Services

The Belgian ELIXIR node offers specialized bioinformatics resources accelerating research in life-science. These include databases, data resources, tools, workflows, web services, trainings, … that have applications in Plant Sciences, Human Data and Proteomics. Services that have been positively evaluated by the international ELIXIR Belgium Scientific Advisory Board are added to ELIXIR Belgium’s Service Delivery Plan. These Node Services are labelled as important resources produced by the Belgian bioinformatics community. Below, an overview of all ELIXIR Belgium services is given. A complete service list of all ELIXIR Nodes can be found on this link.

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Logo PLAZA

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. It allows querying and visualising structural and functional annotations, gene families, protein domains, phylogenetic trees, and genome organization. PLAZA 4.0 is the latest iteration of the PLAZA framework. This version provides a large increase in newly available species, and offers access to updated and newly implemented tools and visualisations, helping users with the ever-increasing demands for complex and in-depth analyses.

PLAZA was developed at the Ghent University. Core publications and training material can be found here. The latest training on PLAZA took place in October 2019.  

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Logo Scop3P

Scop3P provides a unique and powerful resource to explore and understand the impact of phospho-sites on human protein structure and function, and can thus serve as a springboard for researchers seeking to analyse and interpret a given phosphosite or phosphoprotein in a structural, biophysical, and biological context.

The resource re-uses public domain data from a variety of leading international resources, including UniProtKB and PDB, but also uses reprocessed mass spectrometry-based phospho-proteomics data from PRIDE/ProteomExchange, which is in turn globally collected and thus wholly international-driven.

Scop3P was developed at Ghent University and is online since June 2019. The manuscript describing Scop3P is available as a preprint in BioRXiv.

Service Tags

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Logo Tabloid Proteome

The online Tabloid Proteome is a database of protein association network generated using publically available mass spectrometry based experiments in PRIDE. These associations represent a broad scala of biological associations between pairs of proteins that goes well beyond mere binary protein interactions. As such, the provided information is almost completely complementary to traditional direct protein interaction studies.

In addition to the collection of co-occurring protein pairs, Tabloid Proteome also links to their biological relation in existing knowledgebases. Moreover, pathway links from Reactome, protein-protein interactions from IntAct and BioGRID, protein complexes from CORUM, and paralog information from Ensembl are also superimposed. Functional annotation is provided by disease information from DisGeNET, and Gene Ontology annotations.

Tabloid Proteome was developed at the Ghent university in 2017 and published in Nucleid Acids Research (manuscript). In October 2018, the first training on Tabloid Proteome took place in Gent.

Service Tags

Logo TCRex

The TCRex webtool allows functional interpretation of full human T-cell repertoire data derived from next generation sequencing.

TCRex is the first tool of its kind and is able to link T-cell receptor sequences to a rapidly expanding list of 49 different important immunogenic epitopes, consisting of 44 viral and 5 cancer epitopes. Additional epitopes can be added by users for their own use. The tool is able to calculate enrichment statistics and baseline prediction rates to evaluate full repertoires. It is unique among TCR-epitope prediction tools in that it allows processing of full human repertoires. It has also brought together the largest database on TCR-epitope data to train the underlying machine learning models through manual curation of various online resources and scientific literature.

TCRex was developed at the University of Antwerp and has been released for public use in 2018. The manuscript describing the webtool is available as a preprint in BioRXiv.  TCRex can also be followed on Twitter: @TCRexTool.

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Logo Unipept

Unipept is an open source web application developed at Ghent University that is designed for metaproteomics data analysis with a focus on interactive data visualizations. Unipept is powered by an index containing all UniProt entries, a tweaked version of the NCBI taxonomy and a custom lowest common ancestor algorithm. This combination enables a blazingly fast biodiversity analysis of large and complex metaproteome samples. Next to these core functions, Unipept also has a tool for selecting unique peptides for targeted proteomics and for comparing genomes based on peptide similarity.

Unipept 4.0 is the latest release of the Unipept framework and includes a completely new functional analysis tool and an updated database based on UniProt 2018.06. A tutorial on Unipept has been published in 2018. All Unipept journal articles can be found on this page. Unipept can be followed on Twitter: @unipept.

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Logo VariantDB

VariantDB is a web-based interactive annotation and filtering platform that automatically annotates variants with allele frequencies, functional impact, pathogenicity predictions and pathway information. VariantDB allows filtering by all annotations, under dominant, recessive or de novo inheritance models. VariantDB is therefore a user-friendly and powerful tool to help in the interpretation of NGS data.

VariantDB was developed at the University of Antwerp and published in Genome Medicine (manuscript).

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Logo WiNGS

WiNGS is being developed to succeed NGS-Logistics, the genomics data sharing platform established at KULeuven. The NGS-Logistics platform is currently deployed at 6 of the 8 genetic centres in Belgium and lets users identify clinically relevant mutations at other genetic centres. Its scope is similar but broader than the more recent Beacon project of the Global Alliance for Genomics and Health (GA4GH) and ELIXIR Europe, which provides a framework for public web services for variant discovery against distributed genomic data collections. The ELIXIR Belgium Human Data consortium, led by KULeuven, has been participating in the ELIXIR Beacon project and maintains a Belgian Beacon node.

The WiNGS (Widely integrated NGS) platform holds significant scalability improvements to tackle the complexity of analysing of Whole-Genome Sequencing (WGS) data. Because of the sensitivity of patient genomes and GDPR requirements, enhanced access control and privacy protection for this integrated platform will be developed. The first manuscript of the platform can be downloaded here.