The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome

Abstract

The Arabidopsis Information Resource (TAIR) is a continuously updated, online database of genetic and molecular biology data for the model plant Arabidopsis thaliana that provides a global research community with centralized access to data for over 30,000 Arabidopsis genes. TAIR's biocurators systematically extract, organize, and interconnect experimental data from the literature along with computational predictions, community submissions, and high throughput datasets to present a high quality and comprehensive picture of Arabidopsis gene function. TAIR provides tools for data visualization and analysis, and enables ordering of seed and DNA stocks, protein chips, and other experimental resources. TAIR actively engages with its users who contribute expertise and data that augments the work of the curatorial staff. TAIR's focus in an extensive and evolving ecosystem of online resources for plant biology is on the critically important role of extracting experimentally based research findings from the literature and making that information computationally accessible. In response to the loss of government grant funding, the TAIR team founded a nonprofit entity, Phoenix Bioinformatics, with the aim of developing sustainable funding models for biological databases, using TAIR as a test case. Phoenix has successfully transitioned TAIR to subscription-based funding while still keeping its data relatively open and accessible.

Keywords: genome database; plant; sustainable funding.

Figure 1. A TAIR Locus Detail page

The locus page aggregates and summarizes all the information in TAIR about any given locus with the most frequently used data towards the top. Each locus is referred to by its unique AGI identifier along with other names from the literature. The graphical representation of the locus is linked to GBrowse for viewing within the chromosomal context. GO and PO annotations are presented in summary form; the detailed view is accessible from the link to annotation detail page (red circle). Similarly, links within each data subtype (e.g. Protein Data, Polymorphism) can be followed to access more detailed information from TAIR. Hyperlinks from the external links section go directly to resources outside of TAIR. Manually validated associated publications are shown at the bottom.

Figure 2. A TAIR Annotation Detail page

This secondary page linked from the annotation summary on the locus page presents additional details and links about the origins of each annotation including publication (linked to publication detail page), keyword (linked to keyword detail page) annotation contributor (linked to the community detail page), evidence code, and evidence description.

Figure 3. Genome Browsers at TAIR

a. SeqViewer Close-Up View. Each of the five chromosomes is represented by a green line on top. A subset of any given chromosome is shown in the blue-boxed area along with the specific tracks of data selected using the check boxes in the upper left. b. SeqViewer Nucleotide View. Drilled down nucleotide level view of locus AT3G57280 showing the exact positions of exons (orange), introns (light blue), UTR (red), TDNA/transposon insertions (purple track), translation start/stop (boxed blue area) c. GBrowse showing similar data as 3a but with a different presentation. d. Additional data tracks in GBrowse. Some examples of data types are shown that are visible in GBrowse but not in SeqViewer such as phosphorylation sites and transcriptional regulatory sequences.