The next-generation Open Targets Platform: reimagined, redesigned, rebuilt.

The Open Targets Platform (https://platform.opentargets.org/) is an open source resource to systematically assist drug target identification and prioritisation using publicly available data.

A decoupled, modular and scriptable architecture for tools to curate data platforms.

Motivation: Curation is essential for any data platform to maintain the quality of the data it provides. Today, more effective curation tools are often vital to keep up with the rapid growth of existing, maintenance-requiring databases and the amount of newly published information that needs to be surveyed. However, curation interfaces are often complex and challenging to be further developed.

Identifiers.org: Compact Identifier services in the cloud.

Motivation: Since its launch in 2010, Identifiers.org has become an important tool for the annotation and cross-referencing of Life Science data. In 2016, we established the Compact Identifier (CID) scheme (prefix: accession) to generate globally unique identifiers for data resources using their locally assigned accession identifiers.

The PRIDE database and related tools and resources in 2019: improving support for quantification data.

The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.

The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and dissemination of mass spectrometry proteomics data worldwide.

Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks.

Unlabelled: Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.

HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.

Recent advances in mass-spectrometry-based proteomics are now facilitating ambitious large-scale investigations of the spatial and temporal dynamics of the proteome; however, the increasing size and complexity of these data sets is overwhelming current downstream computational methods, specifically those that support the postquantification analysis pipeline. Here we present HiQuant, a novel application that enables the design and execution of a postquantification workflow, including common data-processing steps, such as assay normalization and grouping, and experimental replicate quality control and statistical analysis. HiQuant also enables the interpretation of results generated from large-scale data sets by supporting interactive heatmap analysis and also the direct export to Cytoscape and Gephi, two leading network analysis platforms.