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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= 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