DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species

Abstract

Tomato is the most economically important horticultural crop used as a model to study plant biology and particularly fruit development. Knowledge obtained from tomato research initiated improvements in tomato and, being transferrable to other such economically important crops, has led to a surge of tomato-related research and published literature. We developed DES-TOMATO knowledgebase (KB) for exploration of information related to tomato. Information exploration is enabled through terms from 26 dictionaries and combination of these terms. To illustrate the utility of DES-TOMATO, we provide several examples how one can efficiently use this KB to retrieve known or potentially novel information. DES-TOMATO is free for academic and nonprofit users and can be accessed at http://cbrc.kaust.edu.sa/des_tomato/, using any of the mainstream web browsers, including Firefox, Safari and Chrome.

Figure 1

Workflow used within DES to create a KB such as DES-TOMATO.

Figure 2

Step-by-step illustration of how DES-TOMATO can be used to identify components of genetic resistance for P. syringae (marked in yellow). The pink octagons represent the “Solanaceae Genes” dictionary; the dark green triangles represent the “Bacteria (NCBI Taxonomy)” dictionary; and the pale green trapezoids represent “Plant-related Vocabulary” dictionary. The edge color is distributed across a color spectrum from hot/red (high frequency co-occurrence/strong association) to cold/blue (small number of co-occurrences, weaker association). The numbers on the edges provide the number of publications that link the associated nodes.

Figure 3

Step-by-step illustration of how DES-TOMATO can be used to find relevant candidate genes involved in salinity tolerance by focusing on Na⁺ homeostasis and plasma membrane H⁺-ATPases (in yellow). In the network, the pink octagons represent the “Solanaceae Genes” dictionary. The edge color is distributed across a color spectrum from hot/red (high frequency co-occurrence/strong association) to cold/blue (small number of co-occurrences, weaker association). The numbers on the edges provide the number of publications that link the associated nodes.

Figure 4

A simple demonstration of how a use “Explore hypotheses”. Boxed in yellow are the criteria used to direct or test the hypotheses generated.

Figure 5

A simple demonstration of how S. lycorpersicum enriched pathways can be explored using “KOBAS Pathways”. Boxed in yellow are the criteria adapted for this exploration process.