War of ontology worlds: mathematics, computer code, or Esperanto?

Area of Science:

• Biomedical informatics
• Knowledge representation
• Ontology engineering

Background:

• Structured knowledge representations, including ontologies and terminologies, are integral to modern biomedicine.
• Existing definitions and underlying philosophies of ontologies vary significantly.
• Understanding these diverse perspectives is crucial for advancing the field.

Purpose of the Study:

• To explicate the varied perspectives of leading ontologists regarding biomedical ontologies.
• To identify and summarize distinct philosophical and practical approaches to ontology development.
• To explore how these diverse views can inform the future of biomedical ontologies.

Main Methods:

• Conducted and summarized interviews with a dozen prominent ontologists.
• Analyzed interview data to identify recurring themes and philosophical clusters.
• Categorized the identified perspectives into three broad groups: mathematics, computer code, and Esperanto.

Main Results:

• Identified three primary perspectives on ontology development: mathematics (emphasizing rigor, logic, and consistency), computer code (prioritizing utility and custom design for diverse applications), and Esperanto (focusing on cross-disciplinary communication and data integration).
• Demonstrated alignment between these perspectives and historical divisions within scientific thought.
• Highlighted the potential for a synthesized approach to enhance next-generation biomedical ontologies.

Conclusions:

• The diverse philosophical underpinnings of biomedical ontologies can be broadly categorized into three main viewpoints.
• Recognizing and integrating these distinct perspectives offers a pathway to more robust and versatile biomedical knowledge representations.
• A synthesis of mathematical rigor, computational utility, and communicative facilitation is key to advancing biomedical ontology development.