Xianfeng Jeff Chen Ph.D. Research Investigator/Project Manager Overview and Implementation Overview and Implementation Strategy of the NIAID-Funded Bio- Strategy of the NIAID-Funded Bio- defense defense Proteomics Database System Proteomics Database System
34
Embed
Xianfeng Jeff Chen Ph.D . Research Investigator/Project Manager
Overview and Implementation Strategy of the NIAID-Funded Bio-defense Proteomics Database System. Xianfeng Jeff Chen Ph.D . Research Investigator/Project Manager. (1) Introduction. Agenda Today. VBI responsibility in Admin Center PRCs datatype and organism - PowerPoint PPT Presentation
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Xianfeng Jeff Chen Ph.D.
Research Investigator/Project Manager
Overview and Implementation Strategy of Overview and Implementation Strategy of the NIAID-Funded Bio-defense the NIAID-Funded Bio-defense Proteomics Database SystemProteomics Database System
• VBI responsibility in Admin Center
• PRCs datatype and organism
• Proteomics data submission and storage work flow
• VBI computing system architecture (CPU and storage)
• VBI database system prototype and functionality
• VBI existing database schema and status
• Example Y2H schema for design logics and case study
• Proposed data integration and knowledgebase construction
Agenda TodayAgenda Today
(1) Introduction
(2) Database Development
(3) Strategy on Knowledgebase Development
IntroductionIntroduction
Proteomics Data ManagementProteomics Data Management
(processed data)
Tasks of Proteomics Data Management
RAWDATA
Data Storage& Visualization
Tools(VBI)
Analysis,Annotation,& Curation
(GU)
DataQA/QC,
Interoperability (VBI/GU)
SOP, LIMS, & Adm DB
(SSS)
University of Michigan Microarray and mass spectrometry
Caprion Mass spectrometry
Harvard Proteomics Institute Genomics and protein expression array
Albert Einsten College of Medicine Mass spectrometry
PNNL Mass spectrometry
Scripps NMR structural and X-ray crystal diffraction data
Myriad Genetics Yeast two-hybrid system
PRCs Major Data TypePRCs Major Data Type
Organization Major Data Type
PRCs OrganismsPRCs Organisms
Einstein Toxoplasma gondii, Cryptosporidium parvum
Production Website InstanceProduction Website Instance
Functionalities:Functionalities:
Search By Experiment
•Select Experiment•Retrieve list of Bait protein and nucleotide, Prey protein & nucleotide•Links to details of bait and Prey example: Drosophila melanogaster
Conclusion and Hypothesis (Processed and Analyzed Data)
Generic Experiment Data Components-------Example of Database Design Logics
People
Experiment
Project
Sample
ResultsConclusion HypothesisDNA /Protein
Detail
Y2H Data Component Modeling
Experiment
Experiment Design
Experiment Factor
Factor Value
Design Description
Ontology Entry
Ontology entries are taking care of the annotation cases1) There are diverse choices and there exist ontologies that can better capture the information 2) What are essentially controlled vocabularies which are limited in number of choices but might grow in the future or vary by technology type
Experiment Component Object Model
Y2H Partial Database Schema
Proteomics DB System Architecture
Public File Server
Private File ServerOracle Relational Database
JDBC,
Perl DBI/DBD,
ODBC
Batch Processing
(1) Data uploading;
(2) Data validation;
(3) Data analysis;
(4) Data processing
JSP, CGI,
Java
Perl,
Java
Virtual Database/ Warehouse
Application Layer
Web Display and Data Visualization
System Architecture of Putative VBI Proteomics KnowledgebaseSystem Architecture of Putative VBI Proteomics Knowledgebase
Security
Security
Security
Security
Temporary data
Service-Oriented MiddleWare with Process Control
Array Express Mass Spectrometry Two Component System 2D Gel Structure Data Genomics Data
------- Data, Tool, Project, and Team Interoperability------- Data, Tool, Project, and Team Interoperability
Strategy on Data Integration and
Construction of Knowledge Warehouse
Biological Information WorkflowBiological Information Workflow
Information Storage, Queries & DB Management
Cleaning, Processing Algorithms
Curation and Annotation of Data
Knowledge Generation
Biological Research
Target Discovery
Diagnostics, Therapeutics &
Vaccines
Data Management Knowledge Management
Bio-IT Scope Data IntegrationKnowledge generationKnowledge managementKnowledge presentation
Phase I Phase II Phase III
First 2 years 3rd-4th years 5th year
•Raw data management•Schema development•Data visualization•Data standardization
•Integration at interface level•Integration of data at DB level•Interoperability of datasets•Normalization and warehousing