:   2.214


  12 in total

1.  OpenGALEN: open source medical terminology and tools.

Authors:  A L Rector; J E Rogers; P E Zanstra; E Van Der Haring
Journal:  AMIA Annu Symp Proc       Date:  2003

2.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

Authors:  Barry Smith; Michael Ashburner; Cornelius Rosse; Jonathan Bard; William Bug; Werner Ceusters; Louis J Goldberg; Karen Eilbeck; Amelia Ireland; Christopher J Mungall; Neocles Leontis; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; Richard H Scheuermann; Nigam Shah; Patricia L Whetzel; Suzanna Lewis
Journal:  Nat Biotechnol       Date:  2007-11       Impact factor: 54.908

3.  Modeling biomedical experimental processes with OBI.

Authors:  Ryan R Brinkman; Mélanie Courtot; Dirk Derom; Jennifer M Fostel; Yongqun He; Phillip Lord; James Malone; Helen Parkinson; Bjoern Peters; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; Larisa N Soldatova; Christian J Stoeckert; Jessica A Turner; Jie Zheng
Journal:  J Biomed Semantics       Date:  2010-06-22

4.  Modeling functional Magnetic Resonance Imaging (fMRI) experimental variables in the Ontology of Experimental Variables and Values (OoEVV).

Authors:  Gully A P C Burns; Jessica A Turner
Journal:  Neuroimage       Date:  2013-05-16       Impact factor: 6.556

5.  The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process.

Authors:  Erick Antezana; Mikel Egaña; Ward Blondé; Aitzol Illarramendi; Iñaki Bilbao; Bernard De Baets; Robert Stevens; Vladimir Mironov; Martin Kuiper
Journal:  Genome Biol       Date:  2009-05-29       Impact factor: 13.583

6.  Analysing Syntactic Regularities and Irregularities in SNOMED-CT.

Authors:  Eleni Mikroyannidi; Robert Stevens; Luigi Iannone; Alan Rector
Journal:  J Biomed Semantics       Date:  2012-12-17

7.  BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Authors:  Patricia L Whetzel; Natalya F Noy; Nigam H Shah; Paul R Alexander; Csongor Nyulas; Tania Tudorache; Mark A Musen
Journal:  Nucleic Acids Res       Date:  2011-06-14       Impact factor: 16.971

8.  Uberon, an integrative multi-species anatomy ontology.

Authors:  Christopher J Mungall; Carlo Torniai; Georgios V Gkoutos; Suzanna E Lewis; Melissa A Haendel
Journal:  Genome Biol       Date:  2012-01-31       Impact factor: 13.583

9.  CLO: The cell line ontology.

Authors:  Sirarat Sarntivijai; Yu Lin; Zuoshuang Xiang; Terrence F Meehan; Alexander D Diehl; Uma D Vempati; Stephan C Schürer; Chao Pang; James Malone; Helen Parkinson; Yue Liu; Terue Takatsuki; Kaoru Saijo; Hiroshi Masuya; Yukio Nakamura; Matthew H Brush; Melissa A Haendel; Jie Zheng; Christian J Stoeckert; Bjoern Peters; Christopher J Mungall; Thomas E Carey; David J States; Brian D Athey; Yongqun He
Journal:  J Biomed Semantics       Date:  2014-08-13

10.  Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology.

Authors:  Mikel Egaña Aranguren; Erick Antezana; Martin Kuiper; Robert Stevens
Journal:  BMC Bioinformatics       Date:  2008-04-29       Impact factor: 3.169

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