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Towards refactoring the Molecular Function Ontology with a UML profile for function modeling.

Patryk Burek1, Frank Loebe2, Heinrich Herre1

  • 1Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, Leipzig, 04107, Germany.

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|October 6, 2017
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Summary
This summary is machine-generated.

We introduce the Function Modeling Language (FueL), a UML dialect for structuring the Molecular Function Ontology (MFO). FueL enhances the graphical representation of gene functions and supports ontology refactoring.

Keywords:
Function decompositionGene OntologyIntensional subsumptionMolecular Function OntologyOntologyUnified Modeling Language

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Area of Science:

  • Bioinformatics
  • Ontology Engineering

Background:

  • Gene Ontology (GO) is a vast and growing resource for gene product cataloging.
  • Managing and refactoring large ontologies like GO presents structural challenges.
  • Human-friendly graphical modeling languages may aid ontology management.

Purpose of the Study:

  • To investigate the use of Unified Modeling Language (UML) for explicit structural organization of the Molecular Function Ontology (MFO).
  • To present a UML dialect, Function Modeling Language (FueL), for ontologically sound function capture.
  • To explore refactoring options for MFO fragments using FueL.

Main Methods:

  • Developed Function Modeling Language (FueL), a UML dialect tailored for ontologies.
  • Utilized FueL to capture the structure of molecular functions within MFO.
  • Analyzed MFO fragments using FueL and identified refactoring strategies.

Main Results:

  • FueL provides systematic, graphical representation of functions and their interrelations.
  • FueL makes implicit information within MFO explicit, supplementing textual descriptions.
  • Subsumption patterns in FueL facilitate methodical analysis of MFO refactoring options.

Conclusions:

  • FueL enhances the comprehensibility of MFO structure for human users.
  • The approach supports communication and collaboration in ontology revision and development.
  • FueL offers a valuable tool for managing and refining large biological ontologies.