{"id":19053927,"url":"https://github.com/tcp-lab/mtp-db","last_synced_at":"2026-05-11T09:30:19.771Z","repository":{"id":156374814,"uuid":"539987341","full_name":"TCP-Lab/MTP-DB","owner":"TCP-Lab","description":"The Membrane Transport Protein Database","archived":false,"fork":false,"pushed_at":"2025-01-20T15:00:41.000Z","size":383,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-20T15:44:44.903Z","etag":null,"topics":["phd-project","transcriptomics","transportome"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/TCP-Lab.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"COPYING","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":"ROADMAP.md","authors":"AUTHORS.md","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-09-22T13:08:52.000Z","updated_at":"2025-01-20T14:53:20.000Z","dependencies_parsed_at":"2024-11-14T11:26:58.542Z","dependency_job_id":"d9ea25d7-1ef0-45b5-b2d3-d428f92ddedc","html_url":"https://github.com/TCP-Lab/MTP-DB","commit_stats":null,"previous_names":["tcp-lab/mtp-db"],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TCP-Lab%2FMTP-DB","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TCP-Lab%2FMTP-DB/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TCP-Lab%2FMTP-DB/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TCP-Lab%2FMTP-DB/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/TCP-Lab","download_url":"https://codeload.github.com/TCP-Lab/MTP-DB/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240109715,"owners_count":19749182,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["phd-project","transcriptomics","transportome"],"created_at":"2024-11-08T23:35:58.240Z","updated_at":"2026-05-11T09:30:18.389Z","avatar_url":"https://github.com/TCP-Lab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MTP-DB - The Membrane Transport Protein Database\n[![DOI](https://zenodo.org/badge/539987341.svg)](https://zenodo.org/badge/latestdoi/539987341)\n[![Python](https://img.shields.io/badge/Python-v3.10-blue)](https://www.python.org/downloads/release/python-31011/)\n[![Docker](https://img.shields.io/docker/pulls/cmalabscience/mtpdb)](https://hub.docker.com/r/cmalabscience/mtpdb)\n[![All Contributors](https://img.shields.io/github/all-contributors/CMA-Lab/MTP-DB?style=flat)](#contributors-)\n\nWelcome to the repository for the MTP-DB, a database that aims to collect information regarding the transportome, and the proteins that make it up.\n\nThe 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](https://github.com/CMA-Lab/MTP-DB/releases) with pre-generated database files.\n\nDaedalus 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.\n\nYou can take a look at the [CHANGELOG.md](CHANGELOG.md) file for a changelog of each release of the database.\n\nTo browse the database locally, we suggest SQLite browsers such as [this FOSS program](https://sqlitebrowser.org/).\nCommon SQL queries to solve some routine problems are detailed in the [How to guide](HOW_TO.md).\n\nThe structure of the MTP-DB is detailed [in this excel file](https://docs.google.com/spreadsheets/d/16vb_2FvZdaUSVOc8m9yRPT6eYP8cGl4UsOzauI2Qbek/edit?usp=sharing). \n\n## Citing the MTP-DB\n\nIf you use the MTP-DB in your research, please cite:\n\u003e Luca Visentin, Federico Alessandro Ruffinatti, The MTP-DB, DOI: [10.5281/zenodo.7868055](https://doi.org/10.5281/zenodo.7868055)\n\nMore information is present in the [CITATION.cff](CITATION.cff) file.\n\n## Generating the MTP-DB locally\nYou have two options if you wish to regenerate the MTP-DB locally.\n\nYou can download the pre-built Docker container from our DockerHub repository and execute that. You will need to install [Docker](https://www.docker.com/) to do this:\n```bash\ndocker run -it --rm -v \"OUT_DIR:/app/out\" \"cmalabscience/mtpdb:VERSION\" \"/app/out\" --help\n```\nJust replace `OUT_DIR` with the full path to the output directory of your choice and `VERSION` with a valid version (see our [releases](https://github.com/CMA-Lab/MTP-DB/releases) and our [Docker Hub repository](https://hub.docker.com/r/cmalabscience/mtpdb)). 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`](https://github.com/CMA-Lab/MTP-DB/blob/main/src/scripts/run_remote_docker)) that does this in a more user-friendly way in the scripts folder.\n\nIf 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:\n```bash\ngit clone git@github.com:CMA-Lab/MTP-DB.git\ncd MTP-DB/src\n# It is optional, but highly reccomended to work in a\n# Python virtual environment\npython -m venv env\nsource env/bin/activate\n\npip install -r requirements.txt\n```\n\nYou can then run Daedalus with:\n```bash\npython -m daedalus --help\n```\n\nAs 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:\n```bash\ngit clone git@github.com:CMA-Lab/MTP-DB.git\ncd MTP-DB/src\n./scripts/rrun --help\n```\nBe aware that these scripts are working-directory sensible, and will only work if your current WD is in `MTP-DB/src/`.\n\n# Contributing\nWe are very fond of contributors and collaborators. Please take a look at the [contributing guide](CONTRIBUTING.md) if you wish to contribute.\n\n## Contributors ✨\n\nThanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):\n\n\u003c!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section --\u003e\n\u003c!-- prettier-ignore-start --\u003e\n\u003c!-- markdownlint-disable --\u003e\n\u003ctable\u003e\n  \u003ctbody\u003e\n    \u003ctr\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/Feat-FeAR\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/88393554?v=4?s=100\" width=\"100px;\" alt=\"Federico Alessandro Ruffinatti\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eFederico Alessandro Ruffinatti\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/CMA-Lab/MTP-DB/issues?q=author%3AFeat-FeAR\" title=\"Bug reports\"\u003e🐛\u003c/a\u003e \u003ca href=\"https://github.com/CMA-Lab/MTP-DB/commits?author=Feat-FeAR\" title=\"Code\"\u003e💻\u003c/a\u003e \u003ca href=\"#maintenance-Feat-FeAR\" title=\"Maintenance\"\u003e🚧\u003c/a\u003e\u003c/td\u003e\n    \u003c/tr\u003e\n  \u003c/tbody\u003e\n\u003c/table\u003e\n\n\u003c!-- markdownlint-restore --\u003e\n\u003c!-- prettier-ignore-end --\u003e\n\n\u003c!-- ALL-CONTRIBUTORS-LIST:END --\u003e\n\nThis project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!\n\n\n## Licensing\n\nDaedalus itself and all associated software in this repository is licensed following the [`COPYING`](COPYING) file. We are not sponsored or licensed by any of the data sources that we use.\n\nThe data downloaded and parsed by Daedalus is licensed under:\n- The IUPHAR database: [CC BY-SA 4.0](https://creativecommons.org/licenses/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](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab1010/6414576). PMID: 34718737.\n- The COSMIC database: [Custom License](https://cancer.sanger.ac.uk/license/COSMIC_Non_Commercial_Use_Terms_October2021.pdf). Data is remixed and parsed, so the content of the COSMIC database is not redistributed as-is (which would be forbidden).\n- The Gene Onthology: [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/). Current Zenodo DOI: https://dx.doi.org/10.5281/zenodo.7504797\n- The TCDB: [CC BY 3.0](https://creativecommons.org/licenses/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](https://pubmed.ncbi.nlm.nih.gov/33170213/)\n- Ensembl places its data in the Public Domain ([more info](https://www.ensembl.org/info/about/legal/disclaimer.html)).\n- The Human Gene Nomenclature Committee places its data in the Public Domain ([CC0](https://creativecommons.org/share-your-work/public-domain/cc0/), [more info](https://www.genenames.org/about/license/))\n- The Human Protein Atlas: [CC BY 3.0](https://creativecommons.org/licenses/by/3.0/) - Uhlén M et al., Tissue-based map of the human proteome. Science (2015)\nPubMed: 25613900 DOI: 10.1126/science.1260419 ([more info](https://www.proteinatlas.org/about/licence))\n\n\n(Last updated on the 22nd of June, 2023)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftcp-lab%2Fmtp-db","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftcp-lab%2Fmtp-db","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftcp-lab%2Fmtp-db/lists"}