title: Plant Omics Data Center: an integrated web repository for interspecies gene expression networks with NLP-based curation.
abstract: Comprehensive integration of large-scale omics resources such as genomes, transcriptomes and metabolomes will provide deeper insights into broader aspects of molecular biology. For better understanding of plant biology, we aim to construct a next-generation sequencing (NGS)-derived gene expression network (GEN) repository for a broad range of plant species. So far we have incorporated information about 745 high-quality mRNA sequencing (mRNA-Seq) samples from eight plant species (Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum, Sorghum bicolor, Vitis vinifera, Solanum tuberosum, Medicago truncatula and Glycine max) from the public short read archive, digitally profiled the entire set of gene expression profiles, and drawn GENs by using correspondence analysis (CA) to take advantage of gene expression similarities. In order to understand the evolutionary significance of the GENs from multiple species, they were linked according to the orthology of each node (gene) among species. In addition to other gene expression information, functional annotation of the genes will facilitate biological comprehension. Currently we are improving the given gene annotations with natural language processing (NLP) techniques and manual curation. Here we introduce the current status of our analyses and the web database, PODC (Plant Omics Data Center; http://bioinf.mind.meiji.ac.jp/podc/), now open to the public, providing GENs, functional annotations and additional comprehensive omics resources.
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan Tsukuba Division, Mitsubishi Space Software Co., Ltd., Tsukuba, 305-0032 Japan Plant Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540 Japan These authors contributed equally to this work.
authors.forename: Hajime
authors.initials: H
authors.lastname: Ohyanagi
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan These authors contributed equally to this work.
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Takano
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan These authors contributed equally to this work.
authors.forename: Shin
authors.initials: S
authors.lastname: Terashima
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan.
authors.forename: Masaaki
authors.initials: M
authors.lastname: Kobayashi
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan.
authors.forename: Maasa
authors.initials: M
authors.lastname: Kanno
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan.
authors.forename: Kyoko
authors.initials: K
authors.lastname: Morimoto
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan.
authors.forename: Hiromi
authors.initials: H
authors.lastname: Kanegae
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan.
authors.forename: Yohei
authors.initials: Y
authors.lastname: Sasaki
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan.
authors.forename: Misa
authors.initials: M
authors.lastname: Saito
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan.
authors.forename: Satomi
authors.initials: S
authors.lastname: Asano
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan.
authors.forename: Soichi
authors.initials: S
authors.lastname: Ozaki
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan.
authors.forename: Toru
authors.initials: T
authors.lastname: Kudo
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Yokoyama
authors.affiliation: Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan.
authors.forename: Koichiro
authors.initials: K
authors.lastname: Aya
authors.affiliation: Graduate School of Bioresources, Mie University, Tsu, 514-8507 Japan.
authors.forename: Keita
authors.initials: K
authors.lastname: Suwabe
authors.affiliation: Division of Natural Science, Osaka Kyoiku University, Kashiwara, 582-8582 Japan.
authors.forename: Go
authors.initials: G
authors.lastname: Suzuki
authors.affiliation: Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, 599-8531 Japan.
authors.forename: Koh
authors.initials: K
authors.lastname: Aoki
authors.affiliation: Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan.
authors.forename: Yasutaka
authors.initials: Y
authors.lastname: Kubo
authors.affiliation: Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan.
authors.forename: Masao
authors.initials: M
authors.lastname: Watanabe
authors.affiliation: Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan.
authors.forename: Makoto
authors.initials: M
authors.lastname: Matsuoka
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan kyano@isc.meiji.ac.jp.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yano
mesh_terms: D066289:Data Curation; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D016247:Information Storage and Retrieval; D020407:Internet; D058977:Molecular Sequence Annotation; D009323:Natural Language Processing; D010944:Plants / Q000235:genetics*; D059467:Transcriptome
keywords: Correspondence analysis; Database; Gene expression network; Manual curation; Natural language processing (NLP); Omics