Transcript RightField Rich Annotation of Experimental Biology through Stealth

RightField
Rich Annotation of Experimental
Biology through Stealth Using
Spreadsheets
Katy Wolstencroft, Stuart Owen, Matthew Horridge,
Olga Krebs, Wolfgang Mueller Carole Goble
RightField
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A tool for embedding ranges of ontology terms
into spreadsheets
Speeds up annotation
Makes annotation more efficient
Hides the ontology complexity from the users
Managing Biological Data
Describe experiments and results of experiments
Minimal Information Models
Guidelines,
Checklists,
Ontology terms
Minimum
Information
Models
CIMR Core Information for Metabolomics Reporting
MIABE Minimal Information About a Bioactive Entity
MIACA Minimal Information About a Cellular Assay
MIAME Minimum Information About a Microarray Experiment
MIAME/Env MIAME / Environmental transcriptomic experiment
MIAME/Nutr MIAME / Nutrigenomics
MIAME/Plant MIAME / Plant transcriptomics
MIAME/Tox MIAME / Toxicogenomics
MIAPA Minimum Information About a Phylogenetic Analysis
MIAPAR Minimum Information About a Protein Affinity Reagent
MIAPE Minimum Information About a Proteomics Experiment
MIARE Minimum Information About a RNAi Experiment
MIASE Minimum Information About a Simulation Experiment
MIENS Minimum Information about an ENvironmental Sequence
MIFlowCyt Minimum Information for a Flow Cytometry Experiment
MIGen Minimum Information about a Genotyping Experiment
MIGS Minimum Information about a Genome Sequence
MIMIx Minimum Information about a Molecular Interaction Experiment
MIMPP Minimal Information for Mouse Phenotyping Procedures
MINI Minimum Information about a Neuroscience Investigation
MINIMESS Minimal Metagenome Sequence Analysis Standard
MINSEQE Minimum Information about a high-throughput SeQuencing Experiment
MIPFE Minimal Information for Protein Functional Evaluation
MIQAS Minimal Information for QTLs and Association Studies
MIqPCR Minimum Information about a quantitative Polymerase Chain Reaction experiment
MIRIAM Minimal Information Required In the Annotation of biochemical Models
MISFISHIE Minimum Information Specification For In Situ Hybridization and Immunohistochemistry
Experiments
STRENDA Standards for Reporting Enzymology Data
TBC Tox Biology Checklist
BioPAX : Biological Pathways Exchange http://www.biopax.org/
FuGE Functional Genomics Experiment
MGED: Microarray Experimental Conditions
tp://www.mibbi.org/index.php/MIBBI_portal
MIBBI Model
Data
Microarray
Ontologies
MIAME:Minimum
MGED
Information about a
Microarray Experiment
Standards Body
Functional Genomics
Data Society
Proteomics
MIAPE:
Minimum PSI-MI, PSI-MS, PSI- Proteomics Standards
Information about a MOD
Initiative
Proteomics Experiment
Interaction
experiments
MIMIX:Minimum
PSI-MI
Information about a Protein-Protein
Molecular Interaction Interaction
Experiment
Systems
Biology
Models
MIRIAM:Minimal
SBO: Systems Biology BioModels.net
Information Required In Ontology
the
Annotation
of
biochemical Models
Proteomics Standards
Initiative
Systems
MIASE:Minimum
KISAO:Kinetic
BioModels.net
Biology Model Information About a Simulation
Algorithm
Simulation
Simulation Experiment Ontology
SysMO Project
SysMO Consortium
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Systems Biology of
MicroOrganisms
Pan-European consortium
> 100 research groups
> 320 scientists
Microbiologists, molecular
biologists, biochemists,
mathematicians....not many
informaticians
SysMO-DB
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SysMO-SEEK – a platform
for systems biology data
sharing
Web based environment for
sharing in the consortium
and disseminating to the
community
Experiments in SysMO
Investigation
Study
Assay
SOP
SOP
SOP
http://isatab.sourceforge.net/
Construction
Validation
Experiments in SysMO
Metabolomics
SOP
Proteomics
Metabolomics
SOP
Mass
Spec
Fluxomics
Transcriptomics
http://isatab.sourceforge.net/
SOP
Construction
Validation
Fitting in with Laboratory practices
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Excel, excel, excel.....
Embedding semantics into the tools already in
use
Scientists can continue to do what they have
always done
RightField
Excel Workbook
Terms Embedded into
Excel Workbook
Ontology
“Portion” of ontology terms
RightField Application
Loading Ontologies
Published ontologies
Multiple versions
You can also load local ontologies from file or URL
Loading Ontologies
Excel workbook loaded into
RightField with multiple
worksheets
Class hierarchies of
loaded ontologies
Selected parent term
from the ontology
Methods for specifying
ontology terms
Term lists for
selected cells
Excel workbook with
marked-up cells
Marking-up Columns or Rows
The End Result
Ontology terms for markedup cells in drop-down boxes
Ontology Information
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Ontologies encapsulated
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Scientists can work offline
Ensures same versions of ontologies used for a series
of experiments
No special macros or plugins required, just Excel or
Open Office
Versions and URIs captured in hidden
worksheets
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Provenance
Comparisons between sheets
Linking back to the vocabularies
Provenance
The human readable term
Term Label
label
The (unique) term
Term IRI
identifier
The ontology that defines the
Ontology IRI
term
Ontology Version The version of the ontology
The (web) location of the
Physical Location
ontology
RightField Technologies
Java
Platform Independent
OWL API
Loading ontologies and reasoning
Apache POI HSSF libraries
Loading and saving of Excel Spreadsheets
Ontology Languages
RDFS - RDF Schema
OWL - Web Ontology Language
OBO - Open Biomedical Ontologies
Current Work
Populate
Extract
RDF Graph
Store / Reuse
RightField in Use
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SysMO – Systems Biology of MicroOrganisms
E-Lico - a virtual laboratory for interdisciplinary
collaborative research in data mining and data-intensive
sciences. Case Studies in kidney research
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Populous extension to RightField for building ontologies from
simple spreadsheet like templates
Helps biologists with ontology design patterns
http://www.e-lico.eu/?q=populous
BioBanking in the Netherlands (Scott Marshall)
Oil and Gas industry
Egyptology specimen classification
Availability
Acknowledgements
Stuart Owen
Matthew Horridge
Katy Wolstencroft
Carole Goble
Wolfgang Mueller
Olga Krebs