The Big Picture: The Industrial Revolutiona talk in berlin, 2008, about industrialising...
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Transcript of The Big Picture: The Industrial Revolutiona talk in berlin, 2008, about industrialising...
The Big Picture: The Industrial Revolution
Robert [email protected] University of Manchester, UK
Industrialisation
• Biology has industrialised data production
• Beginning to industrialise data analysis
• Need to automate experimentation
• Need to join them all together
Data Integration
• Data integration is possible
• We know how to do it (technically)
• We know how to do plumbing
• What is left is a social issue
Classic and Modern Biology
Genotype Phenotype
Modern biology
Classic biology
Semantic Knowledge Base
Experimentation,Data generation
Consistency checkingQuerying
Automated reasoning
Hypothesis formulationExperimental design
Information extraction,Knowledge formalization
Semantic Systems
Biology Cycle
What’s in a Lab?
• People
• Equipment, reagents, etc.
• Protocols
• Policy, governance
• All there to facilitate and manage investigation
What’s in an e-Lab?People
Data Process
Investigation
Data: BioGateway
• Uses Virtuoso Open Server– Open Source software that can host a triple store
– Can build this from RDF files
– Has a DB backend
• Supports SPARQL* language which allows querying RDF data (graphs)
• Its syntax is similar to that of SQL.
*http://www.w3.org/TR/rdf-sparql-query/
http://www.openlinksw.com/virtuoso/
BioGateWay Resources
Uniprot/SWISS-PROT OBO GOA CCONCBI Taxonomy RO
RDF
Data as Input: Asking Questions
• Cancer: what candidate genes are involved in cell cycle control, S-phase to G2 transition, DNA damage response and skin cancer?
• Gastrin: what genes correlate with cancer and the use of anti-acids, and are involved in the gastrin response, and are associated with cell cycle control?
• Inflammation: give me genes that are mentioned in the context of high carbohydrate intake and play a role in (process #1 to be named) and are within x steps from a GO ontology term related to inflammation
Processes: Genotype to Pathway
Created by Paul Fisher
Pathway to Phenotype
Created by Paul Fisher
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Processes: Finding and Curating Services
Processes: Finding and Curating Services
http://www.biocatalogue.org
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Finding, curating and reusing workflows
Data & Processes: Hypotheses
• Run workflow
• Make new data to put in repository
• Also generate hypotheses
• Generate plan from hypothesis
• Execute plan and make more data
• Automated?
The Robot Scientist
myExperiment
Big PicturePeople
Workflows
BioGateWayRobot ScientistKnowledge
BioCatalogue