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ICAR 2015 Workshop - Agnes Chan
Araport is a database and web portal that aims to be a "one-stop shop" for Arabidopsis thaliana data. It contains genome annotations, gene expression data, variants from 1001 genomes, and tools for viewing, analyzing and curating this data. The core components are ThaleMine, a data warehouse, JBrowse, a genome browser, and tools for community curation of gene models. Araport integrates multiple external public datasets and provides programmatic access via web services and APIs.
ICAR 2015 Workshop - Agnes Chan
- 1. araport.org@araport A Guided Tour of Araport Your “One-Stop” DataShop Agnes Chan J Craig Venter Institute July 7, 2015
- 2. araport.org@araport Araport • 2012: ACommunity 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
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- 4. araport.org@araport Araport Warehousing Users Chado JBrowse Science Apps Custom analysis Real-time Federation ThaleMine Gene List Analysis Gene Report Query, Web Services DataSources Biologists/ Bioinformaticians Software Developers
- 5. araport.org@araport What can youfind 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
- 6. araport.org@araport 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
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- 8. araport.org@araport ThaleMine – GeneReport Explore & Export Data Tables Data Summary Categorical Summary Numerical Summary
- 9. araport.org@araport ThaleMine – Germplasm(Demo) Links to Genotype and Phenotype
- 10. araport.org@araport ThaleMine – GeneList Analysis
- 11. araport.org@araport ThaleMine – GeneList Analysis Test for Functional Enrichments Chromosome Distribution GO Enrichment Pathway Enrichment
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- 13. araport.org@araport ThaleMine – DataQueries Custom Export Selected Data
- 14. araport.org@araport ThaleMine – DataQueries Export GO terms for a Custom Gene List
- 15. araport.org@araport ThaleMine – WebServices Tools -> Web Services -> ThaleMine API
- 16. araport.org@araport ThaleMine – WebServices Programmatically access any data you see
- 17. araport.org@araport Community Data Tools Science Apps Araport Science Apps Custom analysis qRT-PCR GFPimages Demo 1 (AtExpress Profiling) Expression study of 1000 hypothetical genes JCVI Real-time
- 18. araport.org@araport Demo Science App GFPExpression for Hypothetical Genes
- 19. araport.org@araport Community 1001 Genomes Variants (Ensembl) Epigenetic (EPIC-CoGe) Real-time Araport11 Community TDNA-seq Over70 tracks TAIR10 • Gene models, etc. JBrowse – Genome Browser Warehouse Araport Data Sources • Updated gene models • RNA-seq expression by tissue JBrowse
- 20. araport.org@araport JBrowse View Gene Modelswith TDNA-seq, RNA-seq, 1001 Genomes Variants,
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- 24. araport.org@araport JBrowse Upload your OwnTrack • File > Open
- 25. araport.org@araport Araport11 Pre-release Col-0 GenomeAnnotation 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
- 26. araport.org@araport Araport11 Pre-release View Araport11Gene Models in JBrowse
- 27. araport.org@araport Araport11 Pre-release Download GFF/FASTAFiles • Data -> Downloads
- 28. araport.org@araport Araport11 Pre-release Web ApolloCommunity Annotation
- 29. araport.org@araport Araport11 Pre-release Edit andCurate Gene Models Gene Edit Form
- 30. araport.org@araport www.Araport.org Gene Report Custom Queries Araport11annotation GFF/FASTA
- 31. araport.org@araport Araport iPad Competition ScienceApps 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
- 32. araport.org@araport And More… Android Appwith 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
- 33. araport.org@araport Acknowledgements J Craig VenterInstitute • 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