Difference between revisions of "Data storage and AmiGO2 Working Group"

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* Zhang Lab (OSU, EECS):'' Eugene Zhang (Co-PI), Botong Qu (CS Ph.D. student)
 
* Zhang Lab (OSU, EECS):'' Eugene Zhang (Co-PI), Botong Qu (CS Ph.D. student)
  
=Data storage and AmiGO 2 Working Group Meetings:=
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= Link to [[Data storage and AmiGO 2 Working Group Meetings]]=
==Data storage and AmiGO 2 call 1-30-15==
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* Who: PJ, CM, Seth, EZ, LC, JP, JE
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* Discussion of the planned transition to the AmiGO 2.0 platform
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* JE is working on installing SolR database - View details and progress reports here: [[AmiGO2_install]]
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== Data Storage and AmiGO2 call 2-18-15==
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* Who: JE, JP, EZ
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* Link to video recording:  [[Media:Data_Storage_2-18-15.mp4]]
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* Link to audio recording: [[File:Data Storage Meeting audio only 2-18-15.m4a|thumbnail|Data_Storage_Meeting_audio_only_2-18-15.m4a]]
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* Further discussion of AmiGO2 progress and overview of AmiGO2 interface
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== Planteome Interface meeting 3-2-15==
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Who: EZ, LC, JE, PJ ...??
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* Link to video recording:  [[File:Planteome Interface mtg video 3-2-15.mp4|thumbnail|Planteome_Interface_mtg_video_3-2-15.mp4]]
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* Link to audio recording:  [[File:Planteome Interface mtg audio 3-2-15.m4a|thumbnail|Planteome Interface mtg audio 3-2-15.m4a]]
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* EZ: First thing: focus of the project, speed up queries, data visualization, data organization
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* User Interface: it would be good to see how the users operate and what kinds of questions they would ask.
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* Amigo 2, could build enhanced interface so users could inspect their data and build queries.
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* what functionalities are needed?
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* Questions:
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**How will the users access the interface?
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** How will they use the interface?
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===Involvement of other organisms? e.g. viruses, animals, etc===
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* Could the tools be expanded to other organisms
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* Crops are interacting with the environment, other organisms
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=== AmiGO2 introduction===
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* show filtered image
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* Cytoscape Sif file, ontology network
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* bring in other ontologies, Rice Xanthomanas example
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* ontology formats
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==Data storage and AmiGO2 Working Group Meeting 4-16-15==
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Who: EZ, BQ, PJ, JP, LC, JE
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* Link to video recording:  [[File:Data_storage_and_AmiGO2_video_4-16_15.mp4|thumbnail|Data_storage_and_AmiGO2_video_4-16_15.mp4]]
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* Link to audio recording:  [[File:Data storage and AmiGO2 audio 4-16 15.m4a|thumbnail|Data storage and AmiGO2 audio 4-16 15.m4a]]
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* Introductions
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* Storing code developed on Planteome project on Github
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* posting notes on wiki
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* data visualization aspect within AmiGO2- work with JE on
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* Data annotation- wikipedia style?
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* different levels of access
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* To do: Send link to Eugene and Botong- circulate the developer position ad
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==Relevant links:==
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* https://github.com/geneontology/amigo
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* Demo: http://amigo.geneontology.org/
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* http://amigo2.berkeleybop.org/ - dev server
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==May 1st meeting==
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===Demo of GO enrichment tool===
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*At the GO website (www.geneontology.org)
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*See how it  works there compared to the one at AGRIGO (http://bioinfo.cau.edu.cn/agriGO/analysis.php). See if your NIH proposal work with Yanmin Di overlaps and can be adopted.
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*Set of genes you can get a list of Arabidopsis thaliana genes from the attached file. (email)
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* Gene pages at Gramene e.g. http://archive.gramene.org/db/genes/search_gene?acc=GR:0101175 or elsewhere
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*Start thinking about building a gene database, with different access levels for admins and curators, limited in what fields are allowed to be edited by what level.
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This is for building the community gene annotation tools. The annotated data from this database can be synced with the AmiGOdb version that Justin Elser and Chris are working on.
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I hope this will give Bo, enough width to work until the AMIGO build and datasets mature.
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BinGO
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http://bioinformatics.oxfordjournals.org/content/21/16/3448.full
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AgriGO
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896167/
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Latest revision as of 12:04, 2 June 2015

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)

Link to Data storage and AmiGO 2 Working Group Meetings