War of Ontology Worlds: Mathematics, Computer Code, or Esperanto?

Abstract

The use of structured knowledge representations—ontologies and terminologies—has become standard in biomedicine. Definitions of ontologies vary widely, as do the values and philosophies that underlie them. In seeking to make these views explicit, we conducted and summarized interviews with a dozen leading ontologists. Their views clustered into three broad perspectives that we summarize as mathematics, computer code, and Esperanto. Ontology as mathematics puts the ultimate premium on rigor and logic, symmetry and consistency of representation across scientific subfields, and the inclusion of only established, non-contradictory knowledge. Ontology as computer code focuses on utility and cultivates diversity, fitting ontologies to their purpose. Like computer languages C++, Prolog, and HTML, the code perspective holds that diverse applications warrant custom designed ontologies. Ontology as Esperanto focuses on facilitating cross-disciplinary communication, knowledge cross-referencing, and computation across datasets from diverse communities. We show how these views align with classical divides in science and suggest how a synthesis of their concerns could strengthen the next generation of biomedical ontologies.

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

“…EDAM is founded on logic, and on relevance and utility to the bioinformatics community. This is in accordance with Lord and Stevens (2010), Merrill (2010, 2011) and Rzhetsky and Evans (2011) that all indicate, using separate sets of arguments, that it is the relevance of scientific ontologies with respect to their practical applications that is more important than an imposed metaphysical ideology. EDAM concepts are not concepts existing only in minds of the EDAM authors, but common notions shared within the bioinformatics community.…”

Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project

“…Our experience in SPARC highlights the difficulty of working with large ontologies, as searching across their entirety, including terms and relationships, remains a challenge. Ontologies sit between the realm of human knowledge and computer code ( Rzhetsky and Evans, 2011 ). They contain some classes and relationships that are understandable to a domain expert, but also a lot of opaque relationships and intermediate classes that are difficult for non-experts to understand ( Dietze et al, 2014 ).…”

Clustered Iconography: A Resurrected Method for Representing Multidimensional Data

“…For example, the first World Esperanto Congress took place in 1905 to promote a universal language to foster world peace and international understanding. In some respects, this initiative had objectives similar to those pursued by Playfair, that is, “to allow for the transfer of knowledge and insight between areas, even if imperfectly” (Rzhetsky and Evans 2011:3). The same period saw the development of purely visual international systems of communication.…”