To empower the use of metabolomics data in the development of

hypotheses concerning the organization and regulation of metabolic

networks we have developed PlantEukaryotic and Microbial Systems

Resource (PMR httpwwwmetnetdborgpmr)[1] and its RESTful Web

APIs a platform that stores visualizes and statistically analyzes

metabolomics data from multiple plants and microbial species

Currently PMR is populated with data from 23 plant species 14 of

which are medicinal species and a microbial species

PMR supports co-analysis of metabolomics and transcriptomics

data from the same samples allowing discovery of genes whose

expression is associated with accumulation of particular metabolites

We present a proof-of-concept for the utility of the API as a research

science app using Araport to provide Arabidopsis metabolomics data

and its functionality to diverse users

Here we detail unique features of PMR and how they are being used

by the wider research community

The big-data computational capabilities of PMR are enabled by its

database structure PMR is built on two kinds of databases An SQL-

based system MySQL is used to efficiently store metabolomics data

NoSQL-based systems include a document-oriented database

MongoDB that stores transcriptomics and metabolomics data and a

graph database Neo4j that stores metabolic and regulatory pathways

for Arabidopsis Hypericum gentianoides and zebrafish (Danio rerio)

The user-interface of PMR is implemented in PHP JavaScript and CSS

RESTful Web APIs are implemented in ASPNET Web API 20 (C)

Data sources

PMR and RESTful Web APIs PlantEukaryotic and Microbial Systems ResourceManhoi Hur1 Jason R Miller2 Erik Ferlanti3 Irina Belyaeva2 Christopher D Town2 and Eve Syrkin Wurtele1

1Iowa State University Ames IA USA 2J Craig Venter Institute Rockville MD USA 3Texas Advanced Computing Center(TACC) Austin TX USA

Conclusion

AcknowledgementThis material is based in part upon work supported by the National Science Foundation under award numbers EEC-0813570 (ESW and BJN) MCB-0951170 (to ESW and LL)

Medicinal Plant Consortium GM092521 National Institutes of Health and the Center for Metabolic Biology Iowa State University (to ESW) The Arabidopsis Information Portal is funded by

a grant from the National Science Foundation (DBI-1262414) and co-funded by a grant from the Biotechnology and Biological Sciences Research Council (BBL0271511)

PMR is a novel integrated system to study metabolomics

transcriptomics and pathways It facilitates to develop hypotheses

concerning the organization and regulation of metabolic networks

RESTful Web APIs for PMR are available on ARAPORT[3]

To submit your data to PMR please contact to Eve Wurtele (mash

iastateedu) or Manhoi Hur (mhhuriastateedu)

References

[1] Hur Manhoi et al A global approach to analysis and interpretation of metabolic data for plant natural product discovery Natural product reports(2013)

[2] Pandurangan Sudhakar et al ldquoRelationship between asparagine metabolism and protein concentration in soybean seedrdquo

[3] Krishnakumar V Hanlon M R Contrino S Ferlanti E S Karamycheva S Kim M amp Stubbs J (2014) Araport the Arabidopsis information portal Nucleic acids research gku1200

1 Workflow on PMR

Introduction

Methods

Results

WM Keck Metabolomics Research Laboratory

2 Case study metabolomics analysis on Soybean by using Volcano plots

3 RESTful Web APIs simply designed for use by other resources

Metabolomics data

from LCMS GCMS TOF and FT-ICR MS

profile data processed or identified metabolites

Transcriptomics data

from RNA-Seq (eg FPKM) Samples

WT

hcar

mutant

Samples

Data analysis by using Volcano plots

WT

hcar

mutant

Reproducibility check by scatterplot matrix

Pathways

from AraCyc HypericumCyc and ZebraCyc

50DAF45DAF40DAF30DAF25DAF

30DAF

25DAF

40DAF

45DAF

50DAF

Example of PMR RESTful Web API for visualization (Box Plot)

Co-analysis combined the over-

represented pathways[2]

AA

eFA

fFA

ST

STeFA

AAfFA

Developing Evans seeds were sampled at 25 30 40 45 and 50 days after flowering (DAF) and submitted for metabolomics amp

transcriptomics analysis to gain insights as to the biochemical program that determines soybean seed development

Metabolomics analysis indicates that amino acid (AA) fatty acid (eFA and fFA) and sterol (ST) classes are increased during seed

development till maturity

http(s)BaseURL + Input parameters

mId 4349

metaboliteName 18-

hydroxyoctadeca-912-dienoic acid

profileValues [

sId 2528

sampleName SALK_000817

genoType At3g56130

avgValue 001722133434

reps [

0028003763

0011330011

0001075435

0009188839

0000579592

00531503

]

Output JSON (JavaScript Object Notation)

CSV TSV and XML

Example URL to retrieve metabolomics

data httppmr-webapi-

gdcbiastateedupmrWebApiapiv1

profileslistspecies=Arabidopsis_thalianaampexpId=1

06ampomicsType=valMetabolomicsamppId=84ampmId=4349

ampdataVersion=10ampminLod=trueampoutputFormat=JSO

N

Retrieved JSON data

JSON format

httppmr-webapi-gdcbiastateedupmrWebApiapiv1

boxplotlistspecies=Arabidopsis_thalianaampexpId=106ampomicsType=valMetabolomicsamppId=84amp

mId=4348ampdataVersion=10ampminLod=trueamplegendColor=chemicalgroup

Boxplot

Plotlyjs

Htmlwidgetsjs - httpwwwhtmlwidgetsorg Plotlyjs- httpsplotly

JavaScript applications

External Web ServerRetrieved data

Htmlwidgetsjs

User interfaces to test out ARAPORT APIs

httppmr-webapi-

gdcbiastateedupmrW

ebApiapiv1boxplotlis

tspecies=Arabidopsis

_thalianaampexpId=106ampo

micsType=valMetabolo

micsamppId=84ampmId=434

8ampdataVersion=10ampmin

Lod=trueamplegendColor

=chemicalgroup

Python code to

adapt PMR API to

ARAPORT API

PMR boxplot API

Bringing PMR data and functions into ARAPORT

Pathways graph tool using Cytoscapejs