Aligning Design Patterns across Multiple Ontologies in the Life Sciences
November 2, 2020 5 Comments
I was delighted to give the keynote at http://ISWC 2020 Workshop on Ontology Design and Patterns today. You can see a video or my slides, I’m including a brief summary here.

As this was a CS audience that may be unfamiliar with some of the issues we are tackling in OBO I framed this in terms of the massive number of named entities in the life sciences, all of which have to be categorized if we are to be able to find, integrated, and analyze data:

We created OBO to help organize and integrate the ontologies used to categorize these things

When we started, many ontologies were quite ‘SKOS-like’ in their nature, with simple axiomatization, and a lack of integration:

OWL gives us a framework for more modular development, leveraging other ontologies, and using reasoning to automate classification:

This is all great, but when I look at many ontologies I often see two problems, often in the same ontology, under- and over- axiomatization:

In some ontologies I see what I sometimes call ‘Rococo OWL’, over-axiomatization in an elaborate dense set of axioms that looks impressive but don’t deliver much functional utility (I plan to write about this in a future post).

We developed Dead Simple OWL Design Patterns (DOSDPs) to make it easier to write down and reuse common OWL patterns of writing definitions, primarily for compositional classes following the Rector Normalization pattern.

I gave an example of how we used DOSDPs to align logical definitions across multiple phenotype ontologies (the uPheno reconciliation project). I would like to expand on this in a future post.

I finished with some open-ended questions about where we are going and whether we can try and unify different modeling frameworks that tackle things from different perspectives (closed-world shape-based on object-oriented modeling, template/pattern frameworks, lower level logical modeling frameworks).

Unfortunately due to lack of time I didn’t go into either ROBOT templates or OTTR templates.
And in closing, to emphasize that the community and social aspects are as important or more important than the technology:

And some useful links:
●http://obofoundry.org/resources
●https://github.com/INCATools/
○ dead_simple_owl_design_patterns (dos-dps)
Special thanks to everyone in OBO and the uPheno reconciliation effort, especially David-Osumi Sutherland, Jim Balhoff, and Nico Matentzoglu.
And thanks to Pascal Hitzler and Cogan Shimizu for putting together such a great workshop.