MTP-DB version 1.25.24

This is the latest build of the MTP-DB, with updated databases as of the 10th of June, 2025.

Changelog

• New post-build hook fixing FXYD genes, which were wrongly listed in the channels table instead of the transporters table.

MTP-DB Version 1.25.16

This is the newest release of the MTP-DB.

Changes

• Added new post-build hooks targeting calcium transporters.

MTP-DB Version 1.25.04

This is the newest release of the MTP-DB.

Changes

• BREAKING: Changed table name from atp_driven_transporters to pumps.
• Update run_rebuilder to be compatible with the new CLI;
• Added tables structure, function and origin with information about the structure, physiological function and tissue of expression of genes.
• Updated some post-build hooks.
• Updated download links so that we leverage the latest version of the IUPHAR database.
• A lot of missing carried solutes and other miscellaneous issues were fixed.
• Write better READMEs.

Added the mazeinspector module to check the quality of the MTP-DB with some statistics.

MTP-DB Version 1.24.46

This version was compiled on the 15 November 2024.

News

• Compatibility with new and old endpoints;
• Fixed issues #34, #10 and #9;
• Added an how-to guide in the Documentation on Github;
• Many ID cols have been indexed to provide much, much faster access with chained SELECT statements.

I've attached the datacache used to create this release for reproducibility.

MTP-DB version 1.24.09

The MTP-DB was regenerated with current data, as of today (February the 27th, 2024).

Fixes

• Compatibility Fixes with remotes were applied;

Changes

• ! Due to changes in data availability policy, this release does not contain COSMIC mutational data.

The MTP-DB version 1.23.25-beta

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.

This release is (hopefully) very close to what we can use for the MTPDB preprint. A lot of issues have been addressed:

• BREAKING: The gene_names > gene_synonyms column was removed;
• BREAKING: The atp_driven_transporters table was renamed to pumps;
• Update run_rebuilder to be compatible with the new CLI;
• Added tables structure, function and origin with information about the structure, physiological function and tissue of expression of genes. Additionally, information on the role of genes in disease settings is also added. All of these information is taken from IUPHAR.
  • Especially useful should be the pore-forming loops information.
• The thesaurus was not being applied correctly to the data, so that some synonyms were not inserted correctly. It is now applied recursively, fixing the problem.
• The aquaporins now have a tissue of origin.
• Various small fixes, like removing useless duplicates in some tables.

For developers

Some extra infrastructure was added for developers:

• Added a tiny subpackage called mazeinspector that looks at the database and provides some (potentially useful) statistics in order to catch bugs.
• Written better READMEs.
• Updated CONTRIBUTING.md to add some missing information.
• Added a small data-dumping script to dump to loose .csv files the data in the MTPDB_datacache.pickle file. It is useful while developing to keep the data you are iterating upon open on the side as a reference.
• Some code was refactored.

Merged pull requests

• Bump requests from 2.28.1 to 2.31.0 in /src by @dependabot in #38
• Bump certifi from 2022.9.24 to 2022.12.7 in /src by @dependabot in #40
• Add the Gene Onthology data to the MTP-DB by @MrHedmad in #39
• Big review of the MTP-DB by @MrHedmad in #41

New Contributors

• @dependabot made their first contribution in #38

Full Changelog: 0.23.17-beta...1.23.25-beta

MTP-DB v. 0.23.17-beta

The first public release of the MTP-DB! We are all very excited. Taking it from the top:

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.

Not much has changed code-wise in respect of the last pre-release, but the fact that we are now open-source and fully accept contributions. Please check out the README for more information on how you can contribute! We are also on Docker Hub! Check the README, again, for info!

MTP-DB v. 0.23.15-beta

This is the first release of the database. The DB features data from 7 different databases, all joined up for ease of consumption. We include:

• ENSEMBL gene IDs and information, making the backbone of the database IDs;
• HGNC for up-to-date, official gene names and gene grouping;
• IUPHAR for target (in our case transporters) and ligand (i.e. drugs/internal compounds) interactions, as well as gene grouping, ion channel conductances, and more;
• COSMIC for mutational information;
• SLC tables for solute carrier information, such as their class and carried solute;
• TCDB for transporter classification information.

We apply manual patches to the data where expert information is lacking from the above databases.

The database is released as a .sqlite file at each release.