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A document-centric approach for developing the tolAPC ontology.

Aisha Blfgeh1,2, Jennifer Warrender3, Catharien M U Hilkens4

  • 1School of Computing Science, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK. a.blfgeh1@newcastle.ac.uk.

Journal of Biomedical Semantics
|November 29, 2017
PubMed
Summary

We developed a new method for building scientific ontologies using domain expert data in spreadsheets. This approach allows for easy updates, ensuring the ontology remains current and accurate for immunological cell types.

Keywords:
Document-centricExcel workflowOntologyTawny-OWL

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Area of Science:

  • Immunology
  • Bioinformatics
  • Computational Biology

Background:

  • Ontology building is complex, requiring diverse expertise (domain knowledge, formalisms, software, philosophy).
  • Collaboration is essential, but remote teamwork faces challenges with diverse data formalisms, commonly office files like spreadsheets.
  • Traditional methods can be costly and time-consuming for distributed teams.

Purpose of the Study:

  • To develop an ontology of immunological cell types.
  • To create a streamlined and collaborative ontology development process.
  • To enable domain specialists to contribute directly to ontology creation using familiar tools.

Main Methods:

  • Developed an ontology of immunological cell types programmatically using ontology design patterns.
  • Utilized an Excel spreadsheet, created by domain specialists, as the primary data source.
  • Implemented a pattern-driven, programmatic approach to transform spreadsheet data into a formal ontology.

Main Results:

  • Successfully created a novel ontology for immunological cell types.
  • The ontology is directly linked to the source spreadsheet, allowing for dynamic updates.
  • Demonstrated a method for generating ontologies from expert-generated spreadsheet data.

Conclusions:

  • The developed methodology facilitates ontology creation using domain expert data in spreadsheets.
  • The process allows for unconstrained updates to the source spreadsheet, which automatically propagate to the ontology.
  • This approach offers a generalizable solution for collaborative and efficient ontology development.