Plant Data Hackathon



Motivation and Scope
During the Barcelona all hands meeting we have committed to prepare a procedure and example on how to use Google Spreadsheets to record and standardise data in WP7.
Our idea is to guide the ateendees in the procedure that we have devised, and enable them to work on their data using a tool (OntoMaton) to facilitate searching for terms in Bioportal Ontologies.
The procedure attempts to provide standardisation to both column names and the data within their rows. This should facilitate the access to ISA-tools and to publishing standardised data sets in repositories.

Organizing Team

  • Inês Chaves - iBET
  • Bruno Costa - iBET
  • Pedro Fernandes - IGC
  • Daniel Faria - IGC
  • João Cardoso - INESC-ID

Agenda

  • 11:00h - Session 1 - Plant Metadata Annotation
    • Presentation of the methodology and results of the metadata annotation effort - Faria and/or Inês and/or Bruno
    • Discussion of the limitations of the methodology and data format, and of potential alternatives
  • 12:30h - Lunch Break
  • 13:30h - Session 2 - Plant Data Revision & Annotation
    • Who (institutions, groups, researchers) has phenotypic data about woody plants in Portugal (particularly Cork Oak and/or Maritime Pine)? What type of data do they have? - Célia
    • Revision of iBET datasets (microarrays and RNA-seq) - Célia and/or Inês
    • Revision of CorkOak database - Sobral
    • Revision of Casuarina phenotypic data from Ana Ribeiro (as a use case for phenotypic data) - Faria and/or Sobral
    • Discussion of dataset annotation solutions (namely ISA-Tools)
  • 15:30h - ELIXIR-EXCELERATE Regular Meeting Part I: Node Planning and Discussion
    • ELIXIR-PT Services: Data Management Plans; Ethical, Legal and Social Implications; Data Annotation and Integration; Data Quality; ...
    • ELIXIR-PT Resources: Dataset hosting? Computing?
    • Outreach: Engaging the life scientists
  • 16:15h - Coffee Break
  • 16:30h - ELIXIR-EXCELERATE Regular Meeting Part II: EXCELERATE progress
    • Progress report by WP
  • 17:00-17:20h - End of Workshop
Start date: 
2016-03-03
End date: 
2016-03-03
Location: 
INESC-ID
Rua Alves Redol, 9
1000-029 Lisboa
Portugal
PT
Name: 
João Cardoso
Host organization: 
Event type: 
Workshops and courses
Topic: