Within the realm of scientific classification, there appear to be three prominant methodus: heirarchical categorization, cladistics, and phenetics.
The first method for classifying the biosphere is based on heirarchical categorization, as per the familiar derivative of the Linnean system: (kingdom (phylum (class (order (family (genus (species))))))). The actual objects that are categorized are individual organisms, with the most specific and exclusive category - species - describing a population of organisms that are similar in some aspect (there are many perspectives on the relative importance of similarities - some definitions of species are biased toward sexually reproducing organisms, while others focus on common ancestry). Perhaps the most important aspect of the species category is that it is the only level of classification that is based on physical objects. All higher, more abstract levels of the heirarchy are based on similarities between and among categories, not on physical objects (because of genetic variability within a population of individuals, I reject the notion that there can be an actual physical instance of species, even among asexual organisms - this debate is even less appropriate among sexual organisms). The system terminates in the most general and inclusive category of kingdom, although the inherent difficulty of such abstract processing has resulted in the recent recognition of a 6th kingdom (archaebacteria) and the suggestion of a category more abstract than kingdom, called domain.
The second method of biological classification is known as cladistics, and is based on the notion of binary pathways forming tree-like branching patterns that demonstrate the relationships of organisms with regard to common ancestry. In this system, the most specific and exclusive category of organisms is still the species, but this method differs from heirarchical categorization because the more abstract connections between species are not guided by categorical similarity, but by the degrees of separation between two species and a common ancestor. Terms used to describe abstract groups of species use the root "phyletic", with prefix modifiers "mono", "para", and "poly".
Coming up: a brief summary of phenetics, and the beginnings of applying these methods to the cognitive domain. In short, I started my thinking about classifying cognitive resources using the familiar heirarchical categorization method, with resources as "species", groups of resources as more abstract "classes", and functions of groups of resources in conceptual change as the most abstract level of categorization, or "kingdoms". While I think that this system will present more utility than currently available, I'm beginning to think that a cladistic representation might also have utility, especially with respect to the developmental patterns observed in long-term learning (specifically I'm interested by the late onset of epistemological resource maturation mentioned in a Hofner article I have in a stack somewhere...). Further, the phenetic system appears to be most useful at the species level of biological classification, so I'm going to explore its utility at the interface between neurological activity and cognitive resources.