Json

namespace: SMRUCC.genomics.Model.BIOM.v10

The biom file format: Version 1.0

The biom format is based on JSON to provide the overall structure for the format.
JSON is a widely supported format with native parsers available within many programming
languages.

Properties

columns

<list of objects> An ORDERED list of obj describing the columns

comment

<string> A free text field containing any information that you
feel Is relevant (Or just feel Like sharing)

data

<list of lists>, counts of observations by sample

If matrix_type Is “sparse”,

1
2
3
[[row, column, value],
[row, column, value],
...]

If matrix_type Is “dense”,

1
2
3
[[value, value, value, ...],
[value, value, value, ...],
...]

date

<datetime> Date the table was built (ISO 8601 format)

format

<string> The name and version of the current biom format

format_url

<url> A string with a static URL providing format details

generated_by

<string> Package and revision that built the table

id

<string or null> a field that can be used to id a table (or null)

matrix_element_type

Value type in matrix (a controlled vocabulary)
Acceptable values :

  • “int” Integer
  • “float” : floating point
  • “unicode” : unicode string

    matrix_type

    <string> Type of matrix data representation (a controlled vocabulary)
    Acceptable values :

  • “sparse” : only non-zero values are specified

  • “dense” : every element must be specified

    rows

    <list of objects> An ORDERED list of obj describing the rows

    shape

    <list of ints>, the number of rows and number of columns in data

    type

    <string> Table type (a controlled vocabulary)
    Acceptable values :

  • “OTU table”

  • “Pathway table”
  • “Function table”
  • “Ortholog table”
  • “Gene table”
  • “Metabolite table”
  • “Taxon table”