PMR metabolomics and transcriptomics database and its RESTful web APIs: A data sharing resource
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The document discusses the PMR (Plant & Microbial Resource) platform, which offers a database for metabolomics and transcriptomics data along with RESTful web APIs for data sharing. It highlights the need for community resources in metabolomics and presents the platform's capabilities for integrating various omics datasets, enabling statistical analysis, and visualization tools. Future plans include enhancing data integration with other platforms and providing comprehensive documentation for community use.
PMR metabolomics and transcriptomics database and its RESTful web APIs: A data sharing resource
- 1. 1/19/2016 1 Manhoi Hur (mhhur@iastate.edu) Iowa State University Plant & Animal Genomes Conference (PAG) 2016 PMR metabolomics and transcriptomics database and its RESTful web APIs: A data sharing resource API= ApplicationProgram Interface Proteomics Metabolomics Fluxomics Transcriptomics Genomics & Transcriptomics: Sequencing and assembly Draft Metabolic and regulatory model (Reaction set with regulators and transporters) Reconstructed biological network Annotation Experiments to test validity and accuracy of model Communitydatasets Omics datasets as constraint Overall vision Rai A, Saito K. Omics data input for metabolic modeling. Current Opinion in Biotechnology. 2016 Feb 29;37:127-34. Proteomics Metabolomics Fluxomics Transcriptomics Genomics & Transcriptomics: Sequencing and assembly Draft Metabolic and regulatory model (Reaction set with regulators and transporters) Reconstructed biological network Annotation Experiments to test validity and accuracy of model Communitydatasets Omics datasets as constraint Overall vision Absence of available community resources for metabolomics data Rai A, Saito K. Omics data input for metabolic modeling. Current Opinion in Biotechnology. 2016 Feb 29;37:127-34. Community-based needs • Repository for growing collections of defined metabolite abundance data and associated metadata • Clear, consistent formats • Comprehensive metadata • Easy access and download • Computational tools to integrate genome system-scale datasets Hur, et al. "A global approach to analysis and interpretation of metabolic data for plant natural product discovery." Natural Product Reports (2013) PMR: Plant/Eukaryotic and Microbial Systems Resource • Data repository • Metabolomics data and transcriptomics data • Metadata • Statistical analysis and visualization • Data integration • Integrated metabolomics and transcriptomics • Data sharing • Download data directly • Retrieve data and its plots through RESTful web APIs Hur, et al. "A global approach to analysis and interpretation of metabolic data for plant natural product discovery." Natural Product Reports (2013) Data repository Stat analysis Data sharing Data integration Technical basis for PMR Platform • PMR database and its web-application • Back-end: NoSQL database (MongoDB 3.x and Neo4J) • Flexibility and scalability • Front-end: PHP, jQuery, HighChart JS, and Plotly.js • Apache HTTP Server • pmr-RESTful web APIs • Microsoft ASP.NET Web API 2.x • C#, Plotly.js ,and Htmlwidgets.js • Microsoft IIS Web Server
- 2. 1/19/2016 2 PMR website http://metnetdb.org/PMR/ Species and Experiments list Star means samples also have transcriptomicsdata Experiments available for selected species Sample Names Reproducibility test – Spearman correlations Experimental Metadata Platform Metadata Metabolite list
- 3. 1/19/2016 3 Metabolite list Metabolite data as Boxplot Volcano plot: Comparing data between samples Metabolomics data empowers accurate computational modeling and hypothesis development • Hur et al. Natural Product Reports (2013) • Quanbeck et al. Frontiers in Plant Science (2012) • Yeo et al. JBC (2012) • Ngaki et al Nature (2012) • Atsushi et al Plant Physiology (2014) • Vu et al Plant Signaling & Behavior (2015) • Li et al BMC Genomics (2015) pmr-RESTful web APIs to share PMR data and functionality with diverse users • Undergraduate teaching- 6-week Genetics lab unit to determine function of yeast genes (https://db.nanobio.illinois.edu) • Araport- Arabidopsis information portal (https://www.araport.org) Near Future: • Soybase (http://soybase.org) • MaizeGDB (http://www.maizegdb.org) • Sol Genomics Network (http://www.sgn.cornell.edu) Genetics lab: Yeast: Let's Mess it up! pmr-RESTful web APIs simply designed for use by other resources • Based on HTTP requests; detail encoded directly in URL path • Output format: JSON (JavaScript Object Notation) http(s)://BaseURL + Input parameters • Example URL: http://pmr-webapi- gdcb.iastate.edu/pmrWebApi/api/v1 /experiments/list?species=Arabidopsis_thaliana Retrieved data { "species": "Arabidopsis_thaliana", "expName": "At2010-KO5", "expId": 110 }, { "species": "Arabidopsis_thaliana", "expName": "At2010-KO6", "expId": 111 }, { "species": "Arabidopsis_thaliana", "expName": "At2010-KO7", "expId": 199 }, { "species": "Arabidopsis_thaliana", "expName": "At2010-KO8", "expId": 198 }, { "species": "Arabidopsis_thaliana", "expName": "At2010-KO9", "expId": 197 } Example: PMR API for sharing metabolite data http://pmr-webapi- gdcb.iastate.edu/pmrWebApi/api/v1 /metabolites/list?species=Arabidospis_thali ana&expId=106&pId=84&dataVersion=1.0/ Retrieved data [ { "mId": 4348, "metaboliteName":"16-Hydroxyhexadecanoic acid" }, { "mId": 4349, "metaboliteName":"18-hydroxyoctadeca-9,12-dienoic acid" }, { "mId": 4350, "metaboliteName":"18-hydroxyoctadec-9-enoicacid" }, { "mId": 4353, "metaboliteName":"2-hydroxyhexadecanoic acid" }, { "mId": 4354, "metaboliteName":"2-hydroxyeicosanoicacid" }, { "mId": 4355, "metaboliteName":"2-hydroxydocosanoic acid" }, { "mId": 4356, "metaboliteName":"2-hydroxytetracosanoicacid" }, { "mId": 4357, "metaboliteName":"2-hydroxytetracos-2-enoicacid" }, { "mId": 4358, "metaboliteName":"2-hydroxyhexacosanoic acid" },
- 4. 1/19/2016 4 Example of PMR API for visualization (Box Plot) JSON format http://pmr-webapi-gdcb.iastate.edu/pmrWebApi/api/v1 /boxplot/list?species=Arabidopsis_thaliana&expId=106& omicsType=valMetabolomics&pId=84&mId=4348&dataV ersion=1.0&minLod=true&legendColor=chemicalgroup/ Htmlwidgets.js Boxplot Plotly.js Htmlwidgets.js - http://www.htmlwidgets.org/ Plotly.js- https://plot.ly/ JavaScript applications Showing actual plotsRetrieved data Bringing PMR data and functions into ARAPORT Example of Apps on ARAPORT – PMR_Plotter Boxplot on PMR Boxplot on ARAPORT Metabolite: 18-hydroxyoctadeca-9,12-dienoicacid https://www.araport.org/apps/jmiller/pmrplotter Conclusions and Future Directions • PMR is a systems biology platform to support the community • Developed RESTful web APIs for PMR • Integrate additional PMR metabolomics data and functionalities with ARAPORT • PMR will make well-designed documentation for a workflow that can be used within the ARAPORT science apps and other community resources. Data repository Stat analysis Data sharing Data integration Acknowledgments EEC-0813570 MCB-0951170 Medicinal Plant Consortium GM092521 Dr. Jason MillerDr. Chris Town Irina Belyaeva Erik Ferlanti DESC0014038 ARAPORT team at J. Craig Venter Institute Iowa State University Center for Metabolic Biology Dr. Basil J Nikolau Dr. Ling Li PI: Eve Syrkin Wurtele PMR team at Iowa State University Zebulon Arendsee