Difference between revisions of "Data storage and AmiGO2 Working Group"
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===3.2 Planteome Data Warehouse Development=== | ===3.2 Planteome Data Warehouse Development=== | ||
| − | * Novel data warehouse for storing both the ontologies and annotation data based on [http://nosql-database.org/ NoSQL] | + | * Novel data warehouse for storing both the ontologies and annotation data based on [http://nosql-database.org/ NoSQL] (e.g. MongoDB, http://www.mongodb.org, and Apache™ Hadoop®, http://hadoop.apache.org) |
* Integrate the MapReduce algorithm to increase scalability and performance | * Integrate the MapReduce algorithm to increase scalability and performance | ||
* Investigate using HDF ([http://en.wikipedia.org/wiki/Hierarchical_Data_Format Hierarchical Data Format]), as a storage format for any numerical or sequence-based data. | * Investigate using HDF ([http://en.wikipedia.org/wiki/Hierarchical_Data_Format Hierarchical Data Format]), as a storage format for any numerical or sequence-based data. | ||
Revision as of 11:48, 11 April 2015
Goals and Objectives:
Aim-3: Develop an online informatics portal and data warehouse for ontology-based, annotated plant genome data and plant genomes.
3.1 Planteome Web Portal Development
- Drupal portal will host the AmiGO browser, the ontology database developed by the PO and the GO consortium, 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.
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 Media:Data_Storage_2-18-15.mp4
- Who: JE, JP, EZ
- Further discussion of AmiGO2 progress and overview of AmiGO2 interface
Relevant links:
https://github.com/geneontology/amigo
Demo: http://amigo.geneontology.org/
http://amigo2.berkeleybop.org/ - dev server
