In the previous post (http://blogs.ch.cam.ac.uk/pmr/2013/05/23/sepublica-how-semantics-can-empower-us-scholrev-scholpub-btpdf2/) I outlined some of the reasons why semantics are so important. Here I want to show what we have to do (and a...
In the previous post (http://blogs.ch.cam.ac.uk/pmr/2013/05/23/sepublica-how-semantics-can-empower-us-scholrev-scholpub-btpdf2/) I outlined some of the reasons why semantics are so important. Here I want to show what we have to do (and again stick with me – although you might disagree with my stance).
The absolute essentials are:
We have to be a community.
We have to identify things that can be described and on which we are prepared to agree.
We have to describe them
We have to name them
We have to be able to find them (addressing)
Here Lewis Carroll, a master of semantics shows the basics
And she went on planning to herself how she would manage it. `They must go by the carrier,’ she thought; `and how funny it’ll seem, sending presents to one’s own feet! And how odd the directions will look!
ALICE’S RIGHT FOOT, ESQ.
NEAR THE FENDER,
(WITH ALICE’S LOVE).
Oh dear, what nonsense I’m talking!’
Alice identifies her foot as a foot, and makes gives it a unique identifier RIGHT FOOT. The address consists of another unique identifier (HEARTHRUG) and annotates it (NEAR THE FENDER). There’s something fundamental about this – (How many children have annotated their books with “Jane Doe, 123 Some Road, This Town, That City, Country, Continent, Earth, Solar System, Universe?). Hierarchies seem fundamental to humans. Anything else is much more difficult. (Peter Buneman and I have been bouncing this idea about). I am sure we have to use hierarchies to promote these ideas to newcomers.
Things get unique identifiers. They can be at different levels. Single instances such as Alice’s left foot.
But there are also whole classes – the class of left feet. I have a left foot. It’s distinct from Alice’s. And we need unique names for these classes, such as “left foot“. Generally all humans have one (but see http://en.wikipedia.org/wiki/The_Man_with_Two_Left_Feet ). And we can start making rules, see http://human-phenotype-ontology.org/contao/index.php/hpo_docu.html.
At the moment, all relationships in the Human Phenotype Ontology are is_a relationships, i.e. a simple class-subclass relationships. For instance, Abnormality of the feet
Abnormality of the lower limbs. The relationships are transitive, meaning that they are inherited up all paths to the root. For instance, Abnormality of the lower limbs is_a
Abnormality of the extremities, and thus Abnormality of the feet also is Abnormality of the extremities.
We see a terminology appearing. Some would call this an ontology, others would refute this. I tend to use the concept of “dictionary” fuzzed across language and computability.
This is where the difficulties start. One the one hand this is very valuable – if a disease affects the extremities, then it might affect the left foot. But it’s also where people’s eyes glaze over. Ontology language is formal and does not come naturally to many of us. And when it’s applied like a syllogism:
All men are mortal
Socrates is a man
Therefore Socrates is mortal
Many people think – so what? – we knew that already. On the other hand it’s quite difficult to translate this into machine language (even after realising that “men” is mans (the plural). The symbology is frightening (with upside down A’s and backwards E’s). Here are fundamental concepts in a type system: http://stackoverflow.com/questions/12532552/what-part-of-milner-hindley-do-you-not-understand :
The discussion on Stack Overflow includes:
“Actually, HM is surprisingly simple–far simpler than I thought it would be. That’s one of the reasons it’s so magical”
“The 6 rules are very easy. Var rule is rather trivial rule – it says that if type for identifier is already present in your type environment, then to infer