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.
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.
01 Syntax
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| ToString | 1 | |
| PopulateRows | 1 | |
| ToJSON | 1 | |
| LoadFile | 1 |
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| id | 1 | <string or null> a field that can be used to id a table (or null) |
| comment | 1 | <string> A free text field containing any information that you feel Is relevant (Or just feel Like sharing) |
| format | 1 | <string> The name and version of the current biom format |
| format_url | 1 | <url> A string with a static URL providing format details |
| type | 1 | <string> Table type (a controlled vocabulary) Acceptable values : + "OTU table" + "Pathway table" + "Function table" + "Ortholog table" + "Gene table" + "Metabolite table… |
| generated_by | 1 | <string> Package and revision that built the table |
| date | 1 | <datetime> Date the table was built (ISO 8601 format) |
| matrix_type | 1 | <string> Type of matrix data representation (a controlled vocabulary) Acceptable values : + "sparse" : only non-zero values are specified + "dense" : every element must be sp… |
| matrix_element_type | 1 | Value type in matrix (a controlled vocabulary) Acceptable values : + "int" Integer + "float" : floating point + "unicode" : unicode string |
| shape | 1 | <list of ints>, the number of rows and number of columns in data |
| data | 1 | <list of lists>, counts of observations by sample If matrix_type Is "sparse", [[row, column, value], [row, column, value], ...] If matrix_type Is "dense", [… |
| rows | 1 | <list of objects> An ORDERED list of obj describing the rows |
| columns | 1 | <list of objects> An ORDERED list of obj describing the columns |
04 Members
<string or null> a field that can be used to id a table (or null)
<string> A free text field containing any information that you feel Is relevant (Or just feel Like sharing)
<string> The name and version of the current biom format
<url> A string with a static URL providing format details
<string> Table type (a controlled vocabulary) Acceptable values :
<string> Package and revision that built the table
<datetime> Date the table was built (ISO 8601 format)
<string> Type of matrix data representation (a controlled vocabulary) Acceptable values :
Value type in matrix (a controlled vocabulary) Acceptable values :
<list of ints>, the number of rows and number of columns in data
<list of lists>, counts of observations by sample
If matrix_type Is "sparse",
[[row, column, value],
[row, column, value],
...]
If matrix_type Is "dense",
[[value, value, value, ...],
[value, value, value, ...],
...]<list of objects> An ORDERED list of obj describing the rows
<list of objects> An ORDERED list of obj describing the columns
Boolean)String)