文档介绍：BioMAS: A Multi-Agent System for Automated Genomic Annotation
Keith Decker
Department puter and Information Sciences University of Delaware
Salim Khan, Ravi Makkena, Gang puter & Information Sciences
Dr. Carl Schmidt, Heebal Kim
Animal & Food Sciences
Outline
General class of problems and MAS solution approach
BioMAS: Automated Genomic Annotation
HVDB: HerpesVirus Database
ChickDB: Gallus Gallus Database
GOFigure!
CoPrDom
Signal Transduction Pathway Discovery
What problems are we addressing?
Huge, dynamic “Primary Source” Databases
Highly distributed, overlapping
Heterogeneous content, structure, curation
Multitude of analysis algorithms
Different interfaces, output formats
Create contingent process plans chaining many analyses together
Individual PIs, working on non-anisms
Learn, then hand-navigate sea of DBs and analysis tools
Easily overwhelmed by new sequence and EST data
Struggle to make results available usefully to others
Approach: Multi-Agent Information Gathering
Software agents for information retrieval, filtering, integration, analysis, and display
Embody heterogeneous database technology (wrappers, mediators, …)
Deal with dynamic data and changing data sources
Efficient and robust putation (for both info retrieval and analysis)
Deal with issues of anization and ownership
Natural approach to providing integrated information
To humans via web
To other agents via semantic markup [XML/OIL/DAML]
Example: Multi-Agent System for Automated Herpesvirus Annotation
Input raw sequence data
Output: an annotated database that allows plex queries
BLAST homologs
Motifs
Protein domains [Prodomain records]
PSORT sub-cellular location predictions
GO [Gene Ontology] electronic annotation
“Show me all the genes in Marek’s Disease virus with a tyrosine phosphorylation motif and a transmembrane domain value ≥ 2”
How does this help?
Automates collection of information from various primary source databases
If the info changes, can be updated automatically. PI can