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

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.

[1]  Juancarlos Chan,et al.  Gene Ontology Consortium: going forward , 2014, Nucleic Acids Res..

[2]  Hiroaki Kitano,et al.  The PANTHER database of protein families, subfamilies, functions and pathways , 2004, Nucleic Acids Res..

[3]  Y. Kanayama,et al.  Dynamic Metabolic Regulation by a Chromosome Segment from a Wild Relative During Fruit Development in a Tomato Introgression Line, IL8-3. , 2016, Plant & cell physiology.

[4]  Jeyakumar Natarajan,et al.  Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line , 2006, BMC Bioinformatics.

[5]  Xiaohong Wang,et al.  TCS1, a Microtubule-Binding Protein, Interacts with KCBP/ZWICHEL to Regulate Trichome Cell Shape in Arabidopsis thaliana , 2016, PLoS genetics.

[6]  Barry Smith,et al.  Ontologies as Integrative Tools for Plant Science Nih Public Access Author Manuscript $watermark-text Ontology 101 $watermark-text , 2022 .

[7]  Alan Christoffels,et al.  DESTAF: a database of text-mined associations for reproductive toxins potentially affecting human fertility. , 2012, Reproductive toxicology.

[8]  T. Devarenne,et al.  The Tomato Cell Death Suppressor Adi3 Is Restricted to the Endosomal System in Response to the Pseudomonas syringae Effector Protein AvrPto , 2014, PloS one.

[9]  P. Hasegawa,et al.  NaCl Regulation of Plasma Membrane H+-ATPase Gene Expression in a Glycophyte and a Halophyte , 1993, Plant physiology.

[10]  Jonathan D. Wren,et al.  Knowledge discovery by automated identification and ranking of implicit relationships , 2004, Bioinform..

[11]  T. Altmann,et al.  Metabolic changes in fruits of the tomato dx mutant. , 2006, Phytochemistry.

[12]  A. Handa,et al.  Hormonal Regulation of Tomato Fruit Development: A Molecular Perspective , 2005, Journal of Plant Growth Regulation.

[13]  Rolf Apweiler,et al.  IntEnz, the integrated relational enzyme database , 2004, Nucleic Acids Res..

[14]  G. Martin,et al.  Manipulation of Plant Programmed Cell Death Pathways During Plant-Pathogen Interactions , 2007, Plant signaling & behavior.

[15]  John W. Scott,et al.  High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding , 2012, PloS one.

[16]  Lukas A. Mueller,et al.  From manual curation to visualization of gene families and networks across Solanaceae plant species , 2013, Database J. Biol. Databases Curation.

[17]  Hideki Takahashi,et al.  Tomato as a model plant for plant-pathogen interactions , 2007 .

[18]  K. Dietz,et al.  Salt-induced expression of the vacuolar H+-ATPase in the common ice plant is developmentally controlled and tissue specific. , 2001, Plant physiology.

[19]  V. Bajic,et al.  HCVpro: hepatitis C virus protein interaction database. , 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[20]  Tetsuya Mori,et al.  Jasmonate-Responsive ERF Transcription Factors Regulate Steroidal Glycoalkaloid Biosynthesis in Tomato. , 2016, Plant & cell physiology.

[21]  Vladimir B. Bajic,et al.  Information Exploration System for Sickle Cell Disease and Repurposing of Hydroxyfasudil , 2013, PloS one.

[22]  Vladimir B. Bajic,et al.  INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles , 2013, PloS one.

[23]  Vladimir B. Bajic,et al.  Combining Position Weight Matrices and Document-Term Matrix for Efficient Extraction of Associations of Methylated Genes and Diseases from Free Text , 2013, PloS one.

[24]  Alan R. Powell,et al.  Integration of text- and data-mining using ontologies successfully selects disease gene candidates , 2005, Nucleic acids research.

[25]  D. Spooner,et al.  Comparison of AFLPs with other markers for phylogenetic inference in wild tomatoes [Solanum L. section Lycopersicon (Mill.) Wettst.] , 2005 .

[26]  Vladimir B. Bajic,et al.  Context-Specific Protein Network Miner – An Online System for Exploring Context-Specific Protein Interaction Networks from the Literature , 2012, PloS one.

[27]  Christopher J. Rawlings,et al.  Enhancing Data Integration with Text Analysis to Find Proteins Implicated in Plant Stress Response , 2010, J. Integr. Bioinform..

[28]  Jonathan D. G. Jones,et al.  The tomato DWARF enzyme catalyses C-6 oxidation in brassinosteroid biosynthesis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Jun Li,et al.  The plasma membrane Na+/H+ antiporter SOS1 is essential for salt tolerance in tomato and affects the partitioning of Na+ between plant organs. , 2009, Plant, cell & environment.

[30]  I. Dodd,et al.  Effect of partial rootzone drying on the concentration of zeatin-type cytokinins in tomato (Solanum lycopersicum L.) xylem sap and leaves. , 2006, Journal of experimental botany.

[31]  Y. Yamazaki,et al.  TOMATOMA Update: Phenotypic and Metabolite Information in the Micro-Tom Mutant Resource. , 2016, Plant & cell physiology.

[32]  Yuling Bai,et al.  Domestication and Breeding of Tomatoes: What have We Gained and What Can We Gain in the Future? , 2007, Annals of botany.

[33]  Daniel W. A. Buchan,et al.  The tomato genome sequence provides insights into fleshy fruit evolution , 2012, Nature.

[34]  Tatiana A. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2004, Nucleic Acids Res..

[35]  N. Sinha,et al.  Tomato (Solanum lycopersicum): A Model Fruit-Bearing Crop. , 2008, CSH protocols.

[36]  G. Martin,et al.  Adi3 is a Pdk1‐interacting AGC kinase that negatively regulates plant cell death , 2006, The EMBO journal.

[37]  V. Bajic,et al.  Dragon Plant Biology Explorer. A Text-Mining Tool for Integrating Associations between Genetic and Biochemical Entities with Genome Annotation and Biochemical Terms Lists[w] , 2005, Plant Physiology.

[38]  Jesús Cuartero,et al.  Tomato and salinity , 1998 .

[39]  Lukas A. Mueller,et al.  A Community-Based Annotation Framework for Linking Solanaceae Genomes with Phenomes1[C][OA] , 2008, Plant Physiology.

[40]  J. Feijó,et al.  GABA signalling modulates plant growth by directly regulating the activity of plant-specific anion transporters , 2015, Nature Communications.

[41]  R. Munns Genes and salt tolerance: bringing them together. , 2005, The New phytologist.

[42]  Y. Kamiya,et al.  Brassinosteroid-6-oxidases from Arabidopsis and tomato catalyze multiple C-6 oxidations in brassinosteroid biosynthesis. , 2001, Plant physiology.

[43]  R. Altman,et al.  PharmGKB: understanding the effects of individual genetic variants. , 2008, Drug metabolism reviews.

[44]  Vladimir B. Bajic,et al.  DDMGD: the database of text-mined associations between genes methylated in diseases from different species , 2014, Nucleic Acids Res..

[45]  Hajime Ohyanagi,et al.  Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation , 2014, Plant & cell physiology.

[46]  Vladimir B. Bajic,et al.  Database for exploration of functional context of genes implicated in ovarian cancer , 2008, Nucleic Acids Res..

[47]  W. Raza,et al.  Plant Growth Promotion by Volatile Organic Compounds Produced by Bacillus subtilis SYST2 , 2017, Front. Microbiol..

[48]  Anne Morgat,et al.  UniPathway: a resource for the exploration and annotation of metabolic pathways , 2011, Nucleic Acids Res..

[49]  Zhou Du,et al.  agriGO: a GO analysis toolkit for the agricultural community , 2010, Nucleic Acids Res..

[50]  Amos Bairoch,et al.  The ENZYME database in 2000 , 2000, Nucleic Acids Res..

[51]  Barry Smith,et al.  The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses , 2012, Plant & cell physiology.

[52]  Charles DeLisi,et al.  Data Mining for Systems Biology: Methods and Protocols , 2012 .

[53]  Robert Hoehndorf,et al.  The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants , 2016, J. Biomed. Semant..

[54]  Michael J. Axtell,et al.  Initiation of RPS2-Specified Disease Resistance in Arabidopsis Is Coupled to the AvrRpt2-Directed Elimination of RIN4 , 2003, Cell.

[55]  H. Ezura,et al.  How and why does tomato accumulate a large amount of GABA in the fruit? , 2015, Front. Plant Sci..

[56]  M. Foolad,et al.  Genome Mapping and Molecular Breeding of Tomato , 2007, International journal of plant genomics.

[57]  A. Hoffman,et al.  DP-155, a lecithin derivative of indomethacin, is a novel nonsteroidal antiinflammatory drug for analgesia and Alzheimer's disease therapy. , 2007, CNS drug reviews.

[58]  Zhiyong Li,et al.  A Novel Role for Arabidopsis CBL1 in Affecting Plant Responses to Glucose and Gibberellin during Germination and Seedling Development , 2013, PloS one.

[59]  D. Grierson,et al.  Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening. , 2002, Journal of experimental botany.

[60]  Vladimir B. Bajic,et al.  Dragon exploration system on marine sponge compounds interactions , 2013, Journal of Cheminformatics.

[61]  Alan Christoffels,et al.  DDESC: Dragon database for exploration of sodium channels in human , 2008, BMC Genomics.

[62]  Kazuki Saito,et al.  Tomato Glutamate Decarboxylase Genes SlGAD2 and SlGAD3 Play Key Roles in Regulating γ-Aminobutyric Acid Levels in Tomato (Solanum lycopersicum). , 2015, Plant & cell physiology.

[63]  Robert M. Buels,et al.  The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl , 2010, Nucleic Acids Res..

[64]  D. Shibata,et al.  Biochemical mechanism on GABA accumulation during fruit development in tomato. , 2008, Plant & cell physiology.

[65]  Minoru Kanehisa,et al.  Molecular network analysis of diseases and drugs in KEGG. , 2013, Methods in molecular biology.

[66]  D. Spooner,et al.  Taxonomy of wild tomatoes and their relatives (Solanum sect. Lycopersicoides, sect. Juglandifolia, sect. Lycopersicon; Solanaceae). , 2008 .

[67]  Jun Wang,et al.  Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. , 2014, The Plant journal : for cell and molecular biology.

[68]  G. Giuliano,et al.  Regulation of carotenoid biosynthesis during tomato development. , 1993, The Plant cell.

[69]  Vladimir B. Bajic,et al.  PIMiner: a web tool for extraction of protein interactions from biomedical literature , 2013, Int. J. Data Min. Bioinform..

[70]  Ning Ma,et al.  BLAST: a more efficient report with usability improvements , 2013, Nucleic Acids Res..

[71]  Henning Hermjakob,et al.  The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..

[72]  Vladimir B. Bajic,et al.  DDPC: Dragon Database of Genes associated with Prostate Cancer , 2010, Nucleic Acids Res..

[73]  Vladimir B. Bajic,et al.  DESM: portal for microbial knowledge exploration systems , 2015, Nucleic Acids Res..

[74]  Xiaoyan Ma,et al.  NRGA1, a putative mitochondrial pyruvate carrier, mediates ABA regulation of guard cell ion channels and drought stress responses in Arabidopsis. , 2014, Molecular plant.

[75]  Sylvie Ranwez,et al.  The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies , 2014, Bioinform..

[76]  Henning Hermjakob,et al.  The Reactome pathway Knowledgebase , 2015, Nucleic acids research.

[77]  J. Rathjen,et al.  The changing of the guard: the Pto/Prf receptor complex of tomato and pathogen recognition. , 2014, Current opinion in plant biology.

[78]  Jonathan D. G. Jones,et al.  Patterns of Dwarf expression and brassinosteroid accumulation in tomato reveal the importance of brassinosteroid synthesis during fruit development. , 2005, The Plant journal : for cell and molecular biology.

[79]  E. Schleiff,et al.  Crosstalk between Hsp90 and Hsp70 Chaperones and Heat Stress Transcription Factors in Tomato[W] , 2011, Plant Cell.

[80]  C. Maurel,et al.  Phosphorylation dynamics of membrane proteins from Arabidopsis roots submitted to salt stress , 2014, Proteomics.

[81]  S. Jayaraman,et al.  Novel JAZ co‐operativity and unexpected JA dynamics underpin Arabidopsis defence responses to Pseudomonas syringae infection , 2015, The New phytologist.

[82]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology , 2003, Nucleic Acids Res..

[83]  Ulf Leser,et al.  What makes a gene name? Named entity recognition in the biomedical literature , 2005, Briefings Bioinform..

[84]  D. Swanson,et al.  Indomethacin and Alzheimer's disease , 1996, Neurology.

[85]  D. Weiss,et al.  The Correlation between Heat-Shock Protein Accumulation and Persistence and Chilling Tolerance in Tomato Fruit , 1996, Plant physiology.

[86]  Sarah Melamed,et al.  A new model system for tomato genetics , 1997 .

[87]  Mathieu Andro,et al.  Open Data Platform for Knowledge Access in Plant Health Domain : VESPA Mining , 2015, ArXiv.

[88]  A. Bennett,et al.  Assessment of the Number and Expression of P-Type H+-ATPase Genes in Tomato , 1994, Plant physiology.

[89]  M. Palmgren PLANT PLASMA MEMBRANE H+-ATPases: Powerhouses for Nutrient Uptake. , 2001, Annual review of plant physiology and plant molecular biology.

[90]  Casey S. Greene,et al.  Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery , 2015, Briefings Bioinform..

[91]  E. Woltering,et al.  Multiple mediators of plant programmed cell death: Interplay of conserved cell death mechanisms and plant‐specific regulators , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[92]  Jiye Cheng,et al.  The Coronatine Toxin of Pseudomonas syringae Is a Multifunctional Suppressor of Arabidopsis Defense[W][OA] , 2012, Plant Cell.

[93]  C. Buell,et al.  Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis , 2012 .

[94]  G. Martin,et al.  The β-Subunit of the SnRK1 Complex Is Phosphorylated by the Plant Cell Death Suppressor Adi31[C][W][OA] , 2012, Plant Physiology.

[95]  Christoph Steinbeck,et al.  The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 , 2012, Nucleic Acids Res..

[96]  Xinnian Dong,et al.  Posttranslational Modifications of NPR1: A Single Protein Playing Multiple Roles in Plant Immunity and Physiology , 2016, PLoS pathogens.

[97]  S. Iuchi,et al.  Leucine zipper motif in RRS1 is crucial for the regulation of Arabidopsis dual resistance protein complex RPS4/RRS1 , 2016, Scientific Reports.

[98]  P. M. Bramley,et al.  Carotenoid Biosynthesis during Tomato Fruit Development (Evidence for Tissue-Specific Gene Expression) , 1994, Plant physiology.

[99]  R. Chetelat,et al.  UTILIZATION OF RELATED WILD SPECIES FOR TOMATO IMPROVEMENT , 1995 .

[100]  D. Inzé,et al.  The Potential of Text Mining in Data Integration and Network Biology for Plant Research: A Case Study on Arabidopsis[C][W] , 2013, Plant Cell.

[101]  M. Ganal,et al.  Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato , 2012, PloS one.

[102]  Barbara S. Paugh,et al.  Sphingosine-1-Phosphate and Interleukin-1 Independently Regulate Plasminogen Activator Inhibitor-1 and Urokinase-Type Plasminogen Activator Receptor Expression in Glioblastoma Cells: Implications for Invasiveness , 2008, Molecular Cancer Research.

[103]  Yasukazu Nakamura,et al.  Genome-wide analysis of intraspecific DNA polymorphism in 'Micro-Tom', a model cultivar of tomato (Solanum lycopersicum). , 2014, Plant & cell physiology.

[104]  Vladimir B. Bajic,et al.  OVERVIEW OF TEXT-MINING IN LIFE-SCIENCES , 2005 .

[105]  Alan Christoffels,et al.  Dragon exploratory system on hepatitis C virus (DESHCV). , 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[106]  Chuan-Yun Li,et al.  KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases , 2011, Nucleic Acids Res..

[107]  Miguel A. Andrade-Navarro,et al.  Information extraction from full text scientific articles: Where are the keywords? , 2003, BMC Bioinformatics.

[108]  Sebastian Schmeier,et al.  DDEC: Dragon database of genes implicated in esophageal cancer , 2009, BMC Cancer.

[109]  M. Tester,et al.  Na+ tolerance and Na+ transport in higher plants. , 2003, Annals of botany.

[110]  G. Coaker,et al.  Identification of QTLs controlling resistance to Pseudomonas syringae pv. tomato race 1 strains from the wild tomato, Solanum habrochaites LA1777 , 2015, Theoretical and Applied Genetics.

[111]  Jun Li,et al.  HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks , 2015, Plant & cell physiology.

[112]  V. Bajic,et al.  DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining , 2017, RNA biology.

[113]  G. Martin,et al.  Molecular basis of Pto-mediated resistance to bacterial speck disease in tomato. , 2003, Annual review of phytopathology.

[114]  Frank Eisenhaber,et al.  Discovering Biomolecular Mechanisms with Computational Biology , 2010 .

[115]  Kui Lin,et al.  Genomic analyses provide insights into the history of tomato breeding , 2014, Nature Genetics.

[116]  Christoph Steinbeck,et al.  MetaboLights: An Open‐Access Database Repository for Metabolomics Data , 2016, Current protocols in bioinformatics.

[117]  Martijn J. Schuemie,et al.  Distribution of information in biomedical abstracts and full-text publications , 2004, Bioinform..

[118]  S. Matsuo,et al.  Roles and regulation of cytokinins in tomato fruit development , 2012, Journal of experimental botany.

[119]  Joseph R Ecker,et al.  Ethylene Biosynthesis and Signaling Networks Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.001768. , 2002, The Plant Cell Online.

[120]  D. Zamir,et al.  Regulation of carotenoid biosynthesis during tomato fruit development: expression of the gene for lycopene epsilon-cyclase is down-regulated during ripening and is elevated in the mutant Delta. , 1999, The Plant journal : for cell and molecular biology.

[121]  Vladimir B. Bajic,et al.  Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining , 2004, Nucleic Acids Res..

[122]  Charles DeLisi,et al.  Data Mining for Systems Biology , 2013, Methods in Molecular Biology.

[123]  G. Martin,et al.  The Pto kinase conferring resistance to tomato bacterial speck disease interacts with proteins that bind a cis‐element of pathogenesis‐related genes , 1997, The EMBO journal.

[124]  P. Bramley Regulation of carotenoid formation during tomato fruit ripening and development. , 2002, Journal of experimental botany.

[125]  David S. Wishart,et al.  T3DB: the toxic exposome database , 2014, Nucleic Acids Res..

[126]  R. Serrano Structure and Function of Plasma Membrane ATPase , 1989 .

[127]  R. Peng,et al.  Genome-Wide Identification and Analysis of the MYB Transcription Factor Superfamily in Solanum lycopersicum. , 2016, Plant & cell physiology.

[128]  I. Baldwin,et al.  For security and stability , 2011, Plant signaling & behavior.

[129]  S. Lutts,et al.  Root-synthesized cytokinins improve shoot growth and fruit yield in salinized tomato (Solanum lycopersicum L.) plants , 2010, Journal of experimental botany.

[130]  Scott Federhen,et al.  The NCBI Taxonomy database , 2011, Nucleic Acids Res..

[131]  Jie Zhou,et al.  H2O2 mediates the crosstalk of brassinosteroid and abscisic acid in tomato responses to heat and oxidative stresses , 2014, Journal of experimental botany.

[132]  G. Galili,et al.  Regulatory Role of Cystathionine-γ-Synthase and de novo Synthesis of Methionine in Ethylene Production during tomato Fruit Ripening , 2006, Plant Molecular Biology.

[133]  M. G. Kim,et al.  The phytotoxin coronatine is a multifunctional component of the virulence armament of Pseudomonas syringae , 2014, Planta.