The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing

Harrison, Peter W.; López, Rodrigo; Rahman, Nadim; Allen, Stefan Gutnick; Aslam, Raheela; Buso, Nicola; Cummins, Carla; Fathy, Yasmin; Félix, Eloy; Glonț, Mihai; Jayathilaka, Suran; Kadam, Sonal; Kumar, Manish; Lauer, Katharina B.; Malhotra, Geetika; Mosaku, Abayomi; Edbali, Ossama; Park, Young Mi; Parton, Andrew; Pearce, Matt; Pena, Jose Francisco Estrada; Rossetto, Joseph; Russell, Craig; Selvakumar, Sandeep; Sitjà, Xènia Pérez; Sokolov, Alexey; Thorne, Ross; Ventouratou, Marianna; Walter, Peter; Yordanova, Galabina; Zadissa, Amonida; Cochrane, Guy; Blomberg, Niklas; Apweiler, Rolf

doi:10.1093/nar/gkab417

Cited by 71 publications

(57 citation statements)

References 23 publications

(23 reference statements)

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“…Importantly, as of September 2021, more than 180 COVID-19 related datasets have been submitted to PRIDE Archive. These datasets, once they become publicly available, are integrated into the EMBL-EBI resource COVID-19 Data Portal ( https://www.covid19dataportal.org/ ), enabling researchers to access all public data at EMBL-EBI resources in a unified interface ( 42 ).…”

Section: Pride Archive Submission Statisticsmentioning

confidence: 99%

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Perez‐Riverol

Bai

Bandla

et al. 2021

Nucleic Acids Research

3,909

2,678

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The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is one of the founding members of the global ProteomeXchange (PX) consortium and an ELIXIR core data resource. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2019. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 500 datasets per month during 2021. In addition to continuous improvements in PRIDE Archive data pipelines and infrastructure, the PRIDE Spectra Archive has been developed to provide direct access to the submitted mass spectra using Universal Spectrum Identifiers. As a key point, the file format MAGE-TAB for proteomics has been developed to enable the improvement of sample metadata annotation. Additionally, the resource PRIDE Peptidome provides access to aggregated peptide/protein evidences across PRIDE Archive. Furthermore, we will describe how PRIDE has increased its efforts to reuse and disseminate high-quality proteomics data into other added-value resources such as UniProt, Ensembl and Expression Atlas.

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Section: Pride Archive Submission Statisticsmentioning

confidence: 99%

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Perez‐Riverol

Bai

Bandla

et al. 2021

Nucleic Acids Research

3,909

2,678

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“…In response to the COVID-19 pandemic and in collaboration with the effort of building the COVID Data Portal ( 8 ) at EMBL-EBI, we continue to source and uniformly analyse datasets that contribute to the research community's response to the COVID-19 pandemic. All these efforts have resulted in over 20% growth in the data volume in Expression Atlas during the last two years.…”

Section: Introductionmentioning

confidence: 99%

Expression Atlas update: gene and protein expression in multiple species

Moreno

Fexová

George

et al. 2021

Nucleic Acids Research

119

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The EMBL-EBI Expression Atlas is an added value knowledge base that enables researchers to answer the question of where (tissue, organism part, developmental stage, cell type) and under which conditions (disease, treatment, gender, etc) a gene or protein of interest is expressed. Expression Atlas brings together data from >4500 expression studies from >65 different species, across different conditions and tissues. It makes these data freely available in an easy to visualise form, after expert curation to accurately represent the intended experimental design, re-analysed via standardised pipelines that rely on open-source community developed tools. Each study's metadata are annotated using ontologies. The data are re-analyzed with the aim of reproducing the original conclusions of the underlying experiments. Expression Atlas is currently divided into Bulk Expression Atlas and Single Cell Expression Atlas. Expression Atlas contains data from differential studies (microarray and bulk RNA-Seq) and baseline studies (bulk RNA-Seq and proteomics), whereas Single Cell Expression Atlas is currently dedicated to Single Cell RNA-Sequencing (scRNA-Seq) studies. The resource has been in continuous development since 2009 and it is available at https://www.ebi.ac.uk/gxa.

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“…This technical platform enables the pooling of sequence data throughout Germany, further enriched by in-house-sequenced samples as part of the SARS-CoV-2 Integrated Molecular Surveillance lab-network (IMS-SC2). Data submitted to DESH from sequencing laboratories across the country, as well as IMS-SC2 sequence data, in combination with additional international data from resources such as GISAID [ 9 ] or EMBL-EBIs COVID-19 Data Portal [ 10 ], enabled comprehensive genomic surveillance of the pandemic across Germany.…”

Section: Introductionmentioning

confidence: 99%

Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany

Calvignac‐Spencer

Budt

Huska

et al. 2021

Viruses

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Here, we report on the increasing frequency of the SARS-CoV-2 lineage A.27 in Germany during the first months of 2021. Genomic surveillance identified 710 A.27 genomes in Germany as of 2 May 2021, with a vast majority identified in laboratories from a single German state (Baden-Wuerttemberg, n = 572; 80.5%). Baden-Wuerttemberg is located near the border with France, from where most A.27 sequences were entered into public databases until May 2021. The first appearance of this lineage based on sequencing in a laboratory in Baden-Wuerttemberg can be dated to early January ’21. From then on, the relative abundance of A.27 increased until the end of February but has since declined—meanwhile, the abundance of B.1.1.7 increased in the region. The A.27 lineage shows a mutational pattern typical of VOIs/VOCs, including an accumulation of amino acid substitutions in the Spike glycoprotein. Among those, L18F, L452R and N501Y are located in the epitope regions of the N-terminal- (NTD) or receptor binding domain (RBD) and have been suggested to result in immune escape and higher transmissibility. In addition, A.27 does not show the D614G mutation typical for all VOIs/VOCs from the B lineage. Overall, A.27 should continue to be monitored nationally and internationally, even though the observed trend in Germany was initially displaced by B.1.1.7 (Alpha), while now B.1.617.2 (Delta) is on the rise.

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The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing

Cited by 71 publications

References 23 publications

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Expression Atlas update: gene and protein expression in multiple species

Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany

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