Ontologies in ecology: putting the lessons-learned to good use and moving forward

While most of the headlines and attention in bio-ontologies has gone to the Gene Ontology, later also the FMA, and, most recently, the set of ontologies within or close to the OBO Foundry project, it has been comparatively more modest in the area of ontologies for ecology. This is set to change.

Madin et al [1] published a review article last month in Trends in Ecology and Evolution about not only the state of the art on existing ontologies for ecology, but also an Ode to the development and use of ontologies. The latter is not framed in a bright-vision-follow-me way, but noting (a.o.) the problems of

terminological ambiguity [that] slows scientific progress, leads to redundant research efforts, and ultimately impedes advances towards a unified foundation for ecological science

and showing problems and clear examples of what kind of problems ontologies can help to solve.

Recollecting the OWLED’07 industry panel discussion last year, it seemed as if industry was at the point where bio-ontologies were 5-8 years ago and, moreover, about to reinvent the wheel. Not so with ontologies for ecology. Madin et al has separate information boxes about “building consistent ontologies” explaining the difference between is-a and instance-of, is-a and part-of, and is-a and constitution—those things that early adopters learned the hard way a few years ago is presented as a known basic starting point. Likewise for the info-box on “What is an ontology?” and the straight adoption of OWL and benefits automated reasoners. In the overview presented by Madin et al, there are no issues to resolve on trying to be backward compatible with the obo format, but they go straight to the W3C standardized formal ontology representation languages for the ontologies for ecology. Idem box 2 on finding data (which is also a nice scenario for the OBDA Plugin and DIG-Mastro), OntoClean, foundational ontologies and domain ontologies versus other artifacts with terms, linking of ontologies, and a clear table with task-description-requirements (table 1) that invariably asks for good ontologies.

Aside from the analysis of benefits and usages, the concluding remarks section notes that

[t]hus, the adoption of ontologies is hindered both by the familiarity of current practices and the lack of tools to readily migrate to improved practices.

Point taken.

And last, but not least,

Formal ontologies provide a mechanism to address the drawbacks of terminological ambiguity in ecology, and fill an important gap in the management of ecological data by facilitating powerful data discovery based on rigorously defined, scientifically meaningful terms. By clarifying the terms of scientific discourse, and annotating data and analyses with those terms, well defined, community-sanctioned, formal ontologies based on open standards will provide a much-needed foundation upon which to tackle crucial ecological research while taking full advantage of the growing repositories of data on the Internet.

[1] Joshua S. Madin, Shawn Bowers, Mark P. Schildhauer and Matthew B. Jones. Advancing ecological research with ontologies. Trends in Ecology & Evolution, 23(3): 159-168. doi:10.1016/j.tree.2007.11.007