pmr metabolomics and transcriptomics database and its restful web apis: a data sharing resource
TRANSCRIPT
1/19/2016
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Manhoi Hur ([email protected])
Iowa State University
Plant & Animal Genomes Conference
(PAG) 2016
PMR metabolomics and transcriptomics database and its
RESTful web APIs:
A data sharing resource
API= Application Program 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
Community datasets
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
Community datasets
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
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PMR website
http://metnetdb.org/PMR/Species and
Experiments list
Star means samples also have transcriptomics data
Experiments available for selected species
Sample Names
Reproducibility test – Spearman correlations
Experimental Metadata
Platform Metadata
Metabolite list
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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-KO 5","expId": 110
},{
"species": "Arabidopsis_thaliana","expName": "At2010-KO 6","expId": 111
},{
"species": "Arabidopsis_thaliana","expName": "At2010-KO 7","expId": 199
},{
"species": "Arabidopsis_thaliana","expName": "At2010-KO 8","expId": 198
},{
"species": "Arabidopsis_thaliana","expName": "At2010-KO 9","expId": 197
}
Example: PMR API for sharing metabolite data
http://pmr-webapi-gdcb.iastate.edu/pmrWebApi/api/v1/metabolites/list?species=Arabidospis_thaliana&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-enoic acid"
},{
"mId": 4353,"metaboliteName": "2-hydroxyhexadecanoic acid"
},{
"mId": 4354,"metaboliteName": "2-hydroxyeicosanoic acid"
},{
"mId": 4355,"metaboliteName": "2-hydroxydocosanoic acid"
},{
"mId": 4356,"metaboliteName": "2-hydroxytetracosanoic acid"
},{
"mId": 4357,"metaboliteName": "2-hydroxytetracos-2-enoic acid"
},{
"mId": 4358,"metaboliteName": "2-hydroxyhexacosanoic acid"
},
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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&dataVersion=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-dienoic acid
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-0951170Medicinal 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