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Month: September 2009

Episode 987: Cabinets – A Taxonomic Soap Opera.

Amanita muscaria (fly agaric)In this episode of our longest running soap opera Terry & Tina confuse Eric who takes off with Malcolm.

“Cabinets” is a public service broadcast with the aim of promoting  community understanding of complex taxonomic issues.

— Cue opening credits —

The story so far:Terry is a taxonomist and he works very hard to produce a classification of the family Z. It includes two genera, X and Y and three species A, B and C. Here is a picture of his classification.

Managing The Managing Of The TDWG Ontology

Castle CampbellSeveral years ago I was involved in the developing the “TDWG Ontology”. Quite what the TDWG Ontology was/is remains an enigma for many. Around 2005/6 we tried to move away from modeling things in XML Schema and into some form of frame based modeling with well defined classes and properties – as opposed to the document structures implied by XML Schema.  With the help of Jessie Kennedy’s team at Napier and people around the world we started building an OWL ontology of the whole domain – then ran out of money.

We still needed basic terms for use in LSID RDF metadata. This lead to the  development of the LSID Vocabularies. These were very light weight “ontologies” but were still an attempt at defining terms using OWL.

In all our efforts there was a problem. There was no continuity of resourcing. For two years no one has been paid to manage the TDWG Ontology even though there is an increasing need for the disparate biodiveristy informatics projects to have a formal mechanism for defining shared terms. Because the resource is seen as common no one feels responsible to commit resources to manage it.

In the last few days I have been doing some work with Kehan Harman on establishing a technical fix for this.

Nomenclature is Dead! Long Live Barcode Taxa!

nigella-1Over the past few months I have been working on how to represent biological taxonomy and nomenclature using Description Logics. Here I combine these thoughts with a rather naive view of DNA Barcoding to suggest a new approach to taxonomy.

Description Logic (DL) is an extension of frame based languages (such as those used in object orientated programming paradigms) and semantic networks (e.g. WordNet) to link them to first-order predicate logic thus enabling the representation of application domains in formal, well understood ways that can be reasoned over by machines. DL has come to the fore in recent years with the advent of the Web Ontology Lanugage (OWL) by the World Wide Web Consortium (W3C). Two subsets of which, OWL-DL and OWL-Lite, are based on DL. Notably these two sub-languages guarantee decidability within finite time. From now on I’ll use the terminology of OWL-DL and OWL-Lite rather than generic DL terms. The OWL terms are more likely to be understood by a general reader who can read the OWL documentation as background. A concept in DL is referred to as a class in OWL. A role in DL is a property in OWL.

There are three principal features within OWL:

  • Classes are groups of individuals that belong together typically because they share some properties or property values.
  • Individuals are instances of classes.
  • Properties are statements of relationships between individuals or from individuals to data values.

There are other features within the language that allow the expression of things such as equivalence, cardinality and the domains and ranges of properties. Using OWL principally involves asserting specialization hierarchies of classes and inferring unknown subclass relationships and class membership using an inference engine such as Fact++. A set of OWL assertions is frequently referred to as an ontology.