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Ontomaton: NCBO BioPortal Ontology lookups in Google Spreadsheets produced by ISATeam at University of Oxford e-Research Centre (Eamonn Maguire, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra and Susanna Sansone) and NCBO (Trish Whetzel). The work was presented during ICBO 2013 in Montreal by Trish Whetzel (Thanks Trish!)
Citation preview
OntoMaton: a BioPortal-powered ontology widget for Google Spreadsheets.
Bioinformatics. 2013 Feb 15;29(4):525-7. doi: 10.1093/bioinformatics/bts718
ICBO 2013, Paper Highlight, Presented by Trish Whetzel
Eamonn Maguire, Alejandra González-Beltrán, Patricia L. Whetzel,
Susanna-Assunta Sansone and Philippe Rocca-Serra
Motivations• Geographically distributed collaborators• Spreadsheets used to collect data• Potential for conflicting versions• Need to maintain provenance• Need to provide ontology look-ups• Need for collaborative editing
ISAcreator: Ontology Lookup and Term Selection
ISAcreator: Ontology markup via NCBO Annotator
Curation of datasets imported or converted from other formats
Motivations• Geographically distributed collaboratorsü Spreadsheets used to collect data• Potential for conflicting versions• Need to maintain provenanceü Need to provide ontology look-ups• Need for collaborative editing
a BioPortal-powered ontology widget for Google Spreadsheets
OntoMaton: Leverages Google Spreadsheets
Collaborative editingProvenance trackingVersion control
OntoMaton: Searching
OntoMaton: Searching
OntoMaton: Tagging
h"p://rest.bioon
tology.org
Ontology Services
• Search• Traverse• Comment• Download
Widgets• Tree-‐view• Auto-‐complete• Graph-‐view
AnnotaCon
Data Access
Mapping Services
• Create• Upload• Download
Term recogniCon
Search “data” annotated with a given term
NCBO Web services
h"p://rest.bioon
tology.org
Ontology Services
• Search• Traverse• Comment• Download
Widgets• Tree-‐view• Auto-‐complete• Graph-‐view
AnnotaCon
Data Access
Mapping Services
• Create• Upload• Download
Term recogniCon
Search “data” annotated with a given term
NCBO Web services
h"p://rest.bioon
tology.org
Ontology Services
• Search• Traverse• Comment• Download
Widgets• Tree-‐view• Auto-‐complete• Graph-‐view
AnnotaCon
Data Access
Mapping Services
• Create• Upload• Download
Term recogniCon
Search “data” annotated with a given term
NCBO Web services
OntoMaton: Installation
OntoMaton: Installation
OntoMaton: Installation
OntoMaton: Installation
OntoMaton: Installation
OntoMaton: Installation
OntoMaton: Settings
OntoMaton: Settings
OntoMaton: Settings
OntoMaton: Settings
OntoMaton: Settings
Applications
Application I: Collaborative ISA
Application II: Mapping
Application III: QTTpattern based ontology building / expansion
User Community
A growing ecosystem of over 30 public and internal resources using the ISA metadata tracking framework
to facilitate standards-‐compliant collec@on, cura@on, management and reuse of inves@ga@ons in an increasingly diverse set of life science domains.
Towards interoperable bioscience dataSansone et al, 2012Nature Gene@cs
Source Code & Documentation
https://github.com/ISA-tools/OntoMaton
OntoMaton: a BioPortal poweredOntology widget for Google SpreadsheetsMaguire et al, 2013Bioinformatics
Thank you!
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