Wheat Data Interoperability Guidelines

These recommendations have been prepared by members of the Wheat Data Interoperability Working Group (WG), one of the WGs of the Research Data Alliance and the only WG of the Agriculture Data Interoperability Interest Group. The group is coordinated by members of the Wheat Initiative, a global initiative that aims to reinforce synergies between bread and durum wheat national and international research programmes to increase food security, nutritional value and safety while taking into account societal demands for sustainable and resilient agricultural production systems.

This record is maintained by: ThomasLetellier

Record added: Dec. 26, 2017, 2:36 p.m..
Record updated: May 7, 2018, 11:30 a.m. by ThomasLetellier.

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Taxonomic range

Triticum aestivum

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Edits to 'https://fairsharing.org/bsg-c000042' by 'The FAIRsharing Team' at 11:05, 03 Jan 2018 (approved):

	'standards' has been modified:
		Before:
			Crop Ontology
			Variant Call Format
			Reference Sequence Annotation
			Generic Feature Format Version 3
			Minimum Information about Plant Phenotyping Experiment
			Investigation Study Assay Tabular
			Resource Description Framework
			Darwin Core
			FASTQ Sequence and Sequence Quality Format
			Binary Alignment Map Format
		After:
			Crop Ontology
			Variant Call Format
			Reference Sequence Annotation
			Generic Feature Format Version 3
			Minimum Information about Plant Phenotyping Experiment
			Investigation Study Assay Tabular
			Resource Description Framework
			Darwin Core
			FASTQ Sequence and Sequence Quality Format
			Binary Alignment Map Format
			Multi-Crop Passport Descriptors
		Added:
			Multi-Crop Passport Descriptors
		Removed:

Edits to 'https://fairsharing.org/bsg-c000042' by 'ThomasLetellier' at 11:30, 07 May 2018 (approved):

	'databases' has been modified:
		Before:
			Sequence Read Archive
			Genetic and Genomic Information System
		After:
			Sequence Read Archive
			Genetic and Genomic Information System
			Gramene|a comparative mapping resource for grains
			GrainGenes|a Database for Triticeae and Avena
			The Triticeae Toolbox 
		Added:
			Gramene|a comparative mapping resource for grains
			GrainGenes|a Database for Triticeae and Avena
			The Triticeae Toolbox 
		Removed:

Publications

Wheat Data Interoperability Guidelines, Ontologies and User Cases. Recommendations from the RDA Wheat Data Interoperability Working Group

Dzalé Yeumo, Esther ; Fulss, Richard ; Alaux, Michael; Aubin, Sophie; Arnaud, Elizabeth; Baumann, Ute; Cooper, Laurel; Davey, Richard; Laporte, Marie-Angélique; Larmande, Pierre; Letellier, Thomas; Pommier, Cyril; Protonotarios, Vassilis; Shrestha, Rosemary; Subirats, Imma; Venkatesan, Aravind; Whan, Alex;
2017

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16 records in view

Name	Abbreviation	Type	Subject	Domain	Taxonomy	Related Database	Related Standard	Related Policy	In Collection/Recommendation
Binary Alignment Map Format	BAM	Standard	Life Sciences	Sequence Sequence alignment Deoxyribonucleic acid	All	ENCODE modMine UCSC Genome Browser database The UCSC Archaeal Genome Browser RhesusBase Plus 5 more...	mirGFF3	None	eTRIKS Standards Starter Pack FAIRDOM Community Standards Wheat Data Interoperability Guidelines
Crop Ontology	CO	Standard	Agriculture Anatomy Ontology and Terminology	Phenotype	Plantae	GnpIS MGIS T3 Planteome PeanutBase	TO CO_331 CO_320 CO_321 SPTO Plus 34 more...	None	Wheat Data Interoperability Guidelines
Darwin Core	DwC	Standard	Biodiversity Life Sciences	Geographical location Biological sample annotation Taxonomic classification	All	GBIF FLOW Canadensys Scratchpads OBIS Plus 9 more...	DwC-germplasm DwC_translations OBIS Schema WoRMS AC Plus 2 more...	None	TDWG Biodiversity Information Standards Wheat Data Interoperability Guidelines
FASTQ Sequence and Sequence Quality Format	FASTQ Sequence and Sequence Quality Format	Standard	Life Sciences	Experimental measurement Amino acid sequence Deoxyribonucleic acid	All	GenBank ASPGD DDBJ ENCODE modMine Plus 11 more...	MINSEQE FASTA	None	FAIRDOM Community Standards Wheat Data Interoperability Guidelines
Generic Feature Format Version 3	GFF3	Standard	Life Sciences	Annotation Coding sequence DNA sequence data Gene expression data Transcription factor binding site prediction Plus 4 more...	All	ADHDgene ASPGD CADRE EcoliWiki: A Wiki-based community resource for Escherichia coli FlyBase Plus 43 more...	mirGFF3 SO	None	Wheat Data Interoperability Guidelines
Genetic and Genomic Information System	GnpIS	Database	Life Sciences	DNA sequence data Gene expression data Genetic polymorphism Genetic map Genome map Plus 2 more...	Agaricus subrefescens Arabidopsis thaliana Arabis alpina Botrytis cinerea B0510 Botrytis cinerea T4 Plus 15 more...	Data Inra GrapeMine	ISA-Tab CO GFF3 MIAPPE PO Plus 1 more...	None	ELIXIR node contributed resources Wheat Data Interoperability Guidelines
GrainGenes, a Database for Triticeae and Avena	GrainGenes	Database	Genomics Life Sciences Phenomics	Genetic polymorphism Genetic map Genome map Physical map Quantitative trait loci Plus 4 more...	Aegilops tauschii Avena Hordeum Hordeum vulgare Secale Plus 4 more...	Gramene MaizeGDB UniGene T3	NCBITAXON FASTA	None	AgBioData Wheat Data Interoperability Guidelines
Gramene, a comparative mapping resource for grains	Gramene	Database	Comparative Genomics Functional Genomics Life Sciences	Pathway or network prediction Genome	Arabidopsis thaliana Brachypodium dystachyon Coffea Hordeum Medicago truncatula Plus 6 more...	MetaCyc EcoCyc GrainGenes Ensembl Genomes T3 Plus 5 more...	ENVO SO PECO TO GO Plus 4 more...	None	AgBioData Wheat Data Interoperability Guidelines
Investigation Study Assay Tabular	ISA-Tab	Standard	Functional Genomics Life Sciences	Biological sample DNA microarray Experiment metadata Gene expression data Report Plus 3 more...	All	SCDE MTBLS GMD GigaDB SCC Plus 7 more...	OBI CIMR MINSEQE MIAME MIQE Plus 5 more...	EMBO Recommended Databases and Data Standards GigaScience - Minimum Standards of Reporting Checklist BioMed Central - Minimum Standards of Reporting Checklist	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project bioCADDIE eTRIKS Standards Starter Pack FAIRDOM Community Standards Plus 1 more...
Minimum Information about Plant Phenotyping Experiment	MIAPPE	Standard	Life Sciences	Experiment metadata Report Phenotype	Arabidopsis thaliana Hordeum vulgare Oryza sativa Plantae Populus Plus 3 more...	PGP GnpIS CyVerse Data Common Repository	ISA-Tab CO	None	Wheat Data Interoperability Guidelines
Multi-Crop Passport Descriptors	MCPD	Standard	Agriculture Life Sciences	Germplasm	Plantae	MGIS GLIS of the ITPGRFA	GLIS Descriptors	None	Wheat Data Interoperability Guidelines
Reference Sequence Annotation	RSA	Standard	None	None	All	None	None	None	Wheat Data Interoperability Guidelines
Resource Description Framework	RDF	Standard	Computer Science	None	Not applicable	UniProtKB RegenBase data.eNanoMapper.net BioPortal RDF Portal Plus 7 more...	CellML RDFS AGROVOC Chem2Bio2RDF DC Plus 13 more...	None	Wheat Data Interoperability Guidelines
Sequence Read Archive	SRA	Database	Life Sciences	DNA sequence data Sequence Sequence alignment Nucleic acid sequence alignment Allele Plus 2 more...	All	ImmPort BioSample HWG IPA BIP Plus 5 more...	SRA-XML MIxS - MIMARKS MINSEQE	GigaScience - Minimum Standards of Reporting Checklist Springer Nature - Nature Genetics - Availability of Data and materials Gates Open Research Data Guidelines Cold Spring Harbor Laboratory Press - Genes and Development - Instructions Regarding Data Submission Springer Nature - Nature Materials - Availability of Data and materials Plus 40 more...	Data Citation Implementation Open Science Prize NIH-supported data repositories Wheat Data Interoperability Guidelines
The Triticeae Toolbox	T3	Database	Genomics Phenomics	None	Avena Hordeum vulgare Triticum aestivum	PLEXdb Gramene GRIN GrainGenes Ensembl Plants	CO TO GFF2 VCF FASTA	None	AgBioData Wheat Data Interoperability Guidelines
Variant Call Format	VCF	Standard	Genomics Life Sciences	Sequence position Deoxyribonucleic acid Genome Genotype	All Homo sapiens	UCSC Genome Browser database Ensembl SoyBase dbGaP GnpIS Plus 5 more...	None	None	National Child Development Study (UK) eTRIKS Standards Starter Pack Wheat Data Interoperability Guidelines

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