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Merge pull request #1080 from ScilifelabDataCentre/develop
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@LianeHughes
LianeHughes authored Dec 20, 2023
2 parents 9c53544 + b86fe05 commit 09676db
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4 changes: 2 additions & 2 deletions content/english/dashboards/post_covid.md
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Expand Up @@ -131,8 +131,8 @@ The below plot shows the number of times that patients given the diagnoses of in
Rotating your phone may improve graph layout
</div>

<div class="d-md-none plot_wrapper">
<div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weeklycontacts_healthcare.json" height="300px" >}}</div>
<div class="plot_wrapper mb-3">
<div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weeklycontacts_healthcare.json" height="500px" >}}</div>
</div>

**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare.py).
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200 changes: 199 additions & 1 deletion data/available_datasets.json
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@@ -1,6 +1,204 @@
{
"last_updated": "2023-11-02",
"last_updated": "2023-12-15",
"datasets": [
{
"doi": "10.1136/bmjopen-2022-064240",
"available_items": [
{
"type": "data",
"repo_name": "Zenodo",
"accession_number": "",
"description": "A collection of serology data created by WHO Unity Studies Global SARS-CoV2 Seroepidemiological Investigations. Includes both data published in studies and other data not used in publications.",
"data_type": [
"Serology data"
],
"data_url": "https://zenodo.org/communities/unity-sero-2021?q=&l=list&p=1&s=20&sort=newest"
}
],
"title": "Systematic review of seroprevalence of SARS-CoV-2 antibodies and appraisal of evidence, prior to the widespread introduction of vaccine programmes in the WHO European Region, January–December 2020",
"issue": "11",
"volume": "13",
"publisher": "BMJ",
"published": "2023-11-06",
"author": [
"Vaughan A.",
"Duffell E.",
"Freidl G. S.",
"Lemos D. S.",
"Nardone A."
]
},
{
"doi": "10.1186/s13613-023-01201-1",
"available_items": [
{
"type": "code",
"repo_name": "Zenodo",
"accession_number": "",
"description": "Data curation pipeline for patient data extracted for medical records up to 60th day of ICU stay (written in R, Version v3.0.1 used).",
"data_type": [
"Other data",
"Public health data"
],
"data_url": "https://zenodo.org/records/6063905"
},
{
"type": "data",
"repo_name": "Zenodo",
"accession_number": "",
"description": "Data dictionaries associated with data curation pipeline used.",
"data_type": [
"Other data",
"Public health data"
],
"data_url": "https://zenodo.org/records/6063905"
}
],
"title": "Early mobilisation in critically ill COVID-19 patients: a subanalysis of the ESICM-initiated UNITE-COVID observational study",
"issue": "1",
"volume": "13",
"publisher": "Springer Science and Business Media LLC",
"published": "2023-11-14",
"author": [
"Kloss P.",
"Lindholz M.",
"Milnik A.",
"Azoulay E.",
"Cecconi M."
]
},
{
"doi": "10.1016/j.xcrm.2023.101267",
"available_items": [
{
"type": "data",
"repo_name": "Sequence Read Archive",
"accession_number": "PRJNA1014462",
"description": "Raw sequence reads related to SARS-CoV-2 antibodies from children exhibiting broad neutralisation.",
"data_type": [
"Biochemistry data",
"Health data",
"Serology data"
],
"data_url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1014462/"
},
{
"type": "data",
"repo_name": "Electron Microscopy Databank",
"accession_number": "EMD-41075",
"description": "SARS-CoV-2 spike in complex with Fab 71281-33.",
"data_type": [
"Biochemistry data",
"Health data",
"Serology data"
],
"data_url": "https://www.ebi.ac.uk/emdb/EMD-41075"
},
{
"type": "data",
"repo_name": "Electron Microscopy Databank",
"accession_number": "EMD-41076",
"description": "SARS-CoV-2 spike in complex with Fab 71281-33 (2).",
"data_type": [
"Biochemistry data",
"Health data",
"Serology data"
],
"data_url": "https://www.ebi.ac.uk/emdb/EMD-41075"
}
],
"title": "SARS-CoV-2 antibodies from children exhibit broad neutralization and belong to adult public clonotypes",
"issue": "11",
"volume": "4",
"publisher": "Elsevier BV",
"published": "2023-12-02",
"author": [
"Wall S. C.",
"Suryadevara N.",
"Kim C.",
"Shiakolas A. R.",
"Holt C. M."
]
},
{
"doi": "10.2807/1560-7917.es.2023.28.46.2300595",
"available_items": [
{
"type": "data",
"repo_name": "GISAID",
"accession_number": "",
"description": "Whole genome sequence data from individuals for all Swedish BA.2.86 cases is available on GISAID. The accession numbers are avilable in the supplementary materials (linked here).",
"data_type": [
"Other data",
"Genomics & transcriptomics data"
],
"data_url": "https://www.eurosurveillance.org/docserver/fulltext/eurosurveillance/28/46/23-00595_MOVERT_Supplement.pdf?expires=1702970040&id=id&accname=guest&checksum=39802568B41757067FA9C2CC9B13E7F2"
},
{
"type": "data",
"repo_name": "GISAID",
"accession_number": "",
"description": "The findings of the BA.2.86 marker specificity assessment are based on metadata associated with 13,513 sequences available on GISAID from 1 July to 19 October 2023.",
"data_type": [
"Other data",
"Genomics & transcriptomics data"
],
"data_url": "https://www.epicov.org/epi3/epi_set/EPI_SET_231113ve?main=true"
},
{
"type": "data",
"repo_name": "ENA",
"accession_number": "PRJEB67638",
"description": "Wastewater raw reads from Uppsala, Örebro, Umeå, and Kalmar.",
"data_type": [
"Other data",
"Genomics & transcriptomics data"
],
"data_url": "https://www.ebi.ac.uk/ena/browser/view/PRJEB67638"
}
],
"title": "Early detection of the emerging SARS-CoV-2 BA.2.86 lineage through integrated genomic surveillance of wastewater and COVID-19 cases in Sweden, weeks 31 to 38 2023",
"issue": "46",
"volume": "28",
"publisher": "European Centre for Disease Control and Prevention (ECDC)",
"published": "2023-11-16",
"author": [
"Espinosa-Gongora C.",
"Berg C.",
"Rehn M.",
"Varg J. E.",
"Dillner L."
]
},
{
"doi": "10.1038/s41586-023-06717-x",
"available_items": [
{
"type": "data",
"repo_name": "NCBI database",
"accession_number": "PRJNA989123",
"description": "Raw RNA sequence reads produced when patient whole blood samples were analysed by RNA sequencing in order to monitor global changes in transcript abundance levels post-interferon treatment.",
"data_type": [
"Biochemistry data",
"Genomics & transcriptomics data",
"Health data"
],
"data_url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA989123"
}
],
"title": "Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency",
"issue": "7988",
"volume": "623",
"publisher": "Springer Science and Business Media LLC",
"published": "2023-11-08",
"author": [
"Le Voyer T.",
"Parent A. V.",
"Liu X.",
"Cederholm A.",
"Gervais A."
]
},
{
"doi": "10.1186/s13059-023-03080-y",
"available_items": [
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2 changes: 1 addition & 1 deletion data/publications.json
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