Data storage and AmiGO2 Working Group

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Goals and Objectives:

Aim-3: Develop an online informatics portal and data warehouse for ontology-based, annotated plant genome data and plant genomes.

  • Deliverables: A centralized portal for common reference ontologies for plants and the associated data sets. Novel data store and web user interface.

3.1 Planteome Web Portal Development

  • Drupal portal will host the AmiGO browser, the ontology database (similar to the one developed by the PO and the GO), and a BioMart
  • Transition to AmiGO 2.0 with new features

3.2 Planteome Data Warehouse Development

  • Novel data warehouse for storing both the ontologies and annotation data based on NoSQL (e.g. MongoDB, http://www.mongodb.org, and Apache™ Hadoop®, http://hadoop.apache.org)
  • Integrate the MapReduce algorithm to increase scalability and performance
  • Investigate using HDF (Hierarchical Data Format), as a storage format for any numerical or sequence-based data.
  • Create an efficient way to add annotations incrementally to the database, (not possible in the current AmiGO database)
  • Implementation of OLAP (Online Analytical Processing) data cubes (http://en.wikipedia.org/wiki/OLAP_cube)

3.3 Integration with the iPlant infrastructure

  • Initial design and testing will happen locally at the Center for Genome Research and Biocomputing at Oregon State University
  • Use of virtual machine (VM) images in the iPlant cloud computing environments
  • Utilization of high performance computing resources, such as:
    • The supercomputer 'Stampede' at Texas Advanced Computing Center (TACC)
    • Use of iRODS at iPlant for data file storage and retrieval
    • Image hosting via Bisque hosted on the iPlant infrastructure (See 3.4, below)
  • Interaction with resources such as CoGE, Bisque, and the Integrated Breeding Platform (IBP)

3.4 Library of Publicly-Accessible, Annotated Digital Images

  • Design a relational data schema to support the large-scale storage of annotated images (and their associated metadata)
  • Image library main goal: A training set for a new auto-segmentation and annotation active-learning algorithm
  • Support other visual analysis tools and the integration of image data with ontology data
  • Will also function as a home for community-contributed image data

3.5 Application Programming Interface (APIs)

  • Develop of publicly available APIs for both internal and external data access to ontology terms and annotations
  • Extend the existing lightweight web services providing Plant Ontology terms, synonyms, and definitions to the Planteoem APIs, including direct web service access to annotated data
  • Potential Users:
  • Integrate our data with other external APIs, For example:
    • EBI (the Gene Expression Atlas, Ensembl Plants, IntAct),
    • ERA-CAPS (genotype-to-phenotype data)
    • DOE KBase
    • GCP Integrated Breeding Platform
    • Agave on iPlant which provides web-focused developer access to the iPlant data store and other integration services, providing a direct link to high-performance computing systems such as the TACC.

Participants

  • Jaiswal Lab (OSU, BPP): Justin Elser
  • Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI), Seth Carbon
  • Zhang Lab (OSU, EECS): Eugene Zhang (Co-PI), Botong Qu (CS Ph.D. student)

Data storage and AmiGO 2 Working Group Meetings:

Data storage and AmiGO 2 call 1-30-15

  • Who: PJ, CM, Seth, EZ, LC, JP, JE
  • Discussion of the planned transition to the AmiGO 2.0 platform
  • JE is working on installing SolR database - View details and progress reports here: AmiGO2_install

Data Storage and AmiGO2 call 2-18-15


  • Further discussion of AmiGO2 progress and overview of AmiGO2 interface

Planteome Interface meeting 3-2-15

Who: EZ, LC, JE, PJ ...??

  • first thing:

Questions:

How will the users access the interface?

How will they use the interface?

Involvement of other organisms? e.g. viruses, animals, etc

AmiGO2 introduction

  • show filtered image
  • Cytoscape Sif file, ontology network
  • bring in other ontologies, Rice Xanthomanas example
  • ontology formats

Data storage and AmiGO2 Working Group Meeting 4-16-15

Who: EZ, BQ, PJ, JP, LC, JE

  • Introductions
  • Storing code developed on Planteome project on Github
  • posting notes on wiki
  • data visualization aspect within AmiGO2- work with JE on
  • Data annotation- wikipedia style?
  • different levels of access
  • To do: Send link to Eugene and Botong- circulate the developer position ad

Relevant links:

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