Aptamer Base: a collaborative knowledge base to describe aptamers and SELEX experiments

Abstract

Over the past several decades, rapid developments in both molecular and information technology have collectively increased our ability to understand molecular recognition. One emerging area of interest in molecular recognition research includes the isolation of aptamers. Aptamers are single-stranded nucleic acid or amino acid polymers that recognize and bind to targets with high affinity and selectivity. While research has focused on collecting aptamers and their interactions, most of the information regarding experimental methods remains in the unstructured and textual format of peer reviewed publications. To address this, we present the Aptamer Base, a database that provides detailed, structured information about the experimental conditions under which aptamers were selected and their binding affinity quantified. The open collaborative nature of the Aptamer Base provides the community with a unique resource that can be updated and curated in a decentralized manner, thereby accommodating the ever evolving field of aptamer research. DATABASE URL: http://aptamer.freebase.com.

Figure 1.

Basic type-relation map used by the Aptamer Base to describe SELEX experiments. The Interaction Experiment type ‘has outcome’ an Interaction. Each Interaction ‘has participant’ at least two Interactors (Aptamer and Aptamer Target). The Affinity Experiment type ‘has outcome’ a Dissociation Constant that either ‘confirms’ or ‘disputes’ an interaction. Blue ellipses denote types and arrows represent properties between topics. Overlapping ellipses represent the multiple types associated with a topic. For more details visit http://aptamerbase.semanticscience.org/?q=node/1.

Figure 2.

An overview of the relation map used by the Aptamer Base to describe SELEX experiments, the experimental details and the resulting aptamers. Light blue ellipses denote types and arrows represent either properties between topics or between topics and values (dark blue rectangles).

Figure 3.

Overview of an abridged relation map describing minimal aptamers. Minimal aptamers are captured in the Aptamer Base by creating a new Interaction for each individual Minimal Aptamer, permitting the description of unique Aptamers can then be associated with the unique Interaction topics.

Figure 4.

Summary of target types and aptamer types found in the Aptamer Base. (A) Distribution of the over 900 aptamer types described by the Aptamer Base. (B) Distribution of the 131 aptamer targets found in the Aptamer Base.