Araport, a community portal for Arabidopsis. Data integration, sharing and reuse. sergio contrino University of Cambridge

Transcription

1 Araport, a community portal for Arabidopsis. Data integration, sharing and reuse sergio contrino University of Cambridge

2 Acknowledgements J Craig Venter Institute Chris Town Agnes Chan Vivek Krishnakumar University of Cambridge Gos Micklem Sergio Contrino Former members Jason Miller Ben Rosen Svetlana Karamycheva Eleanor Pence Maria Kim Seth Schobel Chia-Yi Cheng Irina Belyaeva Matt Hanlon Walter Moreira Texas Advanced Computing Center Matt Vaughn Steve Mock Rion Dooley Joe Stubbs Josue Coronel Erik Ferlanti TAIR Eva Huala Bob Muller

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4 Araport11 Col-0 reannotation Cheng, Krishnakumar et al 2016, Plant Journal Protein-coding Genes Non-coding Genes Genomic Features Gene Loci mirna 27,416 -> 27,655 (NCBI, Maker, UniProt; Retired loci: 452 short coding sequences) 177 -> 325 (mirbase) Novel Transcribed Regions NAT 223 -> 1,115 (Publication) Transcript Variants AC 35,386 -> 48,359 (113 RNA-seq Datasets) lincrna Latest gene models from Maker, NCBI, UniProt RNA-seq supported isoforms Updated functional names uorf 58 -> 84 (Publication) 36 -> 2,444 (Publication) snorna 71 -> 287 (Publication) TAIR10 counts -> Araport11 counts (Evidence type) na -> 508 (RNA-seq) snrna Small RNAs na -> 35,846 (Prediction) 13 -> 82 (Publication) trna, rrna No change Data available via NCBI, ThaleMine, JBrowse, FTP, and Araport web services

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6 eplant: Home

7 eplant: example Note: Uses ThaleMine web services

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9 Araport App Store APIs developed by the community and the Araport team

10 Araport App Store: Dev Zone APIs developed by the community and the Araport team

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12 AC JBrowse Over 100 Data Tracks Araport11 RNA-seq T-DNA Phytozome Vista plot

13 JBrowse - Self-Service Data Sharing AC CyVerse Workflow Variants (VCF) Genes (GFF) Features (BED) Your genomic feature files Data Store User upload Publication App Araport JBrowse Publish Output

14 JBrowse Self-Service Prototype Your genomic feature data will be displayed in the JBrowse menu and data tracks Araport11 gene models Community Data Tracks Seeding mirna-seq Seedling RNA-Seq reads Pollen RNA-Seq junctions AC

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17 from: ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery Plant Cell Physiol. 58(1): e4(1-11) 2017 doi: /pcp/pcw200 araport@jcvi.org

18 AC ThaleMine - Gene Report (FT gene, AT1G65480)

19 ThaleMine - Gene Report (Expression, Interaction, Sequence) FT gene, AT1G65480 AC

20 ThaleMine - Gene Report (Seed Stock, Genotype, Phenotype) FT gene, AT1G65480 AC

21 What is InterMine? Open Source Data Warehouse github.com/intermine InterMine has three parts: 1. Database a. Load data from different data sets into single database 2. Webapp a. Mine the data b. Visualise! 3. Web services InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data Bioinformatics December 1; 28(23): YY

22 What sort of data is in InterMine? and in ThaleMine also - transcriptome profiles - GeneRif - Seed stocks and germplasms - Gene Locus History Genomic Pathways Interactions (complex and binary) Protein structures GO and other ontologies (Mammalian phenotype, etc) Protein domains Variation Expression and regulation Lots more

23 How does one get the data from an InterMine? 1. Search tools in UI a. Keyword search b. Sophisticated query tools 2. Web services a. Public API b. - interactive documentation YY

24 ThaleMine Pre-defined Queries Browse and export data in ThaleMine For example: List seed stocks related to flowering List all interactors (genetic and physical) for the FT gene Get gene expression values from different treatment conditions for a gene set AC

25 ThaleMine Build Your Own Query Transparent data model for flexible query construction AC

26 ThaleMine Region search

27 ThaleMine Region search

28 InterMine automatic (query) code generation xml example:

29 InterMine Lists analysis and operations

30 ThaleMine simple use case from: ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery Plant Cell Physiol. 58(1): e4(1-11) 2017 doi: /pcp/pcw200 araport@jcvi.org

31 Common Data Model Enables Crosstalk Between Resources ThaleMine Orthology Synteny Araport Model Organisms Human Legume Federation Cowpea Mine JGI SoyMine Yeast PhytoMine Bean Mine and more AC Medic Mine Peanut Mine and more

32 ThaleMine Recently Added Heatmap for 113 RNA-Seq Studies Ortholog links to other InterMines Gene Report Gene Report (e.g. dicer-like 1/AT1G01040) Gene Human RNA-seq study Medicago Gene List Analysis Genes JGI PhytoMine RNA-seq study AC

33 GO tool: an example using queries across different mines Summary view

34 GO tool: an example using queries across different mines Ontology Ontologyview view

35 Plant InterMines (afawk) ThaleMine - Arabidopsis thaliana PhytoMine - plants MedicMine - Medicago truncatula [HymenopteraMine - Bees, Ants & Wasps] SoyMine - Soybase soy bean data BeanMine - LegFed chado bean data LegumeMine - String bean, Soy, and Peanut PeanutMine - Peanut chado/gff data Wheat3BMine - Wheat chromosome 3B GrapeMine - Grapevine araport@jcvi.org

36 Next: CerealsMine? - choose an icon - choose a colour scheme - follow instructions at happy to help, and there is an active community at dev@lists.intermine.org demo? more info? questions? get in touch during the meeting sergio@intermine.org araport@jcvi.org