JBrowse and Inter-"Mine" Communication - IMDEV 2017

Lightning Talk about InterMine/JBrowse integration and extensions to Inter-"Mine" Communication, presented at the 2017 InterMine Developer Workshop and Hackathon (IMDEV 2017) held at the Joint Genome Institute (JGI) in Walnut Creek, CA

Presented on Thursday, March 30th 2017 by Vivek Krishnakumar

Transcript

1. JBrowse &
   Inter-mine
   communication
   Vivek Krishnakumar
   J. Craig Venter Institute
   vkrishna@jcvi.org
   2017 InterMine Workshop and Hackathon
   Thursday, March 30th @ 11:10am
   

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2. Overview
   ➔InterMine <-> JBrowse Integration
   ➔Extending FriendlyMines
   ➔MedicMine & ThaleMine
   ➔Summary
   ➔Acknowledgements
   ➔FIN
   

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3. InterMine <->
   JBrowse integration
   ➔JBrowse & REST API spec
   ➔Components in InterMine <->
   JBrowse integration
   ➔Issues with initial implementation
   ➔Fixes implemented in InterMine
   core and JBrowse
   

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4. JBrowse & REST API spec
   • JBrowse (http://jbrowse.org)
   • Javascript based portable genome browser tool developed by GMOD community
   • Ships with two REST Store adapters: Features and Names
   • REST Features Store handles genomic features within specified region:
   • :base/stats/global
   • :base/stats/region/:refseq?start=:start&end=:end
   • :base/stats/regionFeatureDensities/:refseq?start=:start&end=:end&basesPerBin=20000
   • :base/features/:refseq?start=:start&end=:end
   • REST Names Store handles search and retrieval of features by identifier:
   • :base/names/?startswith=:searchterm
   • :base/names/?equals=:searchterm
   • Accepted response type: application/json
   http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services
   

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5. Components in InterMine <-> JBrowse integration
   • populate-child-features postprocessor task
   • Processes SequenceFeature entities to ensure that feature hierarchy is correctly structured (based on SO)
   • Genomic feature Engine (API)
   • Returns genomic feature data in JBrowse compatible JSON format
   • Config generator service (API)
   • Returns feature tracks (trackList.json) & reference sequence listing (refSeqs.json)
   • Names service (API)
   • Returns list of genomic features matching the input search term
   • Embedded ReportDisplayer
   • Injects (via iframe) JBrowse visualization into InterMine report page
   http://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/
   

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6. Issues with initial
   implementation
   • populate-child-features postprocessor
   • Failed to correctly construct Gene model JSON
   object
   |- gene:1
   |----- mRNA:1
   |----- exon:1
   |----- exon:2
   |----- mRNA:2
   |----- exon:3
   • Feature Engine & Config generator
   • Failed to properly convert InterMine Class names
   to SO terms
   e.g. AntisenseLncRNA → antisense_lncRNA`
   • Failed to specify transcript type in track
   configuration
   • Data issues
   • Failed to represent Gene model CDS entity as
   disjointed parts due to CDS loading mechanism
   e.g. FlyBaseCDSFastaLoader,
   AraportCDSFastaLoader,
   ChadoSequenceProcessor
   • populate-child-features postprocessor
   • Improved logic populates the childFeatures
   collection appropriately
   |- gene:1
   |----- mRNA:1
   |----- exon:1
   |----- exon:2
   |----- mRNA:2
   |----- exon:3
   • Feature Engine & Config generator
   • Automatically resolves IM Class to SO type
   • Ability to specify which tracks to display and
   define extra parameters via web.properties config
   • Fixes to ProcessedTranscript glyph (in JBrowse)
   • Automatically infers disjointed CDS parts from
   exon parts and total CDS span
   Fixes made to InterMine &
   JBrowse core
   intermine/#1454
   intermine/#1426
   jbrowse/#872
   @sergiocontrino
   @justinccdev
   @vivekkrish
   

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7. Extending
   FriendlyMine
   Functionality
   ➔Current state of Inter-mine
   communication based on standard
   Homology data model
   ➔FriendlyMines extended to
   support alternate Homology data
   model(s)
   ➔Extending FriendlyMines to
   support new Entity types (e.g.
   SyntenyBlocks)
   

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8. Inter-mine communication using Homology data
   1
   2 3
   Homologue data model
   Friendly mine config in web.properties
   

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9. Extending FriendlyMines to support alternate
   Homology model(s)
   Standard Model
   Class Name Homologue
   Primary Entity gene
   Related Entity homologue
   Relationship type (orthologue,
   paralogue, LDO, etc.)
   PhytoMine Data Model
   Homolog
   gene1
   gene2
   type (NO VALUE)
   Method NA method (one-to-one, one-to-
   many, many-to-many)
   

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10. FriendlyMines extended to support alternate
    Homology model(s)
    1
    2
    3
    stable/e93905e
    @vivekkrish
    Homolog data model
    Friendly mine config in web.properties
    

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11. stable/7800633
    @vivekkrish
    Extend FriendlyMines to support new Entity type
    (Synteny Block)
    3
    @sammyjava
    1
    2
    

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12. Medicago Genome &
    Arabidopsis
    Information Portal
    ➔MedicagoGenome.org &
    MedicMine
    ➔Araport.org & ThaleMine
    ➔Additions to ThaleMine
    

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13. MedicagoGenome.org
    

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14. Community
    Orthologs
    (Phytozome, LIS)
    eFP Browser
    (BAR)
    Real-time
    Data Centers
    Community
    RNA-Seq expression
    (NCBI SRA)
    Publications
    (NCBI)
    Pathways
    (KEGG)
    Mt4.0
    • Genome sequence
    • Genome annotation
    MedicMine
    Gene List
    Analysis
    Gene
    Report
    Query, Web
    Services
    MedicMine - Data Warehouse
    Warehouse
    Data Sources
    Mt Gene Indices
    (DFCI)
    Krishnakumar et al. 2014, Plant Cell Physiol
    

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15. Araport.org
    

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16. Community
    Orthologs
    (PhytoMine)
    Co-expression
    (ATTED)
    Real-time
    Data Centers
    Community
    Protein Interactions
    (InAct, BioGrid)
    Gene expression
    (Araport, BAR)
    Publications
    (NCBI, UniProt)
    Pathways
    (KEGG)
    Araport11
    ThaleMine
    Gene List
    Analysis
    Gene
    Report
    Query,
    Data Tables
    Web
    Services
    ThaleMine - Data Warehouse
    Warehouse
    Araport
    Data Sources
    Krishnakumar et al. 2016, Plant Cell Physiol
    Reannotation of
    Col-0 genome
    (Araport)
    

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17. Additions to ThaleMine
    Heatmap for 113 RNA-Seq Studies
    Gene Report
    Gene List Analysis
    Gene Report (e.g. dicer-like 1/AT1G01040)
    Medicago
    JGI PhytoMine
    Human
    RNA-seq study
    RNA-seq study
    Gene
    Genes
    

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18. Summary
    • Issues plaguing the functionality of InterMine’s zero-config JBrowse integration
    have been resolved
    • DISCUSSION: Fold-in changes made to JBrowse code base into InterMine (for maintainability)
    • FriendlyMine functionality extended by implementing link classes to support
    alternative Homology data model(s)
    • FriendlyMine functionality extended further to support Synteny based interlinking of
    InterMine instances
    • Araport and MedicagoGenome.org implement InterMine warehouses, ThaleMine
    and MedicMine, respectively.
    

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19. Acknowledgments
    • JCVI
    • Christopher D. Town (PI: Araport, LegFed)
    • Agnes P. Chan (co-PI: Araport, LegFed)
    • Cambridge
    • Sergio Contrino (Araport Software Dev)
    • Gos Micklem (co-PI: Araport)
    • Justin Clark-Casey
    • Julie Sullivan
    • NCGR
    • Samuel Hokin (LIS Lead Software Dev)
    • Andrew Farmer (co-PI: LegFed)
    • JGI Phytozome
    • Joe Carlson (Lead Software Dev)
    • InterMine and GMOD community
    

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20. Thank you!
    

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