MTP-DB - The Membrane Transport Protein Database

Welcome to the repository for the MTP-DB, a database that aims to collect information regarding the transportome, and the proteins that make it up.

The repository contains Daedalus, a Python package to download, parse and rebuild the MTP-DB on the fly. You can also find database releases in the releases page with pre-generated database files.

Daedalus takes care of connecting to, downloading from, parsing and patching data retrieved from remote databases, compiling them into the MTP-DB. Daedalus is written in Python.

You can take a look at the CHANGELOG.md file for a changelog of each release of the database.

To browse the database locally, we suggest SQLite browsers such as this FOSS program. Common SQL queries to solve some routine problems are detailed in the How to guide.

The structure of the MTP-DB is detailed in this excel file.

Citing the MTP-DB

If you use the MTP-DB in your research, please cite:

Luca Visentin, Federico Alessandro Ruffinatti, The MTP-DB, DOI: 10.5281/zenodo.7868055

More information is present in the CITATION.cff file.

Generating the MTP-DB locally

You have two options if you wish to regenerate the MTP-DB locally.

You can download the pre-built Docker container from our DockerHub repository and execute that. You will need to install Docker to do this:

docker run -it --rm -v "OUT_DIR:/app/out" "cmalabscience/mtpdb:VERSION" "/app/out" --help

Just replace OUT_DIR with the full path to the output directory of your choice and VERSION with a valid version (see our releases and our Docker Hub repository). Any arguments to Daedalus (e.g. --help) can be passed at the end of the command. You can find a script (./src/scripts/run_remote_docker) that does this in a more user-friendly way in the scripts folder.

If you do not wish to use Docker, you wish to use the latest code, or you want to modify the code locally, clone the repository to your local machine. You will need to have Python 3.10.10 and git installed:

git clone git@github.com:CMA-Lab/MTP-DB.git
cd MTP-DB/src
# It is optional, but highly reccomended to work in a
# Python virtual environment
python -m venv env
source env/bin/activate

pip install -r requirements.txt

You can then run Daedalus with:

python -m daedalus --help

As an alternative, you can take a look in the src/scripts folder for helper scripts that regenerate and run a locally-made Docker container. This way, you can work on local code but without having to have Python installed (but having Docker installed). For example:

git clone git@github.com:CMA-Lab/MTP-DB.git
cd MTP-DB/src
./scripts/rrun --help

Be aware that these scripts are working-directory sensible, and will only work if your current WD is in MTP-DB/src/.

Contributing

We are very fond of contributors and collaborators. Please take a look at the contributing guide if you wish to contribute.

Contributors ✨

Thanks goes to these wonderful people (emoji key):

Federico Alessandro Ruffinatti 🐛 💻 🚧

This project follows the all-contributors specification. Contributions of any kind welcome!

Licensing

Daedalus itself and all associated software in this repository is licensed following the COPYING file. We are not sponsored or licensed by any of the data sources that we use.

The data downloaded and parsed by Daedalus is licensed under:

• The IUPHAR database: CC BY-SA 4.0 - Harding SD, Armstrong JF, Faccenda E, Southan C, Alexander SPH, Davenport AP, Pawson AJ, Spedding M, Davies JA; NC-IUPHAR. (2021) The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials. Nucl. Acids Res. 2022. 50(D1) D1282-D1294. doi: 10.1093/nar/gkab1010. Full text. PMID: 34718737.
• The COSMIC database: Custom License. Data is remixed and parsed, so the content of the COSMIC database is not redistributed as-is (which would be forbidden).
• The Gene Onthology: CC BY 4.0. Current Zenodo DOI: https://dx.doi.org/10.5281/zenodo.7504797
• The TCDB: CC BY 3.0 - Latest publication: Saier MH, Reddy VS, Moreno-Hagelsieb G, Hendargo KJ, Zhang Y, Iddamsetty V, Lam KJK, Tian N, Russum S, Wang J, Medrano-Soto A. (2021). The Transporter Classification Database (TCDB): 2021 update. Nucleic Acids Res. 49(D1):D461-7 33170213
• Ensembl places its data in the Public Domain (more info).
• The Human Gene Nomenclature Committee places its data in the Public Domain (CC0, more info)
• The Human Protein Atlas: CC BY 3.0 - Uhlén M et al., Tissue-based map of the human proteome. Science (2015) PubMed: 25613900 DOI: 10.1126/science.1260419 (more info)

(Last updated on the 22nd of June, 2023)