Transcript RightField Rich Annotation of Experimental

RightField
The Semantic Annotation of
Experimental Data using Spreadsheets,
Katy Wolstencroft, Stuart Owen, Matthew Horridge,
Olga Krebs, Wolfgang Mueller Carole Goble
RightField
A tool for embedding ranges of ontology terms
into spreadsheets to allow the users of those
spreadsheets to add semantic annotations from
simple drop-down lists
RightField
A tool for embedding ranges of ontology terms
into spreadsheets to allow the users of those
spreadsheets to add semantic annotations from
simple drop-down lists
Why?
 Makes annotation quicker and more efficient
 Standardises annotation
 Hides the ontology complexity from the users
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Managing Biological Data
Describe experiments and results of experiments
Minimal Information Models
Guidelines,
Checklists,
vocabularies
Necessary for publication, submission to
public databases and sharing
Managing Biological Data
Describe experiments and results of experiments
Minimal Information Models
Guidelines,
Checklists,
MIACA Minimal Information About a Cellular Assay
MIAME Minimum Information About a Microarray Experiment
MIAPE Minimum Information About a Proteomics Experiment
MIARE Minimum Information About a RNAi Experiment
MIASE Minimum Information About a Simulation Experiment
MIBBI >30
Managing Biological Data
Describe experiments and results of experiments
Ontologies and Vocabularies for
Annotation
Gene Ontology
ChEBI
MGED
SBO
BioPortal >270 biomedical ontologies
MIBBI Model
Data
Microarray
Ontologies
MIAME:Minimum
Information MGED
about a Microarray Experiment
Proteomics
MIAPE: Minimum Information PSI-MI, PSI-MS, PSI-MOD
about a Proteomics Experiment
Interaction
experiments
MIMIX:Minimum Information about PSI-MI
a Molecular Interaction Experiment Protein-Protein Interaction
Systems
Models
Biology MIRIAM:Minimal
Information SBO:
Systems
Required In the Annotation of Ontology
biochemical Models
Biology
Systems
Biology MIASE:Minimum
Information KISAO:Kinetic Simulation
Model Simulation
About a Simulation Experiment
Algorithm Ontology
SysMO: Systems Biology of MicroOrganisms
SysMO Consortium
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Pan-European consortium
> 100 research groups
> 320 scientists
Distributed, interdisciplinary
projects
Expected to pool data and
results and disseminate
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
Used in other consortia:
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Virtual Liver, EraSysBio+,
UNICELLSYS and more....
Associating Experiments
Investigation
Study
Assay
SOP
SOP
SOP
http://isatab.sourceforge.net/
Construction
Validation
Data Templates and Vocabularies
Metabolomics
SOP
Proteomics
Metabolomics
SOP
Mass
Spec
Fluxomics
Transcriptomics
SOP
Construction
Validation
Fitting in with Laboratory practices
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Scientists can continue to do what they have
always done
Embedding semantics into the tools already in
use
Excel, excel, excel.....
The End Result
Ontology terms for markedup cells in drop-down boxes
How it Works
Marked-up workbook
Saved in plain Excel
Excel Workbook
RightField Client
Ontology
“Portion” of ontology terms
Informaticians/ontologists
Terms Embedded into
Excel Workbook
End Users
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 User View
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
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
BioBanking in the Netherlands
Outside Biology
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Oil and Gas industry
Egyptology specimen classification
Using RightField Spreadsheets
Populate
Extract
RDF Graph
Store / Reuse
Future Developments
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Auto-complete
Validation of annotation
Populating ontology content - Populous
Populous
http://www.e-lico.eu/populous
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Generic tool for populating ontology templates
Supports validation at the point of data entry
Expressive Pattern language for OWL Ontology
generation
Helps biologists with ontology design patterns
Simon Jupp, Robert Stevens, University of Manchester
Availability
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Open source
http://www.rightfield.org.uk
Acknowledgements
Stuart Owen
Matthew Horridge
Katy Wolstencroft
Carole Goble
Wolfgang Mueller
Olga Krebs