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Open AccessJournal ArticleDOI

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.

TLDR
All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset.
Abstract
IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org).

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STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.

TL;DR: The latest version of STRING more than doubles the number of organisms it covers, and offers an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input.
Journal ArticleDOI

STRING v10: protein–protein interaction networks, integrated over the tree of life

TL;DR: H hierarchical and self-consistent orthology annotations are introduced for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution in the STRING database.
Journal ArticleDOI

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

TL;DR: In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework.
Journal ArticleDOI

CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes.

TL;DR: The structure and content of CellPhoneDB is outlined, procedures for inferring cell–cell communication networks from single-cell RNA sequencing data are provided and a practical step-by-step guide to help implement the protocol is presented.
References
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Journal ArticleDOI

Activities at the Universal Protein Resource (UniProt)

Rolf Apweiler, +133 more
TL;DR: The mission of the Universal Protein Resource (UniProt) is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequences and functional annotation.
Journal ArticleDOI

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions

TL;DR: The Database of Interacting Proteins (DIP) is a database that documents experimentally determined protein-protein interactions and provides the scientific community with an integrated set of tools for browsing and extracting information about protein interaction networks.
Journal ArticleDOI

A travel guide to Cytoscape plugins

TL;DR: A travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5–2.8 and ongoing efforts to distribute, organize and maintain the quality of the collection.
Journal ArticleDOI

MINT, the molecular interaction database: 2012 update

TL;DR: The growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction are reported here.
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