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PFB Files

Overview of the Portable Format for Bioinformatics (PFB) file type

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What is a Portable Format for Bioinformatics?

A Portable Format for Bioinformatics (PFB) allows users to transfer both the metadata from the the Data Dictionary as well as the Data Dictionary itself. As a result, data can be transferred while keeping the structure from the original source. Specifically, a PFB consists of three parts:

  • A schema

  • Metadata

  • Data

For more information and an in-depth review that includes Python tools for PFB creation and exploration, refer to the PyPFB github pagearrow-up-right and install the newest version.

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Note The following PFB example is a direct PFB export from the tutorial-synthetic_data_set_1 found on BioData Catalyst Powered by Gen3arrow-up-right. Due to the large amount of data stored within PFB files, only small sections are shown with breaks (displayed as ... ) occurring in the output.

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Schema

A schema is a JSON formatted Data Dictionary containing information about the properties, such as value types, descriptions, and so on.

To view the PFB schema, use the following command:

pfb show -i PFB_file.avro schema

Example Output

...
  {
    "type": "record",
    "name": "gene_expression",
    "fields": [
      {
        "default": null,
        "name": "data_category",
        "type": [
          "null",
          {
            "type": "enum",
            "name": "gene_expression_data_category",
            "symbols": [
              "Transcriptome Profiling"
            ]
          }
        ]
      },
      {
        "default": null,
        "name": "data_type",
        "type": [
          "null",
          {
            "type": "enum",
            "name": "gene_expression_data_type",
            "symbols": [
              "Gene Expression Quantification"
            ]
          }
        ]
      },
      {
        "default": null,
        "name": "data_format",
        "type": [
          "null",
          {
            "type": "enum",
            "name": "gene_expression_data_format",
            "symbols": [
              "TXT",
              "TSV",
              "CSV",
              "GCT"
            ]
          }
        ]
      },
      {
        "default": null,
        "name": "experimental_strategy",
        "type": [
          "null",
          {
            "type": "enum",
            "name": "gene_expression_experimental_strategy",
            "symbols": [
              "RNA-Seq",
              "Total RNA-Seq"
            ]
          }
        ]
      },
      {
        "default": null,
        "name": "file_name",
        "type": [
          "null",
          "string"
        ]
      },
      {
        "default": null,
        "name": "file_size",
        "type": [
          "null",
          "long"
        ]
      },
      {
        "default": null,
        "name": "md5sum",
        "type": [
          "null",
          "string"
        ]
      },
      {
        "default": null,
        "doc": "The GUID of the object in the index service.",
        "name": "object_id",
        "type": [
          "null",
          "string"
        ]
      }
...

NOTE: To make the outputs more human-readable, the above information was then piped through the program jqarrow-up-right. Example: pfb show -i PFB_file.avro schema | jq

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Metadata

The metadata in a PFB contains all of the information explaining the linkage between nodes and external references for each of the properties.

To view the PFB metadata, use the following command:

Example Output

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Data

The data in the PFB are the values for the properties in the format of the Data Dictionary.

To view the data within the PFB, use the following command:

To view at a certain number of entries in the PFB file, use the flag -n to designate a number. For example, to view the first 10 data entries within the PFB, use the following command:

Example Output

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