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Thoughts: How taxonomically binding is biological nomenclature

Biological nomenclature and taxonomy are both different yet also somehow interconnected. It is sometimes stated that the two kinds of practices are largely independent of each other. Yet we also know that – to some degree – Code-compliant nomenclature must respond to taxonomic change. Pyle & Michel (2008) review the relationship of nomenclature and taxonomy in (what seem to me) often reiterated terms. They write (pages 41-42):

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Opinion: Cynicism in academia

This post on cynicism in academia is off-topic compared to what I usually write about on taxonbytes. And I wish to declare that it is not intended to project a high degree of scholarship on the subject because I lack such scholarship. An internet search of “cynicism academia” (or similar) produces abundant links to both casual and formal treatments. I will not deal with these, but only relate my own current thoughts.

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Weekly reading: Practical introduction to ontologies and OWL

This week we will try out Protégé and pizza ontologies. We will work through an updated version of this tutorial.

New publication: Provenance for explaining taxonomy alignments

A short paper related to the Euler/X toolkit and concept taxonomy alignment project has been published. It deals with the issue of diagnosing inconsistent input constraints in an attempted pairwise taxonomy alignment, analyzing and visualizing their logical provenance so that the user can localize the inconsistencies and proceed towards repairing them. These logic services are already implemented in the toolkit.

Abstract. Derivations and proofs are a form of provenance in automated deduction that can assist users in understanding how reasoners derive logical consequences from premises. However, system-generated proofs are often overly complex or detailed, and making sense of them is non-trivial. Conversely, without any form of provenance, it is just as hard to know why a certain fact was derived. We study provenance in the application of Euler/X, a logic-based toolkit for aligning multiple biological taxonomies. We propose a combination of approaches to explain both, logical inconsistencies in the input alignment, and the derivation of new facts in the output taxonomies.

Chen, M., S. Yu, P. Kianmajd, N. Franz, S. Bowers & B. Ludäscher. 2015. Provenance for explaining taxonomy alignments. In: Ludäscher, B. & B. Plale (Editors), Provenance and Annotation of Data and Processes. Revised Selected Papers of the 5th International Provenance and Annotation Workshop, IPAW 2014, Cologne, Germany, June 9-13, 2014. Lecture Notes in Computer Science 8628: 258-260. Available on-line here.

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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Running list of nomenclatural acts (NMF)

A flat, running list of nomenclatural and taxonomic “novelties” I have been part of. So much more to do. In chronological order:

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Weekly reading: Leonelli on classificatory theory in biology

Sabina Leonelli has authored numerous papers on bio-ontologies that relate to our Spring 2015 theme. For this week we will read:

Leonelli, S. 2013. Classificatory theory in biology. Biological Theory 7: 338-345. Available here.

Also consider my post summarizing where we are right now and might considering going.

Weekly reading: Mikó et al. 2012. On Dorsal Prothoracic Appendages in Treehoppers (Hemiptera: Membracidae) and the Nature of Morphological Evidence

Our next reading is a response to a 2011 article (that paper available here) interpreting the “prothoracic helmet” of treehoppers as serially homologous with wings. Mikó et al. showcase some modern techniques for visualizing morphology, such as confocal laser scanning microscopy (CLSM) and micro-computed tomography (μ-CT) to provide an alternate interpretation, and discuss the importance of having well-defined morphological concepts for interpreting complex morphological structures.

Mikó et al. 2012 is available online here.