Repository: sdsc-ordes/modos-schema
Description: Metadata schema for the Multi-Omics Digital-Object
Primary language: Python
Topics: omics, ontology

# modos-schema

Metadata schema for the Multi-Omics Digital Object System - [MODOS](https://github.com/sdsc-ordes/modos-api).

```mermaid
erDiagram
MODOCollection {

}
MODO {
    datetime creation_date  
    datetime last_update_date  
    uri source_uri  
    uriorcurie id  
    string name  
    string description  
}
Assay {
    OmicsTypeList omics_type  
    uriorcurieList sample_processing  
    uriorcurie id  
    string name  
    string description  
}
DataEntity {
    string data_path  
    DataFormat data_format  
    string data_checksum  
    uriorcurie id  
    string name  
    string description  
}
ReferenceGenome {
    string data_path  
    uriorcurieList taxon_id  
    uri source_uri  
    string version  
    uriorcurie id  
    string name  
    string description  
}
ReferenceSequence {
    string sequence_md5  
    uri source_uri  
    string version  
    uriorcurie id  
    string name  
    string description  
}
Sample {
    uriorcurie cell_type  
    uriorcurie source_material  
    Sex sex  
    uriorcurieList taxon_id  
    stringList collector  
    uri source_uri  
    uriorcurie id  
    string name  
    string description  
}

MODOCollection ||--}o MODO : "entries"
MODO ||--}o Assay : "has_assay"
Assay ||--}o DataEntity : "has_data"
DataEntity ||--}o Sample : "has_sample"
DataEntity ||--}o ReferenceGenome : "has_reference"
ReferenceGenome ||--}o ReferenceSequence : "has_sequence"

```



## Website

[https://sdsc-ordes.github.io/modos-schema](https://sdsc-ordes.github.io/modos-schema)

## Repository Structure

* [examples/](examples/) - example data
* [project/](project/) - project files (do not edit these)
* [src/](src/) - source files (edit these)
  * [modos_schema](src/modos_schema)
    * [schema](src/modos_schema/schema) -- LinkML schema
      (edit this)
    * [datamodel](src/modos_schema/datamodel) -- generated
      Python datamodel
* [tests/](tests/) - Python tests

## Developer Documentation

<details>
Use the `make` command to generate project artefacts:

* `make all`: make everything
* `make deploy`: deploys site
</details>

## Credits

This project was made with
[linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter).

## Acknowledgements and Funding

The development of the Multi-Omics Digital Object System (MODOS) is being funded by the Personalized Health Data Analysis Hub, a joint initiative of the Personalized Health and Related Technologies ([PHRT](https://www.sfa-phrt.ch)) and the Swiss Data Science Center ([SDSC](https://datascience.ch)), for a period of three years from 2023 to 2025. The SDSC leads the development of MODOS, bringing expertise in complex data structures associated with multi-omics and imaging data to advance privacy-centric clinical-grade integration. The PHRT contributes its domain expertise of the Swiss Multi-Omics Center ([SMOC](http://smoc.ethz.ch)) in the generation, analysis, and interpretation of multi-omics data for personalized health and precision medicine applications.
We gratefully acknowledge the [Health 2030 Genome Center](https://www.health2030genome.ch/) for their substantial contributions to the development of MODOS by providing test data sets, deployment infrastructure, and expertise. 

## Copyright
Copyright © 2023-2024 Swiss Data Science Center (SDSC), [www.datascience.ch](http://www.datascience.ch/). All rights reserved. The SDSC is jointly established and legally represented by the École Polytechnique Fédérale de Lausanne (EPFL) and the Eidgenössische Technische Hochschule Zürich (ETH Zürich). This copyright encompasses all materials, software, documentation, and other content created and developed by the SDSC in the context of the Personalized Health Data Analysis Hub.