Batch Submission Help

Guidelines for submitting your own variants to DoCM


Formatting and required fields

Before submitting a batch of variants to DoCM, please review our criteria for inclusion to ensure your batch is suitable.

In order to submit your batch of variants, please use the submission form to upload a tab delimited file. The file should contain the following columns and include headers.

Column Name Description
chromosome Chromosome on which the variant can be found (required)
start Genomic starting position of the variant (required)
stop Genomic end position of the variant (required)
reference Reference bases (genomic '+' strand). "None" should be represented with a "-" character (required)
variant Variant bases (genomic '+' strand). "None" should be represented with a "-" character (required)
doid Disease Ontology id. Formatted either as "DOID:123" or "123" (required)
pubmed_id PubMed id for the publication containing the disease-variant relationship (required)
transcript Ensembl transcript id containing the variant (required)
tags A comma delimited list of tags to apply to this specific disease-source-variant relationship (optional)
meta A JSON data structure of metadata to be displayed on the DoCM website. Please see below for details (optional)

Please note that while the order of the columns is not important, the headers are case sensitive. You can download a template TSV file here.


Submission process

After you submit your batch file, your variants will move through several phases of approval. They are detailed below.

Status Description
submitted We have received your batch file, parsed it successfully, and are preparing to process your submission.
processed This variant has been through our automated validation process which includes annotation with VEP and validation of the DOID and PMID.
accepted This variant has been accepted for inclusion and will be in the next version of DoCM
included This variant is now in the live version of DoCM

Meta Instructions

The meta field allows you to optionally supply external links or metadata to be displayed on the DoCM site. It is a JSON data structure that allows for two top level keys, 'urls', and 'tables'. You may supply either key, both keys or nothing at all. The column is entirely optional.

The 'urls' field should be structured as follows:

{
  "urls": [{
    "path": "http://www.mycancergenome.org/content/disease/melanoma/gna11/101",
    "name": "My Cancer Genome"
  }]
}
and will result in a link appearing in the 'External Links` section of the variant overview page as seen here.

The 'tables' field should be structured as follows:

{
  "tables": [{
    "name": "Drug Interaction Data",
    "columns": ["Therapeutic Context", "Pathway", "Effect", "Association", "Status", "Evidence", "Source"],
    "rows": [{
      "Therapeutic Context": "selumetinib",
      "Pathway": "activation",
      "Effect": "gain-of-function",
      "Association": "response",
      "Status": "early trials",
      "Evidence": "emerging",
      "Source": "J Clin Oncol 2013;31: (suppl; abstr CRA9003)"
    }]
  }]
}
and will result in a table appearing towards the bottom of the variant overview page as seen here.