Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

Ontomaton icbo2013-alternative order-t_wv3

9,447 views

Published on

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!)

Published in: Technology, Education
  • Be the first to comment

  • Be the first to like this

Ontomaton icbo2013-alternative order-t_wv3

  1. 1. 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
  2. 2. 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
  3. 3. ISAcreator: Ontology Lookup and Term Selection
  4. 4. ISAcreator: Ontology markup via NCBO Annotator Curation of datasets imported or converted from other formats
  5. 5. Motivations • Geographically distributed collaborators ü Spreadsheets used to collect data • Potential for conflicting versions • Need to maintain provenance ü Need to provide ontology look-ups • Need for collaborative editing
  6. 6. a BioPortal-powered ontology widget for Google Spreadsheets
  7. 7. OntoMaton: Leverages Google Spreadsheets Collaborative editingProvenance trackingVersion control
  8. 8. OntoMaton: Searching
  9. 9. OntoMaton: Searching
  10. 10. OntoMaton:Tagging
  11. 11. h"p://rest.bioontology.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
  12. 12. h"p://rest.bioontology.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
  13. 13. h"p://rest.bioontology.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
  14. 14. OntoMaton: Installation
  15. 15. OntoMaton: Installation
  16. 16. OntoMaton: Installation
  17. 17. OntoMaton: Installation
  18. 18. OntoMaton: Installation
  19. 19. OntoMaton: Installation
  20. 20. OntoMaton: Settings
  21. 21. OntoMaton: Settings
  22. 22. OntoMaton: Settings
  23. 23. OntoMaton: Settings
  24. 24. OntoMaton: Settings
  25. 25. Applications
  26. 26. Application I: Collaborative ISA
  27. 27. Application II: Mapping
  28. 28. Application III: QTT pattern based ontology building / expansion
  29. 29. User Community
  30. 30. 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  data Sansone  et  al,  2012 Nature  Gene@cs
  31. 31. Source Code & Documentation
  32. 32. https://github.com/ISA-tools/OntoMaton
  33. 33. OntoMaton: a BioPortal powered Ontology widget for Google Spreadsheets Maguire et al, 2013 Bioinformatics Thank you!

×