Databases and Systems

86
A common problem in the construction of databases of mapping information is
how to optimally align or integrate mapping data from different methods, such as
genetic or physical mapping, or different sources, such as radiation hybrid maps
produced by different labs or from different mapping panels. There main motivations
for aligning maps are to support database searches of chromosomal regions of
interest and to produce better graphic displays. Several approaches to these problems
have been explored and implemented within GDB; this article describes and critiques
those methods.
Map Querying
An important query for GDB is to find all loci in a region of interest, sometimes with
additional restrictions as to the type of locus, existence of polymorphisms, or
functional category. The region of interest might in principle be specified in any of
several ways, such as the region between two specified loci, or the neighborhood of a
specified locus for some number of units in each direction. GDB stores many maps of
many different types, and it is desirable to have such positional search across all
maps of a region simultaneously. Intuitively, we want the database to function as a
stack of aligned maps, and a query to cut a thick slice through that stack (see Figure
1). A central concern of this article is how to best align the maps for this purpose.
Figure 1 : Query cutting through a stack of aligned maps
The details of the relational implementation of overlap queries are worth pointing
out briefly. Each locus is considered to have a localization interval, consisting of a
minimum and a maximum coordinate². The query to retrieve stored intervals I
overlapping a query interval Q can be expressed intuitively as the negation of
nonoverlap - find intervals I which are not disjoint from Q. I can be disjoint from Q
² These follow naturally from binned maps, where the coordinates are those of the bin
boundaries; for cytogenetic maps they are the coordinates of the band boundaries,
and in general they are coordinates of backbone markers. Backbone or point-like
markers are represented by zero-width intervals. Distance-based linkages can be
converted to intervals by using a suitable multiplier of the standard error.