ICT::bib

This repository attempts to trace all the published scientific works regarding the transportome, defined as the collection of all the membrane proteins responsible for the translocation of any kind of solutes across the lipid bilayer.

If you use this repository for your research, please cite our paper:

Federico Alessandro Ruffinatti, Giorgia Scarpellino, Giorgia Chinigò, Luca Visentin, Luca Munaron. The Emerging Concept of Transportome: State of the Art Review Physiology (Bethesda). 2023 Nov 1;38(6):0. PMID: 37668550; DOI: 10.1152/physiol.00010.2023

Main Facts

Library Structure

The library (accessible in /Library/) is divided into two different sections:

• the Reviews section collects all reviews about the transportome;
  • the Cancer subsection collects all reviews regarding the transportome in cancer;
  • the Non Cancer section collects all other reviews;
• the Research Articles section collects all research articles investigating the transportome--or, at least, an entire molecular class of transporters (e.g., all SLCs, all ion channels, etc.).

We manually annotate each article in the library with the following information, in addition to the standard bibliographical information:

• Macro-area: the main scientific area the paper covers (e.g., "Breast Cancer", "Cell Motility", "Plants", etc.);
• Topic: the specific topic the paper covers (e.g. "Evolution", "Intestinal Inflammation", etc.);
• Transportomic Target: the specific portion (or layer) of the transportome investigated in the paper, chosen among the following entries:
  • Ion Channels
  • Aquaporins
  • Pores (= Ion Channels AND Aquaporins)
  • SLCs (= solute carriers)
  • Pumps (= ATPase pumps)
  • ABCs (= ATP-binding cassette transporters)
  • Transporters (= SLCs AND Pumps AND ABCs)
  • ICTs (= the whole transportome)

Inside each section, the library is organized in four different categorizations, one for each of the above-mentioned manual annotations, plus by year of publication.

Inside each categorization folder, there is a README.md file with an index of all papers on that section, sorted by the specific categorization criterion.

By navigating into a subsection (e.g., /Library/Reviews/Cancer/by year/2022/) you will find one file per publication, with information such as DOI, Journal of publication, abstract, and more. Each subsection also contains one .library.bib file with the bibliographical information of all the papers in that subsection in .bib format, for ease of inclusion in bibliography managers.

Contributing

We welcome and encourage all contributions! If you find an error, or wish to contribute your own article or an article you find to the library, please open an issue.

If you want to contribute to the repository's code, please take a look at the CONTRIBUTING.md file.