<commit_before>.container-fluid
  .page-background
    .row
      .col-md-8.main.col-md-offset-2
        .col-md-12
          %h1.page-header
            Batch Submission Help
          %p.lead
            Guidelines for submitting your own variants to DoCM
          %hr
          %h4 Formatting and required fields
          %p
            Before submitting a batch of variants to DoCM, please review 
            =link_to('our criteria for inclusion', '/sources')
            to ensure your batch is suitable.
          %p
            In order to submit your batch of variants, please use the 
            =link_to('submission form', '/batches/new')
            to upload a tab delimited file.
            The file should contain the following columns and include headers.
            %table.table.table-striped.table-bordered
              %tr
                %td Column Name
                %td Description
              %tr
                %td chromosome
                %td
                  Chromosome on which the variant can be found
                  %small (required)
              %tr
                %td start
                %td
                  Starting position of the variant
                  %small (required)
                %tr
                  %td
                    stop
                  %td
                    End position of the variant
                    %small (required)
                %tr
                  %td
                    reference
                  %td
                    Reference bases. "None" should be represented with a "-" character
                    %small (required)
                %tr
                  %td
                    variant
                  %td
                    Variant bases. "None" should be represented with a "-" character
                    %small (required)
                %tr
                  %td
                    doid
                  %td
                    =link_to('Disease Ontology', 'http://disease-ontology.org/') 
                    id. Formatted either as "DOID:123" or "123"
                    %small (required)
                %tr
                  %td
                    pubmed_id
                  %td
                    PubMed id for the publication containing the disease-variant relationship
                    %small (required)
                %tr
                  %td
                    transcript
                  %td
                    Ensembl transcript id containing the variant
                    %small (required)
                %tr
                  %td
                    tags
                  %td
                    A comma delimited list of tags to apply to this specific disease-source-variant relationship
                    %small (optional)
                %tr
                  %td
                    meta
                  %td
                    A JSON data structure of metadata to be displayed on the DoCM website. Please
                    =link_to('see below', '#meta-instructions')
                    for details
                    %small (optional)
            %p
            Please note that while the order of the columns is not important, the headers are case sensitive. You can download a template TSV file
            =link_to('here.', '/docm_import_template.tsv')
          %hr
          %h4 Submission process
          %p
            After you submit your batch file, your variants will move through several phases of approval. They are detailed below.
          %table.table.table-striped.table-bordered
            %tr
              %th Status
              %th Description
            %tr
              %td
                submitted
              %td
                We have received your batch file, parsed it successfully, and are preparing to process your submission.
            %tr
              %td
                processed
              %td
                This variant has been through our automated validation process which includes annotation with VEP and validation of the DOID and PMID.
            %tr
              %td
                accepted
              %td
                This variant has been accepted for inclusion and will be in the next version of DoCM
            %tr
              %td
                included
              %td
                This variant is now in the live version of DoCM
          %hr
          %h4#meta-instructions Meta Instructions
          %p
            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.
          %p
            The 'urls' field should be structured as follows:
            %pre
              :preserve
                {
                  "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
            =link_to('seen here.', '/variants/ENST00000078429:c.626A%3EC?version=2')
          %p
            The 'tables' field should be structured as follows:
            %pre
              :preserve
                {
                  "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": "<NAME> 2013;31: (suppl; abstr CRA9003)"
                    }]
                  }]
                }
            and will result in a table appearing towards the bottom of the variant overview page as
            =link_to('seen here.', '/variants/ENST00000078429:c.626A%3EC?version=2')

<commit_msg>explicitly request genomic coordinates in submission<commit_after>.container-fluid
  .page-background
    .row
      .col-md-8.main.col-md-offset-2
        .col-md-12
          %h1.page-header
            Batch Submission Help
          %p.lead
            Guidelines for submitting your own variants to DoCM
          %hr
          %h4 Formatting and required fields
          %p
            Before submitting a batch of variants to DoCM, please review 
            =link_to('our criteria for inclusion', '/sources')
            to ensure your batch is suitable.
          %p
            In order to submit your batch of variants, please use the 
            =link_to('submission form', '/batches/new')
            to upload a tab delimited file.
            The file should contain the following columns and include headers.
            %table.table.table-striped.table-bordered
              %tr
                %td Column Name
                %td Description
              %tr
                %td chromosome
                %td
                  Chromosome on which the variant can be found
                  %small (required)
              %tr
                %td start
                %td
                  Genomic starting position of the variant
                  %small (required)
                %tr
                  %td
                    stop
                  %td
                    Genomic end position of the variant
                    %small (required)
                %tr
                  %td
                    reference
                  %td
                    Reference bases (genomic '+' strand). "None" should be represented with a "-" character
                    %small (required)
                %tr
                  %td
                    variant
                  %td
                    Variant bases (genomic '+' strand). "None" should be represented with a "-" character
                    %small (required)
                %tr
                  %td
                    doid
                  %td
                    =link_to('Disease Ontology', 'http://disease-ontology.org/') 
                    id. Formatted either as "DOID:123" or "123"
                    %small (required)
                %tr
                  %td
                    pubmed_id
                  %td
                    PubMed id for the publication containing the disease-variant relationship
                    %small (required)
                %tr
                  %td
                    transcript
                  %td
                    Ensembl transcript id containing the variant
                    %small (required)
                %tr
                  %td
                    tags
                  %td
                    A comma delimited list of tags to apply to this specific disease-source-variant relationship
                    %small (optional)
                %tr
                  %td
                    meta
                  %td
                    A JSON data structure of metadata to be displayed on the DoCM website. Please
                    =link_to('see below', '#meta-instructions')
                    for details
                    %small (optional)
            %p
            Please note that while the order of the columns is not important, the headers are case sensitive. You can download a template TSV file
            =link_to('here.', '/docm_import_template.tsv')
          %hr
          %h4 Submission process
          %p
            After you submit your batch file, your variants will move through several phases of approval. They are detailed below.
          %table.table.table-striped.table-bordered
            %tr
              %th Status
              %th Description
            %tr
              %td
                submitted
              %td
                We have received your batch file, parsed it successfully, and are preparing to process your submission.
            %tr
              %td
                processed
              %td
                This variant has been through our automated validation process which includes annotation with VEP and validation of the DOID and PMID.
            %tr
              %td
                accepted
              %td
                This variant has been accepted for inclusion and will be in the next version of DoCM
            %tr
              %td
                included
              %td
                This variant is now in the live version of DoCM
          %hr
          %h4#meta-instructions Meta Instructions
          %p
            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.
          %p
            The 'urls' field should be structured as follows:
            %pre
              :preserve
                {
                  "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
            =link_to('seen here.', '/variants/ENST00000078429:c.626A%3EC?version=2')
          %p
            The 'tables' field should be structured as follows:
            %pre
              :preserve
                {
                  "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": "<NAME> Oncol 2013;31: (suppl; abstr CRA9003)"
                    }]
                  }]
                }
            and will result in a table appearing towards the bottom of the variant overview page as
            =link_to('seen here.', '/variants/ENST00000078429:c.626A%3EC?version=2')


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