SingleCellSchema

The SingleCellSchema repository houses developments related to Earlham Institute's (EI’s) CELLGEN ISP metadata mapping and schemas, designed to describe a variety of Single Cell Genomics and Spatial Transcriptomics experiment types, such as those from 10X Genomics and Vizgen.

Visit the SingleCellSchema website at https://singlecellschemas.org.

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The SingleCellSchema repository contains the following directories:

• dist: contains the output files generated from the conversion process.

• schemas/xlsx: contains the xlsx base versions of the schema.

• utils: contains Python helper scripts to convert base Excel files into formats such as HTML, XML and Excel.

The update_and_convert_schema.py script is responsible for updating the Excel base schema files located in the schemas/xlsx directory and generating corresponding JSON files based on these Excel files. The script is located in the utils directory.

The main script, convert.py, is used to convert the Excel schema into Excel, XML, html and JSON files according to the namespace prefix. It is found in the project root directory.

Important note: Please do not directly modify the base JSON files in the schemas/json directory. To make changes, update the data worksheet in one of the base Excel files located in the schemas/xlsx directory.

After making changes to the Excel files, run the update_and_convert_schema.py script in the utils directory to regenerate and update the JSON schema files. To run the update script, execute in the terminal - python3 utils/update_and_convert_schema.py.

Abbreviations:

• SC RNASEQ: Single Cell RNA-Sequencing
• STX: Spatial Transcriptomics

Please follow the instructions below to convert the Excel schema into an excel file, xml, html and json files:

1. Download or clone this repository and navigate to its directory in the terminal

   git clone https://github.com/TGAC/SingleCellSchemas.git

   cd SingleCellSchemas

2. Create a new Python virtual environment called venv

   python3 -m venv venv

3. Activate the virtual environment

   source venv/bin/activate

4. Install dependencies

   pip3 install -r requirements/requirements.txt

5. Different ways to run the convert.py script which is found in the project root directory

   • Use launch.xlsx file to run the script in VSCode by selecting the appropriate configuration

     --OR--

   • python3 convert.py

     This will convert the schema into an excel file, xml and json files using all termsets, namespace prefixes and schemas in the schemas/xlsx directory

     --OR--

   • python3 convert.py <termset>

     where <termset> is the type of terms to be used (extended, core) e.g. python3 convert.py core

     --OR--

   • python3 convert.py schemas/xlsx/<schema-file-path> <termset>

     where <schema-file-path> is the name of the schema file in the schemas/xlsx directory, <termset> is the type of terms to be used (extended, core) e.g. python3 convert.py schemas/xlsx/sc_rnaseq.xlsx core

     --OR--

   • python3 convert.py schemas/xlsx/<schema-file-path> <termset> <namespace_prefix>

     where <schema-file-path> is the name of the schema file in the schemas/xlsx directory, <termset> is the type of terms to be used (extended, core) and <namespace_prefix> is the namespace prefix to be used (e.g. dwc, mixs, tol) e.g. python3 convert.py schemas/xlsx/sc_rnaseq.xlsx core dwc

     --OR--

   • Run the tests (which also runs the converter whilst verifying the output)

     python -m unittest