icar 2015 workshop - agnes chan

araport.org @araport

A Guided Tour of Araport

Your “One-Stop” Data Shop

Agnes Chan J Craig Venter Institute

July 7, 2015


Araport • 2012: A Community White Paper published

in Plant Cell • 2013: Funded by the US National Science

Foundation (NSF) • Goal: An Arabidopsis Data Store,

– “Used” by the Community – “Built-upon/Extended” by the Community


www.Araport.org


Araport

Warehousing

Users

Chado

JBrowse

Science Apps

Custom analysis

Real-time Federation

ThaleMine Gene List Analysis

Gene Report

Query, Web Services

Data Sources

Biologists/ Bioinformaticians

Software Developers


What can you find in Araport? • Col-0 Genome Annotation

– Araport11 Genome Annotation (pre-release) – Web Apollo Community Annotation Tool

• Data & Tools – ThaleMine Data Warehouse – JBrowse Genome Browser – Webservices and Science Apps Store


Community Co-expression

(ATTED)

ePictographs (BAR)

Real-time

Data Centers

Community Interactions

(BAR)

Array expression (BAR)

Publications (NCBI, UniProt)

Pathways (KEGG)

TAIR10 • Gene symbols • Curator summaries

ThaleMine Gene List Analysis

Gene Report

Query, Web Services

ThaleMine – Data warehouse

Warehouse

Araport

Data Sources


ThaleMine


ThaleMine – Gene Report Explore & Export Data Tables

Data Summary

Categorical Summary

Numerical Summary


ThaleMine – Germplasm (Demo) Links to Genotype and Phenotype


ThaleMine – Gene List Analysis


ThaleMine – Gene List Analysis Test for Functional Enrichments

Chromosome Distribution GO Enrichment Pathway Enrichment


ThaleMine – Data Queries


ThaleMine – Data Queries Custom Export Selected Data


ThaleMine – Data Queries Export GO terms for a Custom Gene List


ThaleMine – Web Services Tools -> Web Services -> ThaleMine API


ThaleMine – Web Services Programmatically access any data you see


Community Data

Tools

Science Apps

Araport

Science Apps

Custom analysis

qRT-PCR GFP images

Demo 1 (AtExpress Profiling)

Expression study of 1000 hypothetical

genes

JCVI

Real-time


Demo Science App GFP Expression for Hypothetical Genes


Community 1001 Genomes

Variants (Ensembl)

Epigenetic (EPIC-CoGe)

Real-time

Araport11

Community TDNA-seq

Over 70 tracks

TAIR10 • Gene models, etc.

JBrowse – Genome Browser

Warehouse

Araport

Data Sources

• Updated gene models • RNA-seq expression

by tissue

JBrowse


JBrowse View Gene Models with

TDNA-seq, RNA-seq, 1001 Genomes Variants,


JBrowse Browse 1001 Genomes Variants


JBrowse Upload your Own Track

• File > Open


Araport11 Pre-release Col-0 Genome Annotation

Araport11 Protein Coding Genes

UniProt Update

NCBI Novel

Updated Transcripts

Novel Transcripts

No Change Transcripts

Maker Novel

NCBI SRA RNA-seq

PASA Update

Trinity Assembly

~1,200 ~16,000 ~26,000


Araport11 Pre-release View Araport11 Gene Models in JBrowse


Araport11 Pre-release Download GFF/FASTA Files

• Data -> Downloads


Araport11 Pre-release Web Apollo Community Annotation


Araport11 Pre-release Edit and Curate Gene Models

Gene Edit Form


www.Araport.org

Gene Report Custom Queries

Araport11 annotation GFF/FASTA


Araport iPad Competition Science Apps Ideas Challenge

(Summer 2015) • Describe a use-case-driven

App Idea. • Your idea would integrate

one or more data sources, and/or perform analysis.

How to Submit Your Ideas? • Submission details at

https://www.araport.org. • Opens through August 31,

2015.

Win an iPad

https://www.araport.org/


And More… Android App with ThaleMine

• Download “Intermine” from Google Play Store

• Start searching for your favorite genes (e.g. FT, ABI3)

Araport Poster •Talk 006, near the left exit of Blue Amphi (Systems Biology and New approaches)

•Online demonstration

Android App for ThaleMine

Developers’ Workshop Fall 2015


Acknowledgements J Craig Venter Institute • Chris Town • Jason Miller • Agnes Chan • Erik Ferlanti • Vivek Krishnakumar • Irina Belyaeva • Maria Kim • Chia-Yi Cheng • Seth Schobel

University of Cambridge • Gos Micklem • Sergio Contrino Former members • Ben Rosen • Svetlana Karamycheva • Eleanor Pence

Texas Advanced Computing Center • Matt Vaughn • Steve Mock • Rion Dooley • Matt Hanlon • Joe Stubbs • Walter Moreira • Chris Jordan

TAIR • Eva Huala • Bob Muller

icar 2015 workshop - agnes chan

Science

araport araport11

araport thalemine gene

guided tour of araport

custom gene list

arabidopsis data store

gene models rnaseq expression

araport11 community

tissue jbrowse