Gen3 - TSV Formatting and Templates

TSV Formatting and Templates


TSVs, or tab-separated values files, are the most commonly used format for data submission to a Gen3 Data Commons.

One TSV is submitted per node in the graphical data model starting with the root node program and next its child node project. Note: often a data commons administrator will create these first two nodes for a data submitter, thus the data submitter should begin their submission by preparing TSVs for the child node(s) of project.

The column headers of a TSV are the properties of a node, and the rows in TSVs are individual data records. Thus, the number of rows in a TSV minus the header is the number of records that will be created or updated when the TSV is submitted to a Gen3 Data Commons.


TSV Formatting Checklist

  1. Specify the node type for every row. This is the name of the node (or node_id), and it must be exactly the same for every row.
  2. Specify the submitter_id of every record by entering a unique text identifier in each row. Make sure you don’t use the same value in more than one row of your TSV because every record in a project must have a unique submitter_id!
  3. Specify the links to the parent node(s) for each record. Note: parent records must exist before submitting child records! You can specify either the links with either the parents.submitter_id or the parents.id
  4. Fill in all required properties. Every row in the TSV must have a value for all required properties. Optional properties can be filled in for only some rows or the column can be left out entirely.

Notes about TSV Formatting

  • submitter_id

    Every row in the TSV / record in a node must have a unique submitter_id. This can be any textual identifier, usually something human-readable or encoding some information, e.g., case-1234_lung_cancer, sample_blood_draw2_month6.

  • id

    Every record in every node in the data commons has the property id, which is a UUID, not to be confused with “submitter_id” or “project_id”.

  • links

    Links are a special kind of property. Every node besides the root node program requires a link to it’s “parent node”. The link is specified by “.submitter_id”. The “backref” of the parent node is usually the plural form of the parent node (e.g., “subjects.submitter_id” for a link to a “subject” record; if unsure, the backref will be in the template TSV downloadable from the data dictionary viewer).

    Note: that you can alternatively specify links with the id property using the TSV column header studies.id. The value in this column would be the id (UUID) of your study instead of the submitter_id. When creating links, you can use submitter_id, id, or both, but only one is required. Most users prefer using a parent record’s submitter_id to specify links because they’re typically more human-readable than an id, which is a random 128-bit UUID.

    Some child-parent node relationships are one-to-many or many-to-many (i.e., “-to-many” relationships), meaning that one child record can have multiple parent records in the same parent node. For example, if a single subject belonged to three studies, then the subject TSV would specify the three links by submitting a comma-separated list of the parent submitter_ids: study_1,study_2,study_3.

    Note: Comma-separated lists are generally how “array” variables (properties that take lists as their value), like links, are formatted in a TSV.

    If submitting multiple links in JSON format, the three parent studies would look like this:

  "studies": [
    {
      "submitter_id": "study_1"
    },
    {
      "submitter_id": "study_2"
    },
    {
      "submitter_id": "study_3"
    }
  ],
  • program

    The program node has the property name, the project node has the property code, and every other node has the property submitter_id. These all serve the same basic function, which is to give that record a more human-readable call-name (the internal call-name is the UUID).

  • project

    A project also has the property project_id, which is the unique combination of the program name and the project code. So, for your project, the program is prog and the project code is proj; so your project_id is the dash-separated combination: prog-proj.

Template TSVs for metadata submission


Here are some sample TSV file templates for example nodes in a Gen3 data dictionary.

Look at the “Dictionary” section of a Gen3 data commons to find the complete list of nodes and download template TSVs for that data commons’ data model.

study.tsv

case.tsv

biospecimen.tsv

sample.tsv

aliquot.tsv

analyte.tsv

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