Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design

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.

Towards Advanced Interactive Visualization for Virtual Atlases

“…When virtual atlas data features a spatial aspect, there are many standard and advanced visualization techniques that can be employed to visualize this data efficiently. In the survey by Clarkson (2016), an overview of common design patterns for graphic representation of anatomy is presented. (Smit et al, 2016).…”

“…To access the wealth of information virtual atlases offer, good interaction and navigation strategies are essential. Clarkson (2016) offers a comprehensive overview of textual and graphical design patterns for querying gene expression databases.…”

“…These advantages have given rise to the creation of a multitude of diverse virtual atlases in the biomedical domain, for example the Allen Brain Atlas (Jones et al, 2009), the DigiMouse atlas (Dogdas et al, 2007), and an atlas of the adult human brain transcriptome (Hawrylycz et al, 2012). For an overview of atlases in developmental biology, please refer to the survey of online atlases and gene expression resources for model organisms by Clarkson (2016). Given the wealth of virtual atlases now available, there is an opportunity to employ advanced visualization and interaction techniques that go beyond traditional atlas-use as a static reference collection.…”

The Locare workflow: representing neuroscience data locations as geometric objects in 3D brain atlases

“…This trend has resulted in a growing volume of neuroscience data being made accessible through various data repositories and infrastructures (Ferguson et al, 2014;Jorgenson et al, 2015;Ascoli et al, 2017;Amunts et al, 2019). While free-text searches based on structured metadata are typically implemented in such databases (Clarkson, 2016), possibilities for more sophisticated queries, visualizations, and analysis depend on a harmonization across data files with different formats, scales, and organization (Zaslavsky et al, 2014;Abrams et al, 2022).…”

eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis

“…Open access online atlases and databases are critical in managing the rapidly growing amount of data describing embryogenesis. A recent review ( Clarkson, 2016 ) described multiple criteria that are used by online atlas resources to present stage-focused information, anatomical information, and to provide text and spatial methods for querying gene expression. Importantly, this review stressed the importance of using annotation terms that conform to a community standard ontology, and of supporting these terms with visual definitions.…”