University of Delaware Department of Plant & Soil Sciences, and the Delaware Biotechnology Institute Photo by
Alex Kozik, UC Davis
SMALL RNA INFORMATICS VIA ARAPORT Araport “science apps” for small RNA data
Blake Meyers & Mayumi Nakano
OUR ARABIDOPSIS SMALL RNA WEBSITE
PHASING ANALYSIS TOOL
TAS3a Problem: data is entwined with the app, not an easy
format for external sites/tools to consume; true
for nearly all web apps.
REST INTERFACE (an example from Araport)
JSON output
JSON = JavaScript Object Notation, an open, standard format that uses human-
readable text to transmit data objects
EXPOSING DATA VIA ARAPORT
Original data, different format,
easy to parse
Web page exposes
the data in JSON format
Meyers lab website Araport
Mediator re-exposes
the data
Community API with online
documentation
Science app displays the data
open source, demonstrative
WHY EXPOSE OUR DATA VIA ARAPORT?
• Community: Araport is an open-access online community resource for Arabidopsis research
• Interoperability: Araport is designed to allow users to access and integrate a wide range of Arabidopsis information through a single interface
• Standards: Araport defines standards for data storage, access and interconnectivity
• Scaling: Araport will grow through the contributions of research community (data, computation, visualization tools)
• Security: Araport offers authentication & profiles service that can be shared across different web sites
• Reporting: Araport is maintained by scientists at JCVI, TACC, CSBC and other collaborators
EXPOSING DATA VIA ARAPORT
Step 1: Make data accessible in JSON format from our server
Step 2: Build application programing interfaces (APIs) for JSON web services on Araport
Step 3: Build a Science App using JSON API on Araport
Step 4: Encourage others!
PHASING ANALYSIS TOOL: JSON OUTPUTS
MEYERS LAB JSON WEB SERVICES
MEYERS LAB JSON OUTPUT: Phased Loci
Our phasing analysis pipeline identified 37 loci generating phased siRNAs, which aren’t listed together on any of our web pages, but the list of these
loci is available as a JSON web service. These are now exposed via Araport.
EXPOSING DATA VIA ARAPORT
Step 1: Make data accessible in JSON format from our server
Step 2: Build application programing interfaces (APIs) for JSON web services on Araport
Step 3: Build a Science App using JSON API on Araport
Step 4: Encourage others!
ARAPORT API & JSON OUTPUT
EXPOSING DATA VIA ARAPORT
Step 1: Make data accessible in JSON format from our server
Step 2: Build application programing interfaces (APIs) for JSON web services on Araport
Step 3: Build a Science App using JSON API on Araport
Step 4: Encourage others!
ARAPORT ‘SCIENCE APP’
EXPOSING DATA VIA ARAPORT
Step 1: Make data accessible in JSON format from our server
Step 2: Build application programing interfaces (APIs) for JSON web services on Araport
Step 3: Build a Science App using JSON API on Araport
Step 4: Encourage others!
WHAT’S NEXT?
• Display small RNA abundance data as a new track in JBrowse
• Release sPARTA (small RNA-PARE Target Analyzer) as an Araport science app
• Release more datasets & new tools (e.g. target prediction)
• Add more lists of loci that produce other types of regulatory small RNA.
A PREVIEW OF sPARTA AS A SCIENCE APP
ACKNOWLEDGEMENTS
NSF Plant Genome & MCB Awards
https://mpss.udel.edu
Blake Meyers Mayumi Nakano Deepti Ramachandruni Atul Kakrana Rui Xia & others
Meyers Lab JCVI Chris Town Jason Miller Vivek Krishnakumar Erik Ferlanti
TACC Matt Vaughn Walter Moreira Steve Mock
https://www.araport.org
