Data storage and AmiGO2 Working Group: Difference between revisions
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=Goals and Objectives:= | =Goals and Objectives:= | ||
== Aim-3: Develop an online informatics portal and data warehouse for ontology-based, annotated plant genome data and plant genomes. | == 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=== | ===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 | * Drupal portal will host the AmiGO browser, the ontology database developed by the PO and the GO consortium, and a BioMart | ||
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* 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. | ||
* Create an efficient way to add annotations incrementally to the database, (not possible in the current AmiGO database) | * Create an efficient way to add annotations incrementally to the database, (not possible in the current AmiGO database) | ||
===3.3 Integration with the iPlant infrastructure === | |||
===3.4 Storage of Annotated Digital image collections=== | |||
===3.5 Application Programming Interface (APIs)=== | |||
=Participants= | =Participants= | ||
Revision as of 18:58, 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.
- 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 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.
- Create an efficient way to add annotations incrementally to the database, (not possible in the current AmiGO database)
3.3 Integration with the iPlant infrastructure
3.4 Storage of Annotated Digital image collections
3.5 Application Programming Interface (APIs)
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