PosMed-plus: An Intelligent Search Engine that Inferentially Integrates Cross-Species Information Resources for Molecular Breeding of Plants

Abstract

Molecular breeding of crops is an efficient way to upgrade plant functions useful to mankind. A key step is forward genetics or positional cloning to identify the genes that confer useful functions. In order to accelerate the whole research process, we have developed an integrated database system powered by an intelligent data-retrieval engine termed PosMed-plus (Positional Medline for plant upgrading science), allowing us to prioritize highly promising candidate genes in a given chromosomal interval(s) of Arabidopsis thaliana and rice, Oryza sativa. By inferentially integrating cross-species information resources including genomes, transcriptomes, proteomes, localizomes, phenomes and literature, the system compares a user's query, such as phenotypic or functional keywords, with the literature associated with the relevant genes located within the interval. By utilizing orthologous and paralogous correspondences, PosMed-plus efficiently integrates cross-species information to facilitate the ranking of rice candidate genes based on evidence from other model species such as Arabidopsis. PosMed-plus is a plant science version of the PosMed system widely used by mammalian researchers, and provides both a powerful integrative search function and a rich integrative display of the integrated databases. PosMed-plus is the first cross-species integrated database that inferentially prioritizes candidate genes for forward genetics approaches in plant science, and will be expanded for wider use in plant upgrading in many species.

Prioritization of candidate genes in QTL regions based on associations between traits and biological processes

“…One approach consists of using genes previously identified as influencing the trait under study and test whether these explain a QTL [ 24 , 25 ], but this approach is limited to existing knowledge about genotype-to-phenotype relationships. Other approaches focus on integrating and visualizing existing information for prioritization [ 26 - 28 ] or merely give an overview of previously determined QTL candidate genes [ 29 , 30 ]. Little use has been made of biological pathways or predicted gene functions [ 31 - 33 ].…”

Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes

“…The main limitations of many gene prioritization tools, including Endeavour and BioGraph, are that they are restricted to the analysis of key model species and the data integration process is not easily reproducible and adaptable to other species. PosMed-Plus [68] was one of the first tools to prioritize candidate genes for two plant species ( Arabidopsis thaliana and rice) using a knowledge-based approach and including literature co-occurrence and cross-species information. KnetMiner (http://knetminer.rothamsted.ac.uk/) is one of the first tools to provide a generic and easily configurable approach that works for model and non-model species.…”

Plant systems biology: insights, advances and challenges

“…Also recently, Fouracre (2014), threw light on the application of systems approaches in understanding the Kranz anatomy of the C4 plants. Several web-based resources like PLAN2L (Krallinger et al 2009) and PosMed-plus (positional Medline for plant upgrading science) (Makita et al 2009) are available to integrate literature-derived bioentities and associated information.…”