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Sansone bio sharing introduction

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Susanna Sansone's introduction on Biosharing.

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Susanna-Assunta Sansone, PhD Team Leader, University of Oxford, UK (Updated version of presentation given at) Biocuration, 11 th -14 th October 2010, Tokyo, Japan BioSharing: on Data Policies’s Plans and Reporting Standards  
Information intensive research investigations The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project ,[object Object],[object Object]
Comprehensible, reusable, reproducible research The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project ,[object Object]
The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project ,[object Object],[object Object],[object Object],[object Object],Reporting standards as enablers
Strong advocators The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project ,[object Object],[object Object],[object Object]
...funders are developing data policies... ,[object Object]
....similar trend in the regulatory arena ,[object Object]
....and commercial sector ,[object Object],[object Object]
Escalating number of efforts (omics domain), e.g.
Navigating a sea of ‘standards’
I work on plants, are these just for biomedical applications? Which one are mature enough for me to use or recommend? How can I get involved to propose extensions or modifications? Which tools and databases implement which one? Which one are widely accepted and recognized? What are the criteria to evaluate status and value? ...?.... ...?.... ....?... ...?.... ....?... ...?.... I use HT sequencing technologies, which one are applicable to me? Navigating a sea of ‘standards’ Which tools and databases implement which one? I use HT sequencing technologies, which one are applicable to me?
HT sequencing: public databases and ‘standards’ EBI NCBI ENA SRA
HT sequencing: public databases and ‘standards’ EBI NCBI ENA SRA ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],INSDC feature table
(2008) Vol 26 No 8 http://mibbi.org
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Linking checklists to terminologies http://www.ebi.ac.uk/ontology-lookup/ http://bioportal.bioontology.org/ http://www.obofoundry.org/
Science (2009), Vol 326, 234-236 http://biosharing.org
[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object]
[object Object],[object Object]
‘ Social engineering’ http://biosharing.org
[object Object],[object Object],[object Object],[object Object],[object Object],http://biosharing.org
 
 
 
The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project Launch of prototype in December Iterative development, also based on feedback (enrichment, enhancement and links to other existing/new resources)

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Sansone bio sharing introduction

  • 1. Susanna-Assunta Sansone, PhD Team Leader, University of Oxford, UK (Updated version of presentation given at) Biocuration, 11 th -14 th October 2010, Tokyo, Japan BioSharing: on Data Policies’s Plans and Reporting Standards  
  • 2.
  • 3.
  • 4.
  • 5.
  • 6.
  • 7.
  • 8.
  • 9. Escalating number of efforts (omics domain), e.g.
  • 10. Navigating a sea of ‘standards’
  • 11. I work on plants, are these just for biomedical applications? Which one are mature enough for me to use or recommend? How can I get involved to propose extensions or modifications? Which tools and databases implement which one? Which one are widely accepted and recognized? What are the criteria to evaluate status and value? ...?.... ...?.... ....?... ...?.... ....?... ...?.... I use HT sequencing technologies, which one are applicable to me? Navigating a sea of ‘standards’ Which tools and databases implement which one? I use HT sequencing technologies, which one are applicable to me?
  • 12. HT sequencing: public databases and ‘standards’ EBI NCBI ENA SRA
  • 13.
  • 14. (2008) Vol 26 No 8 http://mibbi.org
  • 15.
  • 16. Linking checklists to terminologies http://www.ebi.ac.uk/ontology-lookup/ http://bioportal.bioontology.org/ http://www.obofoundry.org/
  • 17. Science (2009), Vol 326, 234-236 http://biosharing.org
  • 18.
  • 19.
  • 20.
  • 21. ‘ Social engineering’ http://biosharing.org
  • 22.
  • 23.  
  • 24.  
  • 25.  
  • 26. The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
  • 27. The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
  • 28. The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
  • 29. The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project Launch of prototype in December Iterative development, also based on feedback (enrichment, enhancement and links to other existing/new resources)