Projects

imex-repository

THIS INFORMATION IS NO LONGER USEFUL, AS THE APPROACH WILL BE TO USE PSICQUIC INSTEAD Welcome to the homepage for the IMEx Repository Project. The IMEx consortium is a group of major public interaction data providers sharing curation effort and exchanging completed records on molecular ... [More] interaction data, similar to successful global collaborations for protein and DNA sequences and for macromolecular structures. More information can be found on the IMEx web site. PrincipleExchanging data between IMEx Members is a complex task. This project aims to simplify the exchange by addressing the common technical difficulties that any IMEx database needs to deal with. A Federation of IMEx RepositoriesCurrently, the IMEx Exchange is defined like this: each database exposes its data in a FTP site, in PSI-MI XML format, and the other members need to fetch this data and incorporate it into their database. The process can be simplified if we consider each of these databases or data repositories an IMEx Repository. Then we see all this exchange process as the communication between different nodes in a federation of IMEx Repositories.An IMEx Repository does not need to be an interaction database. It can be any molecular data repository that provides ways to get the data in an organized fashion. For instance, we could consider an IMEx Repository a filesystem that contains PSI-MI XML files. Thus, by considering that everything that contains interaction data is a potential "IMEx Repository" we can greatly simplify the problem of transfering data among the repositories. We can think of IMEx Repositories as black boxes that provide the same way to fetch/store data in the same way, without really needing to know what kind of repository we are dealing with. So, the IMEx Repository Project is a a Java-based open-source project that defines an API to allow you create and work with IMEx Repositories. A well-defined syntax allows you to create this façade around your interaction database/repository so it can be used as an IMEx Repository. In this project, you will find the tools to define your own flows of data between the IMEx repositories of your choice, making it possible to easily create an IMEx Exchange system. Staging IMEx RepositoryA fully-fledged IMEx Exchange system needs to have proper ways to execute certain actions on the data it contains, such as validation or modification (processing) of files. With the libraries in this project you can set up this processes by using provided actions (e.g. PSI-MI XML validator) or custom ones that you can create using the API. It is a rule for the IMEx Exchange Consortium to always keep a copy of the original data, excluding any modifications than a particular IMEx Repository is doing. As this is common to all IMEx members, an Staging IMEx Repository has been devised. The task of this node is modify the data according to pre-defined or custom processes, all this by keeping an original copy of the data. It serves as a gateway for data from other IMEx members and prepares the data from the local member to make it ready for publication through the FTP site. Let's have a look at the following scenario: Each member can have its own Staging Repository. This repository received the data from the other members through the internet and pushes the local member data to be released into the FTP. This IMEx Repository acts as an intermediary between the database and the "exchangeable" data. It can be used as an archive of the original data and as the place where all data validation and processing takes place in order to prepare external data to follow the local policies. IMEx ReleasesThe basic unit of exchange among members is a release. Each member bundles data from different publications and makes it public to the other members in a certan date. Each bundle published is a "release", and the date is used to distinguish between different releases. Not all member release data at the same time, so when new data from different members is available can vary. Each release bundle comes with the interaction data, as well as some metadata about the data released. This metadata is an XML file that lists what publications/interactions are contained in the release bundle and whether they are new, updated or deleted. [Less]