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Sample Metadata object ported over from qiime2.

This implements the Sample_Metadata format which is identical to the Metadata format implemented in qiime2. (see: https://docs.qiime2.org/2024.2/tutorials/metadata/)

An example sample_metadata file:

    id  col1    col2    col3
    #q2:types   categorical     categorical     categorical
    id1 1       a       foo
    id2 2       b       bar
    id3 3       c       42

# Format Support

Has Sniffer: Yes

Reader | Writer | Object Class
--- | --- | ---
Yes | Yes | `skbio.metadata.SampleMetadata`

# Format Specification

## Metadata Formatting Requirements

QIIME 2 metadata is most commonly stored in a TSV (i.e. tab-separated values) file. These files typically have a .tsv or .txt file extension, though it doesn’t matter to QIIME 2 what file extension is used. TSV files are simple text files used to store tabular data, and the format is supported by many types of software, such as editing, importing, and exporting from spreadsheet programs and databases. Thus, it’s usually straightforward to manipulate QIIME 2 metadata using the software of your choosing. If in doubt, we recommend using a spreadsheet program such as Microsoft Excel or Google Sheets to edit and export your metadata files.

The following sections describe formatting requirements for QIIME 2 metadata files, and how to validate your metadata files. Since there is no universal standard for TSV files, it is important to adhere to these requirements and understand how QIIME 2 will interpret the file’s contents to get the most out of your (meta)data!

## Metadata Validation

Sample and feature metadata files stored in Google Sheets can be validated using Keemei. Select Add-ons > Keemei > Validate QIIME 2 metadata file to validate metadata stored in Google Sheets.

QIIME 2 will also automatically validate a metadata file anytime it is used by the software. However, using Keemei to validate your metadata is recommended because a report of all validation errors and warnings will be presented each time Keemei is run. Loading your metadata in QIIME 2 will typically present only a single error at a time, which can make identifying and resolving validation issues cumbersome, especially if there are many issues with the metadata.

## Leading and trailing whitespace characters

If any cell in the metadata contains leading or trailing whitespace characters (e.g. spaces, tabs), those characters will be ignored when the file is loaded. Thus, leading and trailing whitespace characters are not significant, so cells containing the values ‘gut’ and ‘ gut ‘ are equivalent. This rule is applied before any other rules described below.

## Comments and Empty Rows

Rows whose first cell begins with the pound sign (#) are interpreted as comments and may appear anywhere in the file. Comment rows are ignored by QIIME 2 and are for informational purposes only. Inline comments are not supported.

Empty rows (e.g. blank lines or rows consisting solely of empty cells) may appear anywhere in the file and are ignored.

## Identifier Column

The first column in the metadata file is the identifier (ID) column. This column defines the sample or feature IDs associated with your study. It is not recommended to mix sample and feature IDs in a single metadata file; keep sample and feature metadata stored in separate files.

The ID column name (i.e. ID header) must be one of the following values. The values listed below may not be used to name other IDs or columns in the file.

Case-insensitive:

- id

- sampleid

- sample id

- sample-id

- fetureid

- feature id

- feature-id

Case-sensitive (these are mostly for backwards-compatibility with QIIME 1, biom-format, and Qiita files):

- #SampleID

- #Sample ID

- #OTUID

- #OTU ID

- sample_name

The following rules apply to IDs:

- IDs may consist of any Unicode characters, with the exception that IDs must notstart with the pound sign (#), as those rows would be interpreted as comments and ignored. See the section Recommendations for Identifiers for recommendations on choosing identifiers in your study.

- IDs cannot be empty (i.e. they must consist of at least one character).

- IDs must be unique (exact string matching is performed to detect duplicates).

- At least one ID must be present in the file.

- IDs cannot use any of the reserved ID column names listed above.

## Recommendations for Identifiers

Our goal with QIIME 2 is to support arbitrary Unicode characters in all cells of metadata files. However, given that QIIME 2 plugins and interfaces can be developed by anyone, we can’t make a guarantee that arbitrary Unicode characters will work with all plugins and interfaces. We can therefore make recommendations to users about characters that should be safe to use in identifiers, and we are preparing resources for plugin and interface developers to help them make their software as robust as possible. As developer resources become available, we will announce them in the Developer Discussion category on the QIIME 2 Forum.

Sample and feature identifiers with problematic characters tend to cause the most issues for our users. Based on our experiences with QIIME 1, QIIME 2, and other bioinformatics and command line tools, we can recommend the following attributes for identifiers:

- Identifiers should be 36 characters long or less.

- Identifiers should contain only ASCII alphanumeric characters (i.e. in the range of [a-z], [A-Z], or [0-9]), the period (.) character, or the dash (-) character.

An important point to remember is that sometimes values in your sample metadata can become identifiers. For example, taxonomy annotations can become feature identifiers following qiime taxa collapse, and sample or feature metadata values can become identifiers after applying qiime feature-table group. If you plan to apply these or similar methods where metadata values can become identifiers, you will be less likely to encounter problems if the values adhere to these identifier recommendations as well.

To help users become aware of these recommendations, the Keemei metadata validator will warn users about identifiers that don’t meet the above recommendations.

Users may be interested in the cual-id software for assistance with creating sample identifiers. The cual-id paper also provides some discussion on how to design identifiers.

## Metadata Columns

The ID column is the first column in the metadata file, and can optionally be followed by additional columns defining metadata associated with each sample or feature ID. Metadata files are not required to have additional metadata columns, so a file containing only an ID column is a valid QIIME 2 metadata file.

The following rules apply to column names:

- May consist of any Unicode characters.

- Cannot be empty (i.e. column names must consist of at least one character).

- Must be unique (exact string matching is performed to detect duplicates).

- Column names cannot use any of the reserved ID column names described in the section Identifier Column.

The following rules apply to column values:

- May consist of any Unicode characters.

- Empty cells represent missing data. Other values such as NA are not interpreted as missing data; only the empty cell is recognized as “missing”. Note that cells consisting solely of whitespace characters are also interpreted as missing data because leading and trailing whitespace characters are always ignored, effectively making the cell empty.

## Column Types

QIIME 2 currently supports categorical and numeric metadata columns. By default, QIIME 2 will attempt to infer the type of each metadata column: if the column consists only of numbers or missing data, the column is inferred to be numeric. Otherwise, if the column contains any non-numeric values, the column is inferred to be categorical. Missing data (i.e. empty cells) are supported in categorical columns as well as numeric columns.

QIIME 2 supports an optional comment directive to allow users to explicitly state a column’s type, avoiding the column type inference described above. This can be useful if there is a column that appears to be numeric, but should actually be treated as categorical metadata (e.g. a Subject column where subjects are labeled 1, 2, 3, etc). Explicitly declaring a column’s type also makes your metadata file more descriptive because the intended column type is included with the metadata, instead of relying on software to infer the type (which isn’t always transparent).

You can use an optional comment directive to declare column types in your metadata file, either manually or through the q2cli developer tools.

For manual specifications within your metadata file(s), the comment directive must appear directly below the header. The row’s first cell must be #q2:types or #sk:types to indicate the row is a comment directive. Subsequent cells may contain the values categorical or numeric (both case-insensitive). The empty cell is also supported if you do not wish to assign a type to a column (the type will be inferred in that case). Thus, it is easy to include this comment directive without having to declare types for every column in your metadata.

## Number Formatting

If a column is to be interpreted as a numeric metadata column (either through column type inference or by using the #q2:types comment directive), numbers in the column must be formatted following these rules:

- Use the decimal number system: ASCII characters [0-9], . for an optional decimal point, and + and - for positive and negative signs, respectively.

  > - Examples: 123, 123.45, 0123.40, -0.000123, +1.23

- Scientific notation may be used with E-notation; both e and E are supported.

  > - Examples: 1e9, 1.23E-4, -1.2e-08, +4.5E+6

- Only up to 15 digits total (including before and after the decimal point) are supported to stay within the 64-bit floating point specification. Numbers exceeding 15 total digits are unsupported and will result in undefined behavior.

- Common representations of not a number (e.g. NaN, nan) or infinity (e.g. inf, -Infinity) are not supported. Use an empty cell for missing data (e.g. instead of NaN). Infinity is not supported at this time in QIIME 2 metadata files.