title: LAILAPS: the plant science search engine.
abstract: With the number of sequenced plant genomes growing, the number of predicted genes and functional annotations is also increasing. The association between genes and phenotypic traits is currently of great interest. Unfortunately, the information available today is widely scattered over a number of different databases. Information retrieval (IR) has become an all-encompassing bioinformatics methodology for extracting knowledge from complex, heterogeneous and distributed databases, and therefore can be a useful tool for obtaining a comprehensive view of plant genomics, from genes to traits. Here we describe LAILAPS (http://lailaps.ipk-gatersleben.de), an IR system designed to link plant genomic data in the context of phenotypic attributes for a detailed forward genetic research. LAILAPS comprises around 65 million indexed documents, encompassing >13 major life science databases with around 80 million links to plant genomic resources. The LAILAPS search engine allows fuzzy querying for candidate genes linked to specific traits over a loosely integrated system of indexed and interlinked genome databases. Query assistance and an evidence-based annotation system enable time-efficient and comprehensive information retrieval. An artificial neural network incorporating user feedback and behavior tracking allows relevance sorting of results. We fully describe LAILAPS's functionality and capabilities by comparing this system's performance with other widely used systems and by reporting both a validation in maize and a knowledge discovery use-case focusing on candidate genes in barley.
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany Maria.Esch@ipk-gatersleben.de.
authors.forename: Maria
authors.initials: M
authors.lastname: Esch
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany.
authors.forename: Jinbo
authors.initials: J
authors.lastname: Chen
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Colmsee
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Klapperstück
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany.
authors.forename: Eva
authors.initials: E
authors.lastname: Grafahrend-Belau
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Scholz
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Lange
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D018745:Genome, Plant / Q000235:genetics*; D010944:Plants / Q000235:genetics*; D057386:Search Engine; D014584:User-Computer Interface
keywords: Functional gene annotation; Information retrieval; Integrative search engine; Plant genomics resources; Traits