Abstract
BackgroundA large number of online atlases and databases have been developed to mange the rapidly growing amount of data describing embryogenesis. As these community resources continue to evolve, it is important to understand how representations of anatomy can facilitate the sharing and integration of data. In addition, attention to the design of the interfaces is critical to make online resources useful and usable.ResultsI first present a survey of online atlases and gene expression resources for model organisms, with a focus on methods of semantic and spatial representation of anatomy. A total of 14 anatomical atlases and 21 gene expression resources are included. This survey demonstrates how choices in semantic representation, in the form of ontologies, can enhance interface search functions and provide links between relevant information. This survey also reviews methods for spatially representing anatomy in online resources. I then provide a collection of patterns for interface design based on the atlases and databases surveyed. These patterns include methods for displaying graphics, integrating semantic and spatial representations, organizing information, and querying databases to find genes expressed in anatomical structures.ConclusionsThis collection of patterns for interface design will assist biologists and software developers in planning the interfaces of new atlases and databases or enhancing existing ones. They also show the benefits of standardizing semantic and spatial representations of anatomy by demonstrating how interfaces can use standardization to provide enhanced functionality.
Highlights
A large number of online atlases and databases have been developed to mange the rapidly growing amount of data describing embryogenesis
Anatomical atlases For the purpose of this work, an anatomical atlas is defined as a resource that provides spatial representations of a body or region of a body, plus a set of anatomical terms which are associated with regions of the representations
This work documents the variety of ways anatomical information has been communicated in online atlases and databases
Summary
A large number of online atlases and databases have been developed to mange the rapidly growing amount of data describing embryogenesis. As these community resources continue to evolve, it is important to understand how representations of anatomy can facilitate the sharing and integration of data. During the last two decades the primary means of archiving and accessing experimental results has shifted from traditional printed publications to digital repositories and web sites [1, 2] This transition was driven by the need to mange the rapidly growing amount of data describing embryogenesis, integrate heterogeneous data, represent this data within the context of space and time, and enable cross-species comparisons. Many anatomical atlases and gene expression databases have been developed for a number of species, by both individual laboratories and multi-institution teams
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