This topic describes gene entities on the gene analysis platform and explains how to use entity tables to manage gene data files and metadata.
Introduction to gene entity tables
In addition to sequencing files, such as FASTQ and BAM files, gene data also includes related clinical, sample, and experimental metadata. This combination of data constitutes the big data for biomedical multi-omics.
The gene analysis platform uses Alibaba Cloud Object Storage Service (OSS) to provide secure, reliable, and unlimited storage for gene data files. The platform also uses entities to manage biological sample data, such as data for patients, samples, and tissues. An entity's data properties are defined in a CSV table. Entities can reference each other to organize complex multi-omics data.
Entity tables on the platform are fully customizable. You can add, edit, and download entity tables. You can also select data from entity tables to start batch analysis tasks.
Add an entity table
Step 1: You can add a new entity table to your workspace by uploading a CSV file. The platform provides a "Create Empty Template" feature. You can download the CSV template and then edit the name and attribute columns.
Entity name: The name must be unique within the workspace. It can contain digits, letters, underscores (_), and hyphens (-). The name can be up to 64 characters long and cannot start with a digit or a hyphen.
First column name: This is the ID column. You do not need to enter a name for this column. The name is automatically generated in the <entity_name>_id format.
New column: Add any number of columns to describe the entity properties.
Column name: Must be a valid variable name. Column names must be unique within the entity.
Column type: The default type is string, which treats the cell content as text. You can also select another entity from the drop-down list to create a reference. In this case, the cell content must be an ID from the first column of the referenced entity table.
Step 2: Click OK. The browser automatically downloads the CSV template to your local computer. You can use software, such as Microsoft Excel or a text editor, to edit the content and save the file.
You can also prepare the entity table CSV file on your local computer. After you edit and save the data, you can upload the file. The first row of the CSV file is the header row that defines the columns. The first column name must be in the <entity_name>_id format. For example, in the preceding figure, the first column is `sample_id`, which indicates that the entity to be added is named `sample`.
Step 3: Click Upload Table File to upload the data-filled CSV file to the platform.
Click OK. After the upload is successful, the entity data table appears in the workspace.
The maximum size for a single entity file is 2 MB. To upload a larger entity file, you can split it into multiple files, contact the product team, or submit a ticket.
Update an entity table
You can update the data of an existing entity on the gene analysis platform in two ways.
Edit and save the corresponding CSV file for the entity table, and then re-upload it.
You can add new columns and rows. After a successful upload, the new columns and rows are added to the existing table.
If a column name and an ID in the first column match existing data, the content from the CSV file overwrites the existing data in the table.
To edit existing rows, you can select them on the gene analysis platform, download the content as a CSV file to your local computer, and then edit the file.
Edit the data directly on the web page.
Hover the mouse pointer over the content of a cell. An edit icon appears. Click the icon to edit the cell content.
Delete an entity table
You can select rows in the entity table and delete them. When all rows in an entity table are deleted, the table is automatically deleted.
Start a batch analysis
If you have created an application template that uses the entity, you can select rows in the entity table and start a batch analysis on the selected data. The platform displays analysis templates that match the current entity type to help you quickly submit batch analysis tasks. For more information, see Best practices.