Genomics data resources: Frameworks and standards

Abstract

The emergence of genomics tools for the evolutionary and comparative biology community led to a rapid explosion in the number of online resources targeted at this specialized community, including Web-based comparative genomics software, such as the Artemis Comparison Tool (WebACT); databases, such as PaleoDB, Global Biodiversity Information Facility, and TreeBase; and knowledge frameworks, such as the Evolution Ontology. Unfortunately, these providers are largely independent of one another and therefore the individual resources do not share any centralized plan for how the data or tools would or should be provided. As a result, there are a myriad of often incompatible technologies and frameworks being used by this community of providers. In this chapter, we explore approaches to online resource publication, both those already in use by the community, as well as new and emergent frameworks and standards. Exploration of the strengths and weaknesses of each approach, together with a brief exploration of the philosophy or informatics theory behind the varying approaches, will hopefully help readers as they navigate this data space. The discussion is constructed such that it lays the groundwork for exploration of a new global standard for data and knowledge representation-"The Semantic Web"-that holds promise of providing solutions to many of the complexities users face in their attempts to discover and integrate biodiversity data, and examples are provided. © 2012 Springer Science+Business Media, LLC.