PMR database is a community resource for deposition and analysis of metabolomics data and related transcriptomics data. PMR currently houses metabolomics data from over 25 species of eukaryotes. In this talk, we introduce PMRs RESTful web APIs for data sharing, and demonstrate its applications in research using Araport to provide Arabidopsis metabolomics data.

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
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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-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