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 Science	Sequence alignment Deoxyribonucleic acid region	All	ENCODE modMine UCSC Genome Browser database The UCSC Archaeal Genome Browser RhesusBase Plus 10 more...	CRAM mirGFF3	None	FAIRDOM Community Standards eTRIKS Standards Starter Pack Wheat Data Interoperability Guidelines
Crop Ontology	CO	Standard	Agriculture Anatomy Ontology and Terminology	Phenotype	Plantae	GnpIS MGIS T3 Planteome PeanutBase	TO CO_320 CO_331 CO_321 SPTO Plus 34 more...	None	Wheat Data Interoperability Guidelines
Darwin Core	DwC	Standard	Biodiversity Life Science	Geographical location Taxonomic classification Biological sample annotation	All	PANGAEA GBIF FLOW Canadensys Scratchpads Plus 17 more...	AC DwC_translations WoRMS RDF OBIS Schema Plus 12 more...	None	TDWG Biodiversity Information Standards Wheat Data Interoperability Guidelines
FASTQ Sequence and Sequence Quality Format	FASTQ Sequence and Sequence Quality Format	Standard	Life Science	Experimental measurement Deoxyribonucleic acid polypeptide_region	All	GenBank ASPGD DDBJ ENCODE IMG/M Plus 16 more...	MINSEQE FASTA	None	FAIRDOM Community Standards Wheat Data Interoperability Guidelines
Generic Feature Format Version 3	GFF3	Standard	Genomics	Annotation Coding sequence DNA sequence data Gene feature Gene expression data Plus 5 more...	All	ADHDgene ASPGD CADRE EcoliWiki: A Wiki-based community resource for Escherichia coli FlyBase Plus 46 more...	SO mirGFF3	None	AgBioData RDA Covid-19 WG Resources Wheat Data Interoperability Guidelines
Genetic and Genomic Information System	GnpIS	Database	Life Science	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 INRAE GrapeMine	PO ISA-Tab GFF3 VCF CO Plus 1 more...	None	EOSC-Life Wheat Data Interoperability Guidelines ELIXIR Non-CDR and Non-Deposition Database RDA Covid-19 WG Resources
GrainGenes, a Database for Triticeae and Avena	GrainGenes	Database	Genomics Life Science 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 curated, open-source, integrated data resource for comparative functional genomics in plants	Gramene	Database	Comparative Genomics Epigenomics Functional Genomics Genomics Life Science Plus 4 more...	Coding sequence DNA sequence data Differential gene expression analysis Gene Ontology enrichment Gene feature Plus 28 more...	Algae Amborella Arabidopsis thaliana Brachypodium dystachyon Bryophyta Plus 15 more...	Expression Atlas MetaCyc Reactome MaizeGDB GrainGenes Plus 8 more...	BioPAX EO SO ENVO TO Plus 9 more...	None	Open Science Prize AgBioData Wheat Data Interoperability Guidelines
Investigation Study Assay Tabular	ISA-Tab	Standard	Functional Genomics Life Science	Biological sample DNA microarray Experiment metadata Gene expression data Report Plus 3 more...	All	SCDE MTBLS GMD GigaDB SCC Plus 8 more...	CL OBI ECO BTO RNAO Plus 20 more...	EMBO Recommended Databases and Data Standards Advanced Genetics BioMed Central - Minimum Standards of Reporting Checklist GigaScience - Minimum Standards of Reporting Checklist	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project FAIRDOM Community Standards bioCADDIE eTRIKS Standards Starter Pack Plus 7 more...
Minimum Information about Plant Phenotyping Experiment	MIAPPE	Standard	Life Science	Experiment metadata Report Phenotype report	Arabidopsis thaliana Hordeum vulgare Oryza sativa Plantae Populus Plus 3 more...	PGP GnpIS CyVerse Data Common Repository	PPEO ISA-Tab CO	None	Wheat Data Interoperability Guidelines
Multi-Crop Passport Descriptors	MCPD	Standard	Agriculture Life Science	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	ChEMBL Rhea figshare UniProtKB RegenBase Plus 16 more...	CellML RDFS NIFSTD AGROVOC Chem2Bio2RDF Plus 28 more...	None	Wheat Data Interoperability Guidelines
Sequence Read Archive	SRA	Database	Epidemiology Life Science Virology	DNA sequence data Sequence alignment Nucleic acid sequence alignment Allele Gene Plus 2 more...	All	IMG/M GOLD ImmPort BioSample HWG Plus 14 more...	SRA-XML MIxS - MIMARKS MINSEQE FAANG metadata experiment specification standard	MNI Open Research UCL Child Open Health Research Springer Nature Research Data Policy Type 1 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 4 Plus 43 more...	NIH-supported data repositories Data Citation Implementation Open Science Prize Wheat Data Interoperability Guidelines Advanced Genetics Plus 2 more...
The Triticeae Toolbox	T3	Database	Genomics Phenomics Proteomics	Gene report Single nucleotide polymorphism Genotype Phenotype Protein	Avena Hordeum vulgare Triticum aestivum	PLEXdb Gramene GRIN GrainGenes Ensembl Plants	TO FASTA VCF CO GFF2	None	AgBioData Wheat Data Interoperability Guidelines
Variant Call Format	VCF	Standard	Genomics Life Science	Sequence position Deoxyribonucleic acid Genome Genotype	All Homo sapiens	UCSC Genome Browser database Ensembl SoyBase dbGaP GnpIS Plus 9 more...	None	None	National Child Development Study (UK) eTRIKS Standards Starter Pack AgBioData Wheat Data Interoperability Guidelines RDA Covid-19 WG Resources

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