This document discusses the work of the Wheat Data Interoperability Working Group. The working group aims to provide a common framework for describing, representing, linking and publishing wheat data using open standards. It will initially focus on several key data types. The working group's deliverables include a report on existing resources, a cookbook with guidelines for data managers, a library of linked vocabularies and ontologies, and a prototype for integrating and publishing linked wheat data. A survey of 196 wheat researchers found that over half have no data management guidelines. Key data types identified were phenotypes, SNPs, genomic annotations, germplasm, genetic maps and physical maps. The document outlines next steps including a workshop to provide guidance and discuss standards and use

1. Wheat Data Interoperability
Esther DZALE YEUMO KABORE
Richard FULSS

2. 2
Wheat Data Interoperability
 Working Group Focus:
 The WG aims to provide a common framework for describing,
representing linking and publishing Wheat data with respect to open
standards.
 The WG will focus first on the following data types: SNP, Genomic
annotations, Phenotypes, Genetic Maps, Physical Maps, Germplasm,
expression data.

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Wheat Data Interoperability
 Working Group Deliverables:
 A report on the existing resources (vocabularies, ontologies, data formats,
metadata standards). Started
 A cookbook intended for the Wheat data managers community: guidelines on
metadata, vocabularies and ontologies plus a decision tree based on data and
metadata description recommendations and file format recommendations.
Started
 Library of linked vocabularies and ontologies in the with respect to the Linked
Data standards
 A prototype. The goal of the prototype is to propose a ready to use and
streamlined framework for:
 integration of heterogeneous Wheat Data,
 publishing Wheat Linked Data that facilitate the reuse of the mashed up data by
programs and Humans.

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Survey on Wheat standards
 Survey on Wheat standards:
 from April 7 to June 3, 2014
 replies from 196 individuals in at least 31 different countries
 More than 50% of the respondents have not yet established data
management guidelines.

5. Survey results – The respondents (1) 5

6. Survey results – The respondents (2) 6

7. Survey results – Data storage practices 7
114 of the196 respondents currently store their data on local drives; 84 are willing to use shared databases and
repositories.

8. Survey results – Important data types 8
Phenotypes, SNPs, genomic annotations,
germplasm, genetic maps, and physical maps were
listed as the most important data types over the
next five years. Only 24 of the 196 respondents
mentioned other data types.

9. Survey results – data formats (1) 9

10. Survey results – Ontologies 10
Why not ?
•Lack of knowledge (don’t know, too difficult, etc.)
•Lack of trust (lots of talk about their development, but little/no
implementation, no agreement, standards, incomplete)
•Lack of interest (not useful)
•In progress.
•No need/required/relevant
•Too complicated
•Not available
Other ontologies mentioned are:
•ECPGR
•Ontologies to develop conceptual ABM
•PATO, XEML
•Plant Environmental conditions ontology
•plant pathogens:: http://www.pathoplant.de/; PLEXdb;
•QUDT

11. Survey results – Metadata standards 11
Why not ?
•Not applicable
•Not known (majority)
•No need
•Just started
•Lots of talk about their development, but little/no implementation.
•No capacity.
•No existing metadata standard for phenotyping data
•Too complex
•Not a priority
Other metadata standards and tools are:
•AgMIP
•AgMIP/ICASA
•FCDC
•ICASA
•Phenotypic metadata standards developed in Genesys
•PODD science ontology

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How do we move on (1)
 Workshop (1-2 October in Versailles):
 Objectives: provide guidance to the Wheat Data Interoperability Working
Group on
 which priorities should be given to data types with non standardized data formats
(according to the Survey)
 what existing use cases can be used for showcasing the gain of interoperability that
linked data can bring
 discuss and adjust the draft of the cookbook
 prepare a "White Paper" to publicize and communicate the recommended
guidelines
 Expected outcomes:
 List of recommended standards for each data type
 List of standards to develop
 List of interoperability use cases
 Cookbook revised and adjusted
 Draft “White Paper” for publicizing and communicating the recommended
guidelines

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How do we move on (2)
 Prototype and Library of lnked open vocabularies:
 We need volunteers with expertise in
 Software developing
 Linked data
 Metadata and vocabularies
 Web site:
 Wheatdata.org?