Skip to content

Posts tagged ‘ontology’

SPNHC 2015 presentation – Taxonomic concept resolution for voucher-based biodiversity information platforms

Slides are up for our SPNHC 2015 concept taxonomy presentation.

Franz 2015 SPNHC Taxonomic concept resolution for voucher-based biodiversity information platforms from taxonbytes

ETC-Euler Taxonomic Concept Alignment Demonstration Video – Minyomerus 2015 versus Minyomerus 1982

This 8-minute screenshot video, produced in late April, 2015, demonstrates the interaction of the Exploring Taxonomic Concepts (ETC) and Euler/X software tools.

The ETC team has built a highly useful and effective front-end web service to the Euler/X reasoning services, allowing users to import two concept taxonomies through an on-line file management system, provide articulations, run input visualizations, obtain logically consistent alignments, and extract these products from the web interface to the desktop. The underlying ideas and methods are explained in Franz et al. (2015).

The capabilities of the user interface are illustrated with the Minyomerus use case, aligning two classifications authored in 2015 and 1982, respectively.

ETC Euler Taxonomic Concept Alignment Demonstration – Minyomerus 2015 versus 1982 from taxonbytes on Vimeo.

Thoughts: Why stability in nomenclature, and at what cost?

Another post on nomenclature, related to this previous post on the possibly thankfully strong influence of nomenclatural principles on taxonomic practice.

Many taxonomists, including myself certainly, continue to wonder and explore why exactly nomenclature is the way it is. The aim is first and foremost to obtain a sound explanatory account. Whether one likes the explanations, or the practice as illuminated in part by the explanations, is initially another subject.

Read more

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):

Read more

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.”

Read more

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.