Other data

Published Data

Information about available data of the types that do not fit into other categories of data on our portal is displayed on this page.

Data available from research groups in Sweden

The list of available data on this Portal was curated manually until February 2022. After February 2022, we instead began to use a script to query the Europe PMC database (making use of their API) in order to locate relevant publications. We only include data from publications about COVID-19/SARS-CoV-2 that BOTH involve at least one author affiliated with a Swedish research institution AND openly share reusable data and/or code. The code used for the query is written in Python and, as with all of our code, it is openly available in GitHub. We welcome others to reuse it and to repurpose it for other pathogens.

The lists of available data may not be exhaustive as the script used to generate it does not search for every possible database/repository. If you find that a dataset is missing, or that the information related to it is incorrect, please get in touch with us

Last updated: 2024-09-04

Data types

All data types (290)

Biochemistry data (34)

Drug discovery data (15)

Genomics & transcriptomics data (84)

Health data (102)

Imaging data (7)

Other data (47)

Protein data (48)

Public health data (68)

Serology data (22)

Social science and humanities data (64)

Publication	Available dataset and code
A structured course of disease dataset with contact tracing information in Taiwan for COVID-19 modelling Wu Y., Nordling T. E. M. (2024) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41597-024-03627-z	COVID-19 Taiwan data, including individual course of disease data figshare Companion code to Wu and Nordling 2023 for visualisation of Taiwanese COVID-19 data code Github
COVID-19 knowledge and practices in Jigawa State, Nigeria: A cross-sectional survey conducted during the second wave Salako J., Bakare D., Sogbesan A., Colbourn T., et al (2024) Public Library of Science (PLoS) DOI: https://doi.org/10.1371/journal.pgph.0003386	COVID-19 knowledge, and associations with good knowledge of prevention, symptoms data figshare
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 Espinosa-Gongora C., Berg C., Rehn M., Varg J. E., et al (2023) European Centre for Disease Control and Prevention (ECDC) DOI: 10.2807/1560-7917.es.2023.28.46.2300595	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 GISAID 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 GISAID Wastewater raw reads from Uppsala, Örebro, Umeå, and Kalmar. data ENA: PRJEB67638
Early mobilisation in critically ill COVID-19 patients: a subanalysis of the ESICM-initiated UNITE-COVID observational study Kloss P., Lindholz M., Milnik A., Azoulay E., et al (2023) Springer Science and Business Media LLC DOI: 10.1186/s13613-023-01201-1	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). code Zenodo Data dictionaries associated with data curation pipeline used. data Zenodo
Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis Hartman E., Scott A. M., Karlsson C., Mohanty T., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41467-023-41146-4	AKI DIA samples for generalized peakgroup scoring model application data PRIDE: PXD038394 A time-resolved proteomic and prognostic map of COVID-19 data PRIDE: PXD025752 Olink Dataset data Figshare 56 samples from acute kidney injury patients (DIA-MS septic AKI dataset). data PRIDE: PXD044264 Biologically Informed Neural Network (BINN) code code GitHub InfectionMedicineProteomics/BINN: First release code Zenodo DE-score algorithm has been implemented into the data processing package DPKS code GitHub
Cost Effectiveness of Strategies for Caring for Critically Ill Patients with COVID-19 in Tanzania Shah H. A., Baker T., Schell C. O., Kuwawenaruwa A., et al (2023) Springer Science and Business Media LLC DOI: 10.1007/s41669-023-00418-x	POETIC-COVID CEA PROJECT - R code that supports the findings of the study code GitHub
Treating intrusive memories after trauma in healthcare workers: a Bayesian adaptive randomised trial developing an imagery-competing task intervention Ramineni V., Millroth P., Iyadurai L., Jaki T., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41380-023-02062-7	Anonymised databases with the individual participant data and the metadata for Bayesian analyses, along with a data dictionary data Open Science Framework The Study Protocol and Bayesian Statistical Analysis Plan protocol Open Science Framework
Nowcasting COVID-19 Statistics Reported with Delay: A Case-Study of Sweden and the UK Altmejd A., Rocklöv J., Wallin J. (2023) MDPI AG DOI: 10.3390/ijerph20043040	Data related to development of a statistical methodology for predicting true daily quantities and their uncertainty, estimated using historical reporting delays data GitHub R code related to development of a statistical methodology for predicting true daily quantities and their uncertainty, estimated using historical reporting delays code GitHub
Monkeypox outbreaks in the context of the COVID-19 pandemic: Network and clustering analyses of global risks and modified SEIR prediction of epidemic trends Gao J., Zhou C., Liang H., Jiao R., et al (2023) Frontiers Media SA DOI: 10.3389/fpubh.2023.1052946	Information on open data sources used e.g. for socioeconomic factors, environment, biodiveristy, health, among others. data
Association between long-term air pollution exposure and COVID-19 mortality in Latin America Bonilla J. A., Lopez-Feldman A., Pereda P. C., Rivera N. M., et al (2023) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0280355	Aggregated data of COVID-19 mortality and long-term air pollution concentrations data Github Stata scripts used to compile the statitics code Github
Financial incentives for vaccination do not have negative unintended consequences Schneider F. H., Campos-Mercade P., Meier S., Pope D., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41586-022-05512-4	Randomised controlled trial data from Sweden and United States for COVID-19 first dose vaccination data Zenodo Analyses were conducted using STATA 16, the code to replicate the analysis is in the article code Zenodo
Defining post-acute COVID-19 syndrome (PACS) by an epigenetic biosignature in peripheral blood mononuclear cells Nikesjö F., Sayyab S., Karlsson L., Apostolou E., et al (2022) Springer Science and Business Media LLC DOI: 10.1186/s13148-022-01398-1	Analysis and visualisation scripts code GitHub
Family still matters: Human social motivation across 42 countries during a global pandemic Pick C. M., Ko A., Wormley A. S., Wiezel A., et al (2022) Elsevier BV DOI: 10.1016/j.evolhumbehav.2022.09.003	Data related to social motivation data Open Science Framework
Development and cross-national investigation of a model explaining participation in WHO-recommended and placebo behaviours to prevent COVID-19 infection Kłosowska J., Bajcar E. A., Bieniek H., Brączyk J., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41598-022-17303-y	Processed and anonymised demographic and health data. data Open Science Framework
A Mendelian randomization study of genetic predisposition to autoimmune diseases and COVID-19 Li S., Yuan S., Schooling C. M., Larsson S. C. (2022) Springer Science and Business Media LLC DOI: 10.1038/s41598-022-22711-1	Exposure dataset for type 1 diabetes mellitus data MR-base: ebi-a-GCST005536 Exposure dataset for systemic lupus erythematosus data MR-base: ebi-a-GCST003156 Exposure dataset for psoriasis data MR-base: ebi-a-GCST005527 Exposure dataset for multiple sclerosis data MR-base: ieu-b-18 Exposure dataset for primary sclerosing cholangitis data MR-base: ieu-a-1112 Exposure dataset for primary biliary cirrhosis data MR-base: ebi-a-GCST005581 Outcome datasets generated in the current study. data COVID19-hg GWAS
A meta-epidemiological assessment of transparency indicators of infectious disease models Zavalis E. A., Ioannidis J. P. A. (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0275380	The protocol for this study protocol Open Science Framework Data used to evaluate publications and model types, and the code used for analysis. code GitHub
Treating intrusive memories after trauma in healthcare workers: a Bayesian adaptive randomised trial developing an imagery-competing task intervention Ramineni V., Millroth P., Iyadurai L., Jaki T., et al (2022) Cold Spring Harbor Laboratory DOI: 10.1101/2022.10.06.22280777	Anonymised databases with the individual participant data and the metadata for Bayesian analyses. data Open Science Framework Code used for data analysis. code Open Science Framework
Changes in non-communicable diseases, diet and exercise in a rural Bangladesh setting before and after the first wave of COVID-19 King C., Shaha S. K., Morrison J., Ahmed N., et al (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pgph.0001110	Fully anonymised data from two cross-sectional surveys data FigShare
Forecasting the publication and citation outcomes of COVID-19 preprints Gordon M., Bishop M., Chen Y., Dreber A., et al (2022) The Royal Society DOI: 10.1098/rsos.220440	Survey responses collected through Qualtrix data dryad Code used for analysis (in R) code dryad
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity Ambikan A. T., Yang H., Krishnan S., Svensson Akusjärvi S., et al (2022) Elsevier BV DOI: 10.1016/j.cels.2022.06.006	Metabolomics data data FigShare Analysis code code Zenodo
Over half of known human pathogenic diseases can be aggravated by climate change Mora C., McKenzie T., Gaw I. M., Dean J. M., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41558-022-01426-1	All data collected as part of the literature search (list of considered diseases, and references for empirical cases. data GitHub
The effect of herd immunity thresholds on willingness to vaccinate Andersson P. A., Tinghög G., Västfjäll D. (2022) Springer Science and Business Media LLC DOI: 10.1057/s41599-022-01257-7	Data related to herd immunity, willingness to get vaccinated, and demographic factors. data Open Science Framework
Agile software development one year into the COVID-19 pandemic Ågren P., Knoph E., Berntsson Svensson R. (2022) Springer Science and Business Media LLC DOI: 10.1007/s10664-022-10176-9	R code for Bayesian analysis code Zenodo
Dataset: COVID-19 epidemic policy and events timeline (Sweden) Olofsson T., Vilhelmsson A. (2022) Elsevier BV DOI: 10.1016/j.dib.2021.107698	Chronological data on Swedish Governmental COVID-19 policy/actions protocol Zenodo
Epidemic risk perceptions in Italy and Sweden driven by authority responses to COVID-19 Raffetti E., Mondino E., Di Baldassarre G. (2022) Springer Science and Business Media LLC DOI: 10.1038/s41598-022-13218-w	A comparative dataset on public perceptions of multiple risks during the COVID-19 pandemic in Italy and Sweden. data Zenodo Code for processing and visualisations code GitHub
Occurrence and transmission potential of asymptomatic and presymptomatic SARS-CoV-2 infections: Update of a living systematic review and meta-analysis Buitrago-Garcia D., Ipekci A. M., Heron L., Imeri H., et al (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pmed.1003987	Data from the systematic review on asymptomatic and presymptomatic SARS-CoV-2 infection data GitHub Code used to display and synthesise the results code GitHub
Meteorological factors and non-pharmaceutical interventions explain local differences in the spread of SARS-CoV-2 in Austria Ledebur K., Kaleta M., Chen J., Lindner S. D., et al (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pcbi.1009973	Data time series of metereological factors, regional measures and mobility data Zenodo Scripts for the model code GitHub
The required size of cluster randomized trials of nonpharmaceutical interventions in epidemic settings Sheen J. K., Haushofer J., Metcalf C. J. E., Kennedy‐Shaffer L. (2022) Wiley DOI: 10.1002/sim.9365	Code and simulated data code GitHub
COVID-19 collateral damage—psychological burden and behavioural changes among older adults during the first outbreak in Stockholm, Sweden: a cross-sectional study Beridze G., Triolo F., Grande G., Fratiglioni L., et al (2022) BMJ DOI: 10.1136/bmjopen-2021-058422	Data are from the SNAC-K Project, a population-based study on ageing and dementia. Need approval for access. data
COVID‐19‐specific metabolic imprint yields insights into multiorgan system perturbations Cornillet M., Strunz B., Rooyackers O., Ponzetta A., et al (2021) Wiley DOI: 10.1002/eji.202149626	Curated data are available for exploration via the Karolinska KI/K COVID-19 Immune Atlas data
Accessible data curation and analytics for international-scale citizen science datasets Murray B., Kerfoot E., Chen L., Deng J., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41597-021-01071-x	Code used to generate synthetic evalutation datasets code Source code for ExeTera code
Impact of tiered restrictions on human activities and the epidemiology of the second wave of COVID-19 in Italy Manica M., Guzzetta G., Riccardo F., Valenti A., et al (2021) Nature Communications DOI: https://doi.org/10.1038/s41467-021-24832-z	Data from different provinces and analysis code data code Figshare
Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021 Funk T., Pharris A., Spiteri G., Bundle N., et al (2021) European Centre for Disease Control and Prevention (ECDC) DOI: 10.2807/1560-7917.ES.2021.26.16.2100348	Data in supplementary materials/appendices - data on genetic data divided by demogaphic factors data
Epidemiology and transmission characteristics of early COVID-19 cases, 20 January–19 March 2020, in Bavaria, Germany Böhm S., Woudenberg T., Chen D., Marosevic D. V., et al (2021) Cambridge University Press (CUP) DOI: 10.1017/S0950268821000510	Analysis code (R) code Data related to incubation period and patient. data
Assessing relative COVID-19 mortality: a Swiss population-based study Hothorn T., Bopp M., Günthard H., Keiser O., et al (2021) BMJ DOI: 10.1136/bmjopen-2020-042387	R and Stata code related to COVID-19 mortality assessment code GitLab
Ophthalmic Screening in Patients with Coronavirus Disease 2019: A Prospective Cohort Study Papazoglou A., Conen A., Haubitz S., Tschopp M., et al (2021) MDPI AG DOI: 10.3390/jcm10050896	Patient characteristics, medical treatment regiments, symptoms, laboratory findings, ophthalmic findings, systemic symtoms for each patient data
A Novel Olfactory Self-Test Effectively Screens for COVID-19 Snitz K., Honigstein D., Weissgross R., Ravia A., et al (2021) Cold Spring Harbor Laboratory DOI: 10.1101/2021.02.18.21251422	Data related to olfaction tests data Gitlab Analysis code (Matlab) code Gitlab
The effects of school closures on SARS-CoV-2 among parents and teachers Vlachos J., Hertegård E., B. Svaleryd H. (2021) Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.2020834118	Analysis code code Open Science Framework
Community health worker knowledge, attitudes and practices towards COVID-19: Learnings from an online cross-sectional survey using a digital health platform, UpSCALE, in Mozambique Feldman M., Lacey Krylova V., Farrow P., Donovan L., et al (2021) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0244924	Knowledge, attitudes, and practices (KAP) survey results. data
Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples Alekseenko A., Barrett D., Pareja-Sanchez Y., Howard R. J., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41598-020-80352-8	Raw data for amplification curves, and Ct values for clinical samples. data
Malpractice claimed calls within the Swedish Healthcare Direct: a descriptive – comparative case study Björkman A., Engström M., Winblad U., Holmström I. K. (2021) Springer Science and Business Media LLC DOI: 10.1186/s12912-021-00540-3	Data cannot be publicly shared, but applications can be made for access. data
Broadly Active Antiviral Compounds Disturb Zika Virus Progeny Release Rescuing Virus-Induced Toxicity in Brain Organoids Pettke A., Tampere M., Pronk R., Wallner O., et al (2020) MDPI AG DOI: 10.3390/v13010037	Data are available in the article and supplementary materials (effect of novel antiviral compounds against ZIKV in several cell models). data
Mechanisms of a Sustained Anti‐inflammatory Drug Response in Alveolar Macrophages Unraveled with Mathematical Modeling Nyman E., Lindh M., Lövfors W., Simonsson C., et al (2020) Wiley DOI: 10.1002/psp4.12568	Experimental data are in the supplementary material data Code for macrophage model (matlab) code GitLab
Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy Wacker A., Weigand J. E., Akabayov S. R., Altincekic N., et al (2020) Oxford University Press (OUP) DOI: 10.1093/nar/gkaa1013	Nuclear magnetic resonance (NMR) experimental data deposited in COVID19-NMR project data Chemical shift data deposited in BMRB (multiple accession numbers, given in Table 1 in the article). data BioMagResBank
Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2 Custódio T. F., Das H., Sheward D. J., Hanke L., et al (2020) Springer Science and Business Media LLC DOI: 10.1038/s41467-020-19204-y	Microscale thermophoresis (MST) and biolayer interferometry (BLI) data. data GitHub Synthetic nanobody Sybody 23 (Sy23). data SASBDB: SASDJF4 SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD). data SASBDB: SASDJG4 SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD) bound to the synthetic nanobody Sybody 23 (Sy23). data SASBDB: SASDJH4 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23). data Electron Microscopy Data Bank: EMD-11616 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation. data Electron Microscopy Data Bank: EMD-11617 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23). data Protein Data Bank: 7A25 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation. data Protein Data Bank: 7A29 Sequences of all the selected sybodies. data Source data. data
Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19 Sekine T., Perez-Potti A., Rivera-Ballesteros O., Strålin K., et al (2020) Elsevier BV DOI: 10.1016/j.cell.2020.08.017	All data generated during the study (predicted binding affinities, donor characteristics, sample information, and some analyses) are available in the article. data
Natural killer cell immunotypes related to COVID-19 disease severity Maucourant C., Filipovic I., Ponzetta A., Aleman S., et al (2020) American Association for the Advancement of Science (AAAS) DOI: 10.1126/sciimmunol.abd6832	Curated flow cytometry data available via the Karolinska COVID-19 Immune Atlas. data Raw data, clinical characteristics of patients, and various results files are available in supplementary data. data