Added by Louis Felix Nothias, last edited by Louis Felix Nothias on Sep 07, 2017  (view change)

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Metadata table in GNPS

The metadata file describes the samples properties and allows more flexibility for data analysis and visualization. It is an alternative way to assign groups when selecting data input files within the workflow of GNPS.

The latest version of molecular networking allows to use the metadata table as an input. Although it is possible to use group mapping and attribute mapping file, we strongly advise to prepare metadata table instead.

Format. The metadata table is a text file (Tab separated) that users must create these file themselves using a text editor (e.g. Microsoft Excel, Notepad++ for Windows, gedit for Linux, TextWrangler for Mac OS). Using Metadata table or attribute and GROUP mapping can greatly ease the visualization and analysis of data within Cytoscape. We are strongly encourage you to prepare those in advance and to share it publicly with your MassIVE data.

You can download an example and edit it appropriately. Finally users will need to upload just as you would upload data input files and select it in the metadata table file upload selection. For a metadata table file template, you can use the following .txt file [Right-click, and Save link as]

Metadata table are composed of attributes (metadata). Examples of attributes for each sample (file) can be viewed below.

The following column header are Requirements:

- The first column must have a header "filename"

- The attributes are defined in the following columns, and the header must start with "ATTRIBUTE_"

- File must be saved must be text file (TAB separated formatted).

The selection of a metadata table will override the presence of a group or attribute mapping file.

Metadata table: Coordinate attributes for 3D molecular cartography with 'ili

The metadata can also be used to specify spatial coordinates for direct visualization of the data in 'ili toolbox (https://ili.embl.de/). Note that an .STL binary file must selected as an input in the workflow. Note that this is an experimental feature.

The following headers are required:

1. "COORDINATE_X" - X coordinate on the 2D/3D model

2. "COORDINATE_Y" - Y coordinate on the 2D/3D model

3. "COORDINATE_Z" - Z coordinate on the 2D/3D model

4. "COORDINATE_radius" - radius for the spot in 'ili toolbox.