After a meeting in St. Louis on ontology and phylogeny, I spent a couple of days in Missouri State University. Mary Schaeffer,, toni Kazic and I spent an afternoon talking about modelling flowers and the difficulties therein. They wanted to talk about plants in the style of the Plant Ontology (PO) and only use is-a and part-of relationships. The problem was that the variety of combinations of putting bits of flowers together was making building a description of flowers rather tricky. for example, a Perianth is usually both a calyx and a corolla, but may have only one of these horls — so how do you build an anatomy that takes all of this in to account?
Being me, I said "be compositional". As a consequence, I’ve been dabbling over the past few years, in my copious spare time, building a bit of an ontology for the anatomy of flowers. Having started-off knowing nothing about flowers, I’ve now got the stage of being able to bluff my way through talking about flowers; well angiosperm at least. I’ve been helped greatly by David Rhyderheard in our School who is an expert amateur botanist. we’ve spent several hours in my office disssecting flowers and doing some moderately detailed descriptions of their anatomies using my flower ontology.
The initial meeting was in 2006. I thought about it for a few years and have been playing about for a couple of years—and it really has been in my spare time! I make no great claims for the ontology, but it has been an interesting problem. I make no great claims for it and it has no real use case except that of stimulating my own interest.
The basic approach is as follows:-
- I made a little hierarchy of bits of flowers (sepals, petals; stamen (anthers, filaments, etc.); carpels (style, stigma, stypes, etc.).
- These bits can be assembled in to bigger units , such as a calyx is an assembly of sepals; a corrrolla is an assembly of petals; an androecium is an assembly of stamen. Each of these assemblies is a whorl.
- In this way, I can say things about petals and corolla separately. A corolla may be made of five separate petals (apopetalous) or five fused petals (sympetalous) and this fusion may have several properties. we can separate these out in to a hierarchy of qualities that inhere in all these pieces and assemblies of pieces.
- A perianth is made of a calyx or corolla, but one may be missing. Obviusly, male and female "whorls" can be present together or singly to make a single sex or haemaphrodite flower.
- A flower is made of one or more of these whorls (calyx, corolla, androecium, gynoecium). There’s a legion of qualities to add even more variety. In fact, as long as there is one whorl, you have a flower; some flowers can have many of one whorl. So, flower can be described as has part some (calyx or corolla or androecium or gynoecium). Stamen, for example, can have only a filament and miss the anther altogether.
- I haven’t done inflorescence yet, but this a group of flowers; again there is variety in how they are joined together fromm the sunflower to the elderberrry type of inflorescence.
An example of one of my anatomical descriptions of a flower is:
Class: RanunculusRepens
Annotations: [in flower.owl]
comment "Common buttercup",
label "Ranunculus Repens"@
SubClassOf: [in flower.owl]
* ActinomorphicFlower,
* ApopetalousFlower,
* AposepalousFlower,
* HeterosporangiateFlower,
Flower
and (hasFlowerSymmetry some RadialFlowerSymmetry)
and (hasPart some
(Androecium
and (hasAndroecialFusion some Apostemonous)
and (hasPart some
(Stamen
and (hasPart some Filament)
and (hasPart some
(Anther
and (hasAntherAttachment some AdnateAntherAttachment)
and (hasDehiscenceType some LongitudinalDehiscence)))))))
and (hasPart some
(Gynoecium
and (hasGynoecialFusion some Apocarpous)
and (hasPart some
(Pistil
and (hasPart some Carpel)
and (hasPart some Style)
and (hasPart some
(Stigma
and (hasStickiness some Stickiness)
and (hasStigmaShape some HookedStigmaShape)))
and (hasPart only
(Carpel
or Stigma
or Style))))
and (hasSexualPartArrangement some SpiralArrangement)))
and (hasPart exactly 1 (Perianth
and (hasPart some
(Calyx
and (hasSepalousity some Aposepalos)
and (hasPart exactly 5 (Sepal
and (hasColour some Green)
and (hasRegion some
(BaseRegion
and (hasForm some Truncate)))
and (hasRegion some
(MarginRegion
and (hasSepalPetalFeature some Entire)
and (hasSepalPetalFeature some Membranous)))
and (hasRegion some
(SurfaceRegion
and (hasSepalPetalFeature some Pubescent)
and (hasSurfaceSelector some LowerSurfaceSelector)))
and (hasRegion some
(SurfaceRegion
and (hasSepalPetalFeature some Smooth)
and (hasSurfaceSelector some UpperSurfaceSelector)))
and (hasRegion some
(TipRegion
and (hasForm some Truncate)))
and (hasSepalPetalFeature some PalmatelyNetted)
and (hasSepalPetalShape some Ovate)))))
and (hasPart some
(Corolla
and (hasPetalousity some Apopetalos)
and (hasPart exactly 5 (Petal
and (hasColour some Yello)
and (hasRegion some
(BaseRegion
and (hasForm some Acute)))
and (hasRegion some
(MarginRegion
and (hasSepalPetalFeature some Entire)))
and (hasRegion some
(TipRegion
and (hasForm some Acute)))
and (hasSepalPetalFeature some PalmatelyNetted)
and (hasSepalPetalShape some Obovate)
and (hasPart exactly 1 Nectary)))))
and (hasPerianthArrangement some AlternatingPerianthArrangement)
and (hasPart only
(Calyx
or Corolla))))
(In this Manchester OWL Syntax description, the inferred superclasses are indicated by the "e;*" symbol.) This is not a particularly rich description, but it does capture some of the main features of the British common buttercup. I’ve captured what bits are present and limited those with universal quantifications. I’ve got many of the qualities of things. My descriptions of regions of things is poor. I’ve used Alan Rector’s "selector pattern" for choosing between things like upper and lower surfaces. I’ve not done patterns on surfaces or veination as yet. I’ve started putting in some textual definitions, but this is currently woefully inadequate. A version of the flower anatomy ontology may be downloaded.
Flowers are a good example of the separation between the continuant (the thing itself) and the quality that inheres in the independent continuant. take a petal which can be: A colour, colours at different regions of the petal’s surface, have a texture, a shape, different shape features at the base and tit, have features at the ffringes or margins. I also would like a way of saying things like "the petal is white and flushed pink towards the tip", but I’ve not worked out a way yet (though I’ve not even really thought about it). Colour, texture and so on can also be diffeerent on upper and lower surface. Once petals are joined in a corolla, we have another range of qualities. Doing this without separation of aspects of the flower and then taking what Alan rector calls a "conceptual lego" approach this modelling would be even more difficult than at present.
I’ve made quite a lot of use of cardinality constraints. I want to say that the buttercup (usually) has five petals. I’d also like to be able to say that the number of petals is the same as the number of sepals, but I cannot do this in OWL alone. Flower anatomy is full of vagueness — words like "few" and "numerous" are rife in flower books. Words like "usually" are standard in definitions of flower types in books like New Flora of the British Isles
By Clive Stace. a mechanism for optionality would be really useful. Coping with this kind of things in a strict regime like OWL is hard.
Anyway, this “lego” approach has enabled me to describe a few flowers–the main limitation is time, not the ability of the ontology(the botanical ability of the ontologist is, however, a limitation.) . There are more posts to follow about the ability to make a strict ontology of something like flowers where there is such variety and gradation. Evolution doesn’t make modelling easy and one must question how well an evolved system such as a broad range of species sits in the narrow view offered by most ontological approaches and knowledge representation languages.
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