Wheat Data InteroperabilityEsther DZALE YEUMO KABORE

Richard FULSS

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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.

Wheat Data Interoperability

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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.

Wheat Data Interoperability

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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.

Survey on Wheat standards

5Survey results – The respondents (1)

6Survey results – The respondents (2)

7Survey results – Data storage practices

114 of the196 respondents currently store their data on local drives; 84 are willing to use shared databases and repositories.

8Survey results – Important data types

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.

9Survey results – data formats (1)

10Survey results – Ontologies

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

11Survey results – Metadata standards

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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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

How do we move on (1)

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Prototype and Library of lnked open vocabularies: We need volunteers with expertise in

Software developing Linked data Metadata and vocabularies

Web site: Wheatdata.org?

How do we move on (2)