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Posts tagged ‘design’

Thoughts: Bio-ontologies with only minimal predetermined relations

Time for some reflection on this (2015) Spring’s Weekly Discussion on Phenotype ontologies – origins, theory, applications, prospects, and challenges. It gets to be a little (and intentionally) provocative (as opposed to very carefully thought out) towards the end.

We started off three months ago with Daduhl et al. 2010, who provide an inspiring vision on the subject (page 370):

“The application of ontologies to systematics has the potential to force clarification and improve communication about morphological character diversity across taxonomic domains. As a result, ontologies could extend the applicability and level of universality of characters for phylogenetic analysis and improve the knowledge of evolutionary transformations. These computable vocabularies could enable efficient computer processing of vast amounts of data and allow the exploration and aggregation of data across studies that is currently difficult to do in morphology-based phylogenetics.”

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Weekly reading: Nikolov et al. on arthropod cuticle design principles

Hi everyone! For this week’s discussion, we will be reading a paper by Nikolov et al. (found here) discussing the mechanical properties of lobster cuticle as described using a set of nested, hierarchical equations. There are two papers that discuss this topic, of which, this is the less-technical. The other paper can be found here, and has some neat figures outlining the structure of the cuticle. Come ready to discuss how this model might be connected to and incorporated within an anatomy ontology, and how this might (or not) be useful in a phylogenetic context. There a few terms/concepts I really recommend looking up on Wikipedia before reading the paper, simply because they get used frequently (they are easy):

1.) Isotropic vs. Anisotropic

2.) Stress & Strain

3.) Young’s Modulus of Elasticity

4.) Poisson’s Ratio

Enjoy!

http://onlinelibrary.wiley.com/doi/10.1002/adma.200902019/epdf

What might we (systematists) want out of phenotype ontologies

Quick note ahead of the main entry: New paper by István Mikó et al. 2015. Generating semantic phenotypes. Worth a careful read.

The innovative paper by Ramírez & Michalik (2014) made for (another) lively discussion last week. The paper is rich with ideas and densely presented, which motivated an attempt by us to enumerate the sequence of data production and analytical steps. Another interesting question is to what extent (and why!) the authors’ approach moves away from the prevalent multi-taxon phenotype ontology approach. For instance, statements like the following (page 642) depart from the prevalent OBO language:

“As the Spider Ontology arose to manage the morphological concepts used in phylogenetic datasets, it is natural that it incorporated much of the pre-processed homology correspondences on its structure and definitions, to make room for the variety of form and function that the same organ may have in different organisms. In this way, the ontology accommodates the vast majority of homology statements currently accepted in spider systematics.”

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Weekly reading: Ramirez et al. on structural complexity in ancestral ontologies (again)

Last week we read and appreciated Seltmann et al.’s (2012) effort to carefully describe the benefits, use, and user community roll-out of the spectacularly well annotated Hymenoptera Anatomy Ontology Portal. We clearly need and want something like this for Coleoptera. That said, we continue to explore options to maybe do things a little differently. Looking for inspiration, we are reading once more what is to my mind one of the best demonstrations of how phenotype ontologies can be used to address research questions – by phylogenetic systematists, for phylogenetic systematists.

Ramírez, M.J. & P. Michalik. 2014. Calculating structural complexity in phylogenies using ancestral ontologies. Cladistics (Early View). Available here.

We are also starting, based on this semester’s cumulative readings, to formulate some interests of our own. Hence the following homework for all; due by next Wednesday’s discussion.

Formulate three research themes or questions that are comparative/phylogenetic in nature and could possibly make use of phenotype ontologies. Be very specific; ideally starting with the taxonomic group and character system that you are most intimately acquainted with. (in my case, e.g., that might be acalyptine weevil mouthparts). Best to work outward from the current core of your taxonomic expertise. Research ideas might take into account (yet are clearly not limited to):

  • Evolution of phenotype complexity, reduction.
  • Correlations across character systems.
  • Presence/absence of traits across larger phylogenetic groups and within/among subgroups.
  • Relationships of traits to non-organismal variables (e.g., environment).
  • Annotations and inferences targeting the specimen level versus or higher taxon entities.
  • Evolutionary rates, timing.
  • Associations, coevolutionary themes.
  • Information availability, completeness, suitability for analysis.
  • … [insert your favored domain of phenomena or inquiry here]

The idea is to engage in a bit of a reverse engineering exercise. We know that the earliest phenotype ontologies came out of the model organism community – what Nelson & Platnick (1981) might refer to as “general biology” (pages 4-5). Yet systematists tend to ask comparative questions. What (if any) general structures, entities, and relationships do these comparative/phylogenetic questions entail? Which kinds of inferences are we (most) interested in? How would the components needed to accommodate the inferences be fruitfully translated into a logic framework?

In other words, let’s pretend we are well advised to engage in some conceptual modeling for the future design of a Coleoptera Anatomy Ontology (which may not carry such a name in the end). Start with nailing down our most highly domain-specific questions. Abstract overarching design needs from these. Pretend that solutions will follow.

Weekly reading: Seltmann et al. on hymenopterists’ guide to the Hymenoptera Anatomy Ontology

If it were that kind of semester, maybe it would be neat to summarize our thoughts on all the ways in which last week’s paper – one of the theoretical foundations of the OBO Foundry approach – was puzzling to us. But, so far it isn’t (that kind of semester). Just three thoughts then.

1. Many of us seem to want to be realists.

2. Whatever the merits of the theory, implementation matters too. The two need not always be entirely and reciprocally consistent. (that is putting things mildly)

3. Consider this statement by Smith (2004), top of page 79 in the publisher paper.

“Good ontologies are reality representations, and the fact that such representations are possible is shown by the fact that, as is documented in our scientific textbooks, very many of them have already been achieved, though of course always only at some specific level of granularity and to some specific degree of precision, detail and completeness.”

I think it is fair to say that this statement leaves room for both the empiricist and the realist acknowledging the importance of theories and concepts in science while not elevating them a priori to a level where they are either unassailably reliable or misguided. It is a sensible enough statement to make. Strangely, to my thinking at least, Smith takes this statement to work as something of a wedge between reality- and concept-based ontology design maxims. But the statement itself speaks more to the notion of reality (which by the way remains under-defined) and concepts being intertwined in scientific advancement. Whatever else may be said here, we concluded that following his outlined path does require ‘a strong ontological commitment’. I doubt that this message has been received and ratified by most practitioners.

Anyway, onto to more practical issues; up this week:

Seltmann, K., M. Yoder, I. Miko, M. Forshage, M. Bertone, D. Agosti, A. Austin, J. Balhoff, M. Borowiec, S. Brady, G. Broad, D. Brothers, R. Burks, M. Buffington, H. Campbell, K. Dew, A. Ernst, J. Fernandez-Triana, M. Gates, G. Gibson, J. Jennings, N. Johnson, D. Karlsson, R. Kawada, L. Krogmann, R. Kula, M. Ohl, C. Rasmussen, F. Ronquist, S. Schulmeister, M. Sharkey, E. Talamas, E. Tucker, L. Vilhelmsen, P. Ward, R. Wharton & R. Deans. 2012. A hymenopterists’ guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions. Journal of Hymenoptera Research 27: 67-88. Available on-line here.

Weekly reading: Adding a little reality to building ontologies for biology

We are moving from practical designs and implementations of ontologies in systematics to design theory. One issue to understand, or least have an intuitive position on, is the strength of the interaction or interdependency between ontology design and functionality. And “design” could reach as far up the chain of representation as “why Description Logics and not another flavor of logic?” The term “Realism” plays a role. About five years ago there was a fairly spirited debate on this topic, reviewed here. We are reading one paper from the longer list.

Lord, P. & R. Stevens. 2010. Adding a little reality to building ontologies for biology. PLoS ONE 5(9): e12258. Available on-line here.

New taxonbytes T-Shirt designed for outreach program

We have a new ASUHIC / taxonbytes T-shirt, designed by Melody Basham and her team, to be used for upcoming outreach events. Large version here.