Data Submission

How to contribute to PCD

Please contact us to arrange transfer of data to the Pulse Crop Database from accepted peer reviewed work. Manuscripts accepted in scientific journals are highly encouraged to submit data to the PCD prior to publication. After dataset submission, the PCD will provide an accession number and the data will be initially available for download on the publication datasets page. The data will then be integrated with existing PCD data, with full credit given to the submitting authors. As an active member of the AgBioData Consortium, we embrace the Findable, Accessible, Interoperable, and Reusable (FAIR) principles to facilitate and maximize the accessibility and reuse of large-scale data in agricultural research.

Data types and submission requirements

• Genome assembly and annotation data
  
  • At minimum we need the FASTA of the assembly and the GFF3 of the annotated features.  Ideally the data is also deposited into a standard repository (e.g. NCBI) and the accession number(s) are provided.
• Gene annotation data
  
  • If you have functionally characterized a gene from a genome sequence, please provide the information via this template.
• Genome wide expression (RNA-seq) data
  
  • We require the NCBI BioProject and associated BioSample accession numbers as well as expression values (example file)
• High-throughput sequencing data
  
  • We do not accept this data-type.  We recommend all raw sequencing data be deposited in a public repository such as NCBI.
• Map, marker, QTL, and GWAS
  
  • Please see the table below for links to templates and guides to the needed information.  
• Genotype, phenotype, and/or haplotype data from cultivar/breeding line evaluation projects
  
  • We will host genotype, phenotype, and/or haplotype data from cultivar, breeding line, and accessions with primary research importance. Please provide data in appropriate templates that can be downloaded below. SNP genotype data can also be provided in VCF.  Phenotype and/or genotype data of progeny poputlations and panels will be made available for download.

Data templates

Below are the data templates in column 1 and the data types in the remaining columns.  Each row indicates which templates are needed/required for each data type. The templates are downloaded by clicking the template name.  We recommend you contact us before filling in the template so that we can work closely with you to ensure this process is expedited easily and quickly. Use ORCID for contact column and DOI for reference column in every sheet.

*when there are genome position data for markers and/or QTLs, provide the data in genome_position template