ICAR 2015 Workshop 10 (TUESDAY, JULY 7, 2015, 4:30-6:00 PM) The Arabidopsis information portal for users and developers Blake Meyers (University of Delaware) A Community Collaborator Perspective: Case study 2 - Small RNA DBs

1. 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

2. OUR ARABIDOPSIS SMALL RNA WEBSITE

3. 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.

4. 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

5. 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

6. 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

7. 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!

8. PHASING ANALYSIS TOOL: JSON OUTPUTS

9. MEYERS LAB JSON WEB SERVICES

10. 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.

11. 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!

12. ARAPORT API & JSON OUTPUT

13. 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!

14. ARAPORT ‘SCIENCE APP’

15. 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!

17. 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.

18. A PREVIEW OF sPARTA AS A SCIENCE APP

19. 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