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Tripal within the Arabidopsis Information Portal - PAG XXIII

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araport.org @araport Tripal within the Arabidopsis Information Portal Vivek Krishnakumar J. Craig Venter Institute 12/11/2015 Tripal Database Network and Initiatives PAG XXIII, San Diego, CA
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Page 1: Tripal within the Arabidopsis Information Portal - PAG XXIII

araport.org@araport

Tripal within the Arabidopsis Information Portal

Vivek Krishnakumar J. Craig Venter Institute

12/11/2015

Tripal Database Network and Initiatives PAG XXIII, San Diego, CA

Page 2: Tripal within the Arabidopsis Information Portal - PAG XXIII

araport.org@araport

Overview

•  About Araport •  Current architecture •  Planned implementation – Leverage Chado schema – Accommodate inherited data – Serve as point of integration – Facilitate data sharing via web services

Page 3: Tripal within the Arabidopsis Information Portal - PAG XXIII

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About Araport

•  Objectives – Develop community web interface

•  sustainable, fundable and community-extensible •  hosts analysis modules, visualization tools, user data

spaces –  Practice data federation

•  integrate diverse data sets from distributed sources •  consume and expose data via RESTful web services

– Maintain “gold standard” Col-0 annotation •  assemble tissue-specific transcripts from publicly available

RNA-seq datasets •  incorporate novel coding and non-coding genes

Page 4: Tripal within the Arabidopsis Information Portal - PAG XXIII

araport.org@araport

Araport https://www.araport.org •  Explore data

•  ThaleMine •  JBrowse •  Science Apps

•  Search data •  Quick Search •  BLAST •  Raw data downloads

•  Community •  News & Events •  Ask a question •  Job Postings •  Useful Links

Page 5: Tripal within the Arabidopsis Information Portal - PAG XXIII

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Araport Architecture External programs Portal (www.araport.org)

API (api.araport.org)

Agave Core meta data

user profile ADAMA

service manage

service enroll

a b c d e f

CGI

Computing

Storage

Databases

ThaleMine JBrowse

Authentication, metering, logging, versioning, HTTPS, CORS

a b c d e f

Apps

Jobs

Systems

CGI

InterMine

Others

Tripal

SOAP

CGI

REST

Science Apps

Page 6: Tripal within the Arabidopsis Information Portal - PAG XXIII

araport.org@araport

Current implementation

Araport data mart

Combination of flat-files and databases •  TAIR datasets •  Ontologies (GO, PSI) •  Interactions (BAR) •  Orthologs (Panther)

Data Mart •  InterMine schema, PostgreSQL DB •  Indexed and flattened for speed •  Rebuilt periodically

Outputs •  ThaleMine WebApp •  ThaleMine web services

publish

Araport warehouse

Web services

InterMine loader live calls to… •  UniProt web services •  PubMed web services

publish

Page 7: Tripal within the Arabidopsis Information Portal - PAG XXIII

araport.org@araport

Planned implementation

Araport warehouse Araport data mart

Warehouse •  Chado schema, PostgreSQL DB •  General purpose but slow •  Permanent host for core genomic

datasets (assembly, annotation, metadata, etc.)

Inputs •  Genome annotation pipeline •  Community curation data

Outputs •  ThaleMine WebApp •  ThaleMine web services

publish

Data Mart •  InterMine schema, PostgreSQL DB •  Indexed and flattened for speed •  Rebuilt periodically

Page 8: Tripal within the Arabidopsis Information Portal - PAG XXIII

araport.org@araport

•  Functions as our low-level (core) Araport data warehouse –  Preserve legacy datasets with appropriate attributions –  Track any new datasets generated (annotation updates,

community contributions) –  Serve as point of integration and de-duplication of

certain data types –  Integrate with planned community curation interface

•  Supports our pursuit of being open-source (and future-proof)

http://gmod.org/wiki/Chado

Page 9: Tripal within the Arabidopsis Information Portal - PAG XXIII

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•  Drupal CMS based modularized framework, exposing a user-friendly interface to Chado – provides standardized loaders for genomic

datasets (FASTA, GFF3, GenBank, BLAST, GO, InterProScan, KEGG) – supports building custom templates and

materialized views – exposes well documented API

http://tripal.info

Page 10: Tripal within the Arabidopsis Information Portal - PAG XXIII

araport.org@araport

Integrate data inherited from TAIR

•  Currently a combination of flat-files and TAIR’s Oracle database –  Genome Assembly (TAIR9) –  Genome Annotation (TAIR10): genes, pseudogenes, transposons,

ncRNAs –  Annotation properties: gene symbols, confidence ranking, functional

descriptions, curator summary –  GO Annotations (TAIR curated data at geneontology.org) –  Publications (curated gene à publication relationships) –  Variation data: Genetic markers, Polymorphisms (SNPs, TILLing) and T-

DNA Insertions –  Stock data (lines, clones, germplasm)

•  Chado backed Tripal will serve as the core repository for this data

Page 11: Tripal within the Arabidopsis Information Portal - PAG XXIII

araport.org@araport

Integrate with planned Community Curation Interface

Page 12: Tripal within the Arabidopsis Information Portal - PAG XXIII

araport.org@araport

Integrate publication data

•  Existing sources for publication data –  TAIR locus to PubMed ID mapping – NCBI gene2pubmed mapping – UniProt curated Protein to PubMed ID mapping –  Publications missing PMIDs and/or DOIs

•  Chado will act as point of integration – Combine and de-duplicate publication data from 3

sources (more in the future) – Collect and store metadata for publications with and

without PMID and/or DOIs

Page 13: Tripal within the Arabidopsis Information Portal - PAG XXIII

araport.org@araport

Integrate Stock data

•  TAIR stock related tables mapped to corresponding Chado counterpart

•  Custom loaders developed to perform bulk update of Stock information, Phenotypes, Polymorphism data and mappings to AGI locus

Page 14: Tripal within the Arabidopsis Information Portal - PAG XXIII

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Role of Tripal within Araport

•  Tripal is under active development, with plans in place to begin developing rational web services (WS) as well as support interoperability

•  Araport plans to be involved in this working group to satisfy the following needs of our project: –  Expose live data from future annotation update

pipelines to the community directly via WS –  Expose stock data via WS in a standardized manner

to Arabidopsis stock centers (both ABRC and NASC) to aid data synchronization

–  Embrace and support other open-source initiatives

Page 15: Tripal within the Arabidopsis Information Portal - PAG XXIII

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Araport on GitHub

•  GitHub organization: https://www.github.com/Arabidopsis-Information-Portal

•  Relevant repositories: –  tair-chado-batchflow –  chado_pub_loader –  pasa-chado-hook –  GMOD/Apollo (fork)

Page 16: Tripal within the Arabidopsis Information Portal - PAG XXIII

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Acknowledgements

•  JCVI Developers – Maria Kim –  Irina Belyaeva – Svetlana Karamycheva

•  Tripal co-PI Stephen Ficklin and development community

•  TAIR/Phoenix Bio: assistance with data migration

•  Funding Agencies

Page 17: Tripal within the Arabidopsis Information Portal - PAG XXIII

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Chris Town, PI

Lisa McDonald Education and Outreach Coordinator

Chris Nelson Project Manager

Jason Miller, Co-PI JCVI Technical Lead

Erik Ferlanti Software Engineer

Vivek Krishnakumar Bioinf. Engineer

Svetlana Karamycheva Bioinf Engineer

Eva Huala Project lead, TAIR

Bob Muller Technical lead, TAIR Gos Micklem,

co-PI

Sergio Contrino Software Engineer

Matt Vaughn co-PI Steve Mock

Advanced Computing Interfaces

Rion Dooley, Web and Cloud Services

Matt Hanlon, Web and Mobile Applications

Maria Kim Bioinf Engineer

Ben Rosen Bioinf Analyst

Joe Stubbs, API Developer Platform

Walter Moreira API Developer Federation

Chris Jordan Database Manager

Eleanor Pence Intern

Chia-Yi Cheng Bioinf Analyst

Seth Schobel Bioinf. Engineer

Araport Team

Irina Belyaeva Software Engineer

Page 18: Tripal within the Arabidopsis Information Portal - PAG XXIII

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THANK YOU!

Page 19: Tripal within the Arabidopsis Information Portal - PAG XXIII

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Araport @ PAG XXIII Session Details Topic(s) Presenter(s)

Tripal Database Network and Initiatives

Sunday, January 11, 2015 5:30 PM-5:45 PM

California

W876: Tripal within the Arabidopsis Information Portal Vivek Krishnakumar

Arabidopsis Information Portal & IAIC Workshop Monday, January 12, 2015

12:50 PM-3:00 PM Pacific Salon 6-7 (2nd Floor)

W059: Walkthrough the Araport Web Site W061: Exposing Web Services for Araport W062: Developing applications for Araport

Chia-Yi Cheng Jason Miller Matt Vaughn

Computer Demo 2 Tuesday, January 13, 2015

12:30 PM California

C23: Using the Arabidopsis Information Portal Jason Miller

GMOD Wednesday, January 14, 2015

11:30 AM Golden West

W410: JBrowse within the Arabidopsis Information Portal Vivek Krishnakumar

Poster Session – Even Monday, January 12, 2015

10:00 AM-11:30 AM Grand Exhibit Hall

P0790: Data Integration for the Plant Research Community: Araport P0792: Developing Content for the Arabidopsis Information Portal

Chia-Yi Cheng Matt Vaughn


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