2012-02-29

def supertype, supratype, surtype

web.adds/{super, supra, sur}-type:
summary:
. there are uses in the wild of each of
surtype, supratype, and supertype
to mean something like an ancestor type
if not specifically the parent type .

. in genetics, type has a special meaning:
what the gene expresses functionally,
so then the term, supertype,
is used for what the gene expresses incidentally, in tests;
in this system of nomenclature,
the highest type might be called the supratype .

. within knowledge engineering,
the terms are surtype or supertype,
rather than supratype .
. the term surtype was associated with
being complete; ie,
a surtype has several subtypes,
and every instance belongs to a subtype .
. surtype may be related to the term Surjection:
in the surjective mapping,
every instance of the function's codomain
belongs to the mapping .

. wikipedia's take is lean so far:
supertype redirects to Subtype polymorphism;
and neither wiktionary nor wikipedia
have supratype or surtype .
. wiktionary's supertype:
(computing) The data type represented by a superclass .
subtype isIncludedIn surtype .
supertype and surtype (sybase)
The general entity is known as a
supertype (or parent) entity;
The special case entity is known as a
subtype (or child) entity .
In an inheritance link,
one or more subtype (or child) entities inherit,
at the physical level, all or part of the entity attributes
carried by one supertype (or parent) entity
. the Complete Property:
Indicates that all instances of the parent entity (surtype)
must belong to one of the children (subtypes).
For example, entity Person has 2 sub-types {alien, citizen}
every instance of entity Person is one or the other .
supertype and surtype (Olivier Ferret, Brigitte Grau LIMSI-CNRS)
In the lattice of concept types,
a specific mechanism makes more activation
going towards subtypes of a concept type
than towards its SURTYPES .
... Thus it is not interesting to select a SURTYPE
of Supermarket as PublicPlace
because we do not want to activate all the situations which
take place in a public place.
...
The similarity measure we use [Ferret and Grau, 1995]
is decomposed in two steps.
Global similarity is based on the number of similar events,
according to the slots they belong to.
The exact degrees of similarity of slots and events
are examined when this global similarity gives a medium result.
Two events are similar if their predicates contain the same type
and if at least one of their concepts
filling casual roles is similar.
This occurs if their types share a SUPERTYPE
inferior to the reference type of the casual role.
supratype (no combinations with surtype)
Examination of transmission of the
diabetogenic supratype B18 Bf Fl DR3
revealed that this SUPRATYPE
is inherited more frequently than expected from fathers .
The genomic organization of the human MHC was examined
in multiple examples of six different SUPRATYPES .

Kinship mapping and population SUPRATYPES
provide information on order and relative genetic position of loci
within a system too small to map by recombination .

supratype and supertype:
The strategy of creating an MHC-based vaccine
has raised the possibility of designing global vaccines
that would be equally efficient for all MHC SUPRATYPES
(i.e. a combination of alleles in an extended HAPLOTYPE).
In particular, the HLA SUPERTYPE concept
provides a means of designing vaccines that are
universally effective in ethnically diverse populations  .
. extended haplotypes:
 combinations of alleles that tend to occur together .
A haplotype is a combination of alleles (DNA sequences)
at adjacent locations (loci) on the chromosome
that are transmitted together.
haplotype is a set of single-nucleotide polymorphisms (SNPs)
on a single chromosome of a chromosome pair
that are statistically associated.
Assume the first locus has alleles A and T
and the second locus "G" or "C".
Both loci, then, have three possible genotypes
(AA, AT, and TT and GG, GC, and CC respectively).
For a given individual, there are nine possible
configurations (haplotypes) at these two loci
(shown in the Punnett square below).
For individuals who are homozygous at one or both loci,
the haplotypes are unambiguous
- meaning that there is no differentiation in
haplotype T1T2
vs haplotype T2T1;
where T1 and T2 are labeled to show that they are the same locus,
but labeled as such to show it doesn't matter
which order you consider them in, the end result is two T loci.
For individuals heterozygous at both loci,
the gametic phase is ambiguous - in these cases,
you don't know which haplotype you have, e.g., TA vs AT.
human leucocyte antigen (HLA)
class I and II genotypes, class I supertypes
An individual's genotype for a gene is the set of alleles,
which the gene contains. In a diploid organism,
one that has two copies of each chromosome,
two alleles make up the individual's genotype;
the two copies of the gene in diploid organisms are the alleles.
The fact that, in diploid organisms, a gene exists in two copies
makes for possible variations in phenotype,
the expressed characteristics (e.g. blue or brown eyes).
An organism in which the two copies of the gene are identical,
i.e. have the same allele, is called homozygous for that gene.
An organism, which has two different alleles of the gene,
is called heterozygous.
HLA genes that encode immune-associated glycoproteins
are located on chromosome 6p21.
HLA class I and II genes are known to be highly polymorphic,
i.e. they exist in many different forms among humans.
HLA class I and II genes are individually found at
HLA-A, -B and -C and well as HLA-DR, -DQ and -DP loci.
What are supertypes?
Binding patterns obtained from studies of
individual HLA class I molecules
have revealed that some of them within a given allele family
share binding specificities towards the same panel of peptides.
The collection of HLA class I molecules that exhibit this property
is designated as a supertype.
Under this structural classification,
a few HLA class I supertypes are defined
for the numerous allele family that are now known to exist.