Monday, September 13, 2010

Ontology and reality

One of these days, I keep promising myself, I am going to publish something incredibly clever about chemistry, ontology and/or chemical ontology. Then again, I need some incentive to do so, and there’s none in my view. In the meantime, I am happy that somebody else has bothered to write a paper dealing with so-called “realist” approach to ontology [1].

Personally, I never cared much about the “reality” as used in context of OBO Foundry Principles [2]:
Terms in an ontology should correspond to instances in reality.
Worse still is its “corollary”:
Ontologies consist of representations of types in reality — therefore, their preferred terms should consist entirely of singular nouns.
(Why? Does “reality” really consist of singular English nouns?)

Now Lord and Stevens confirm my gut feeling that “realism” (the authors take care to clarify that “realism” in [1] stands for “realism as practiced by BFO”) applied to ontology building often results in unnecessary complexity. Everybody who ever studied physics (or English) in school would agree that expression |dr/dt| is much better definition of speed than the one provided by PATO: “A physical quality inhering in a bearer by virtue of the bearer’s rate of change of position”. To quote [1],
It makes little sense to replicate the models of physics using English instead of a more precise mathematical notation.
Alas, this is exactly what BFO (and most of OBOs) are trying to do. By going “where science has gone before” without learning the language of the science, BFO & Co. keep reinventing the square wheel.

OK, what about chemistry? Chemistry has developed its own language which makes the plain-text definitions for molecular entities redundant. The 2-D diagram (connectivity) defines the molecule of interest better than a paragraph in English. In theory, the systematic name should provide the exactly same information (and thus to be usable as a definition). However, the systematic names for even relatively small molecules often are too complicated to be widely (or ever) used.

Take the systematic name (a) for beauvericin. You are extremely unlikely to either hear it (because it is more or less unpronounceable) or see it (it takes more than one line of text, which is annoying). More importantly, there is a certain limit of molecular complexity above which the systematic names (according the existing nomenclature rules, that is) simply cannot be generated. On the other hand, the diagram (b) is both beautiful and useful.

(a)(3S,6R,9S,12R,15S,18R)-3,9,15-tribenzyl-4,10,16-trimethyl-6,12,18-tri(propan-2-yl)-1,7,13-trioxa-4,10,16-triazacyclooctadecane-2,5,8,11,14,17-hexone
(b)

Not only are the 2-D diagrams self-defining, they provide all the information needed to build the consistent ontology for molecular entities. With a few simple rules, the ontology will build itself from scratch, I promise. But this is a topic for another post.
  1. Lord, P. and Stevens, R. (2010) Adding a little reality to building ontologies for biology. PLoS ONE 5, e12258.
  2. OBO Foundry Principles.

Wednesday, September 08, 2010

Terminology vs nomenclature

First published 8 September 2010 @ just some words

According to The Concise Oxford Dictionary,
nomenclature n. 1 a person’s or community’s system of names for things. 2 the terminology of a science etc. 3 systematic naming. 4 a catalogue or register.
terminology n. (pl. -ies) 1 the system of terms used in a particular subject. 2 the science of the proper use of terms.
I must say that these definitions do not add much clarity. Do you see any difference between “system of names for things” and “system of terms”? Moreover, the nomenclature (2) appears to be equated with the terminology. As for terminology (2), it is akin to terminology as defined by Wikipedia: “the study of terms and their use”, although I have my doubts whether there is such thing as “the science of the proper use of terms”. As was mentioned before, “logy” does not always mean “a subject of study or interest”. And what is “proper”?

On the other hand, Merriam-Webster defines terminology as
1 the technical or special terms used in a business, art, science, or special subject
2 nomenclature as a field of study
No, this does not help at all. Let us agree on the following: terminology is not nomenclature, and nomenclature is not terminology. I suggest these working definitions:
    terminology: a set of terms used in a particular field. nomenclature: a system of generating new terms for a particular field.
Completely different things. Terminology is a subset of vocabulary and, therefore, is part of the language. Nomenclature is a set of external rules. A good nomenclature system has few rules all of which should be understood and applied, preferably with reproducible results, by more than one person.

That is not to say that terminology does not depend on nomenclature or vice versa. Terms can be formed by systematic application of nomenclature rules — that’s what the nomenclature is devised for. But they also can arise by different mechanisms, just like any new words do. Often, terms are recruited from the existing lexicon and conferred new meanings. For instance, the word “residue” acquired specific meanings in fields of math, chemistry or law.

The Russian word for nomenclature, номенклатура, has an additional meaning: the bureaucratic class of Soviet Union and its descendants (as in “post-Soviet nomenklatura”).