Definition of 'exoskeleton' and example given in UBERON

[bionicjules]

Chris - Please note that an exoskeleton is a morphological entity, and that any organism with its main skeletal component on the outer part of its body is regarded as having an exoskeleton. All arthropods have an exoskeleton, although the chemistry can vary widely. The example that you quote - insect cuticle - is therefore being confused with the definition, and it is also wrong in terms of the chemistry. Insects have a variable amount of chitin in their cuticle, and it's only in the untanned (i.e. hydrated and soft) cuticles that the chitin content reaches anywhere near 50% dry weight. Mostly it's between 20% and 30%. The rest is protein and phenolic residues. Other arthropod cuticles can contain significant amounts of calcium carbonate. Hope that's helpful. It's currently bugging my ontology, though!

[cmungall]

Can you tell me which class you are referring to? is it UBERON:0001001 ! chitin-based cuticle

[bionicjules]

UBERON:0001001http://purl.obolibrary.org/obo/UBERON_0001001 has a definition of ‘cuticle’ and the editorial note that it perhaps should be separated from ‘exoskeleton’. But it’s indisputable that the stiff outer covering of arthropods is (a) the skeletal element and (b) is known as the cuticle. Also to say that it’s chitin-based is to hark back to concepts from the 1920’s, when the stiffening reaction was thought to be related to the chitin, and the process of post-ecdysial stiffening of the cuticle was known as ‘chitinisation’. This misconception lingers on. There are many examples of tanned protein structures which are very stiff and durable which contain no chitin. The original example was the egg-case of the cockroach, which was shown to contain no chitin yet was referred to as chitinised. That’s when it was realised that chitin was not essential. It was then thought that the phenols cross-linked the proteins, but it’s now accepted that the stiffening is achieved by dehydration which the phenols drive, using the same chemistry that you get in a red wine, where the phenols cause a dry feeling in the mouth as they mop up the saliva. Another example is the beak of certain cephalopods which can be very durable indeed yet consist only of protein with melanin (polymerised phenolics) particles and which is highly dehydrated. Also, including crustacean cuticle in the mix, you have to admit a material which has around 40% mineral (as calcium carbonate). The lipid content of arthropod cuticles is small and mostly confined to the outer surface. Also UBERON's definition of exoskeleton doesn’t cover the systems developed by DARPA to allow soldiers to manipulate large loads! I know that’s not really biology, but it’s related in that’s where the idea of an external skeleton originates.

I would define an exoskeleton as “A 3-D system of hinged tubes and plates to which most of the muscles are attached, which typically forms a mobile external shell within which the soft parts of the animal reside and by which they are protected. In a technical exoskeleton the muscles are replaced by motors.” This would account for all but gastropod molluscs, slipper-limpets and the like, which have a single chell with no hinges. The shell of an echinoderm doesn’t really count since it has an outer covering of living tissue and anyway is called a test.

I hope this is sufficient clarity!

On a more personal note, I’m slaving away at my ontology, getting as many references as I can from otherontologies. I’ve ‘discovered’ Ontobee (thanks) which helps greatly. I was at an evo-devo conference last week and found significant interest in the implications of my ontology for categorising evolutionary change, so I am sure that there is good intellectual reason for doing this ontology properly. I’ve also contacted Phillipe Rocca-Serra for some face-to-face help.

Many thanks Best wishes Julian

On 31 Jul 2016, at 20:31, Chris Mungall notifications@github.com<mailto:notifications@github.com> wrote:

Can you tell me which class you are referring to? is it ! chitin-based cuticle

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[cmungall]

cc @aszool @mjy @dosumis @teleaslamellatus @balhoff

[gouttegd]

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