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Swedish Pathogens Portal SciLifeLab

Data sources

Resources where users can access data.

Adipose Tissue Knowledge Portal
Adipose Tissue Knowledge Portal
An open-access resource that integrates transcriptomic and proteomic data from diverse clinical cohorts, adipose cell types, and adipocyte studies to enable new discoveries in adipose biology.
AIDA Data Hub
AIDA Data Hub
Data Sharing, Policy Support, and Services for researchers in Swedish medical imaging AI.
Alpha Fold Protein Structure Database
Alpha Fold Protein Structure Database
Contains over 200 million predictions of 3D protein structures based on amino acid sequence. The predictions were generated using AlphaFold, an AI system developed by DeepMind.
Antimicrobial resistance portal
Antimicrobial resistance portal
The AMR Portal is a collaboration between EMBL-EBI research and service teams alongside Imperial College London to deliver a new way to access and explore AMR phenotype and genotype annotations through a user-friendly interface.
BacDive
BacDive
The largest database for standardised bacterial phenotypic data. It includes >600 data fields, e.g. taxonomy, molecular data, and morphology. Integrates data from many sources & makes it freely accessible.
BBMRI-ERIC
BBMRI-ERIC
A biobanking infrastructure that promotes biomedical research. Samples can be accessed with appropriate permissions. Services, software, tools, and support with ELSI are also available.
Cancer Genome Atlas
Cancer Genome Atlas
Has >2.5 petabytes of genomic, epigenomic, transcriptomic, and proteomic data from >10k patients across 33 cancer types. Raw data is under controlled access, but derived data is openly accessible.
Cellosaurus
Cellosaurus
A knowledge resource aiming to describe all cell lines used in biomedical research. Users can browse the cell lines by group.
ChEMBL
ChEMBL
A manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity, and genomic data to enable the translation of information into effective new drugs.
COViMAPP
COViMAPP
A meta-analysis resource showing changes in plasma proteins that occur during COVID-19.
ECDC Avian Influenza
ECDC Avian Influenza
Contains information related to avian influenza, including a distribution map of confirmed human cases, as well as guidelines for surveillance.
ECDC Tuberculosis
ECDC Tuberculosis
Contains open datasets related to tuberculosis, including an atlas showing the distribution of reported cases across Europe.
Ensembl
Ensembl
A browser for vertebrate genomes. Supports research in evolution, transcriptional regulation, and sequence variation. It is part of the Ensembl project, which also includes Ensembl Genomes.
Ensembl Genomes
Ensembl Genomes
A browser for invertebrate genomes that enables comparative analysis, data mining, and visualisation. Information is available for viruses, metazoa, protists, plants, fungi, and bacteria.
European Chemical Biology Database
European Chemical Biology Database
The central hub for data generated within the EU-OPENSCREEN network. The network collaborates with external users to develop novel molecular tool compounds and early therapeautic candidate molecules.
Human Developmental Cell Atlas
Human Developmental Cell Atlas
A molecular atlas of human prenatal development, describing every cell type in detail and showing their spatial and temporal distributions in three dimensions.
Human Protein Atlas
Human Protein Atlas
The Human Protein Atlas aims to map all the human proteins in cells, tissues, and organs using an integration of various omics and imaging technologies.
Infectious Disease Data Observatory
Infectious Disease Data Observatory
Brings together multiple types of infectious disease data to improve the diagnosis and treatment of patients in the clinic. Access to the data held in the IDDO data repository has to be requested.
InParanoiDB
InParanoiDB
A database of orthologs between 640 species, including inparalogs for both protein domains and full-length proteins.
Metabolic Atlas
Metabolic Atlas
Metabolic Atlas is a web platform integrating open-source genome scale metabolic models (GEMs) for easy browsing and analysis.
Molecular Interaction Database
Molecular Interaction Database
A public, open source database detailing protein-protein interactions that are experimentally verified. The interactions have been mined from scientific literature by expert curators.
National Board of Health and Welfare Statistical Databases
National Board of Health and Welfare Statistical Databases
A set of databases related to health and welfare from the National Board of Health and Welfare. This Swedish governmental agency is responsible for ensuring high-quality health and social care.
Nextstrain
Nextstrain
An open-source project to harness the scientific and public health potential of pathogen genome data.
Orphadata Science
Orphadata Science
Provides access to high-quality datasets related to rare diseases and orphan drugs. The data is available in a reusable and computable format.
Precision Medicine Portal
Precision Medicine Portal
Links to multiple data sources, including quality registers and KIARVA (an open-source immunology database).
Protein Data Bank Europe
Protein Data Bank Europe
A repository in which data on biological macromolecular structures can be deposited. A founding member of the worldwide Protein Data Bank (PDB), and works to collate, maintain, and provide access to PDB.
Public Health Agency of Sweden
Public Health Agency of Sweden
The Public Health Agency of Sweden (Folkhälsomyndigheten, FoHM) is responsible for issues related to public health. It collates and collects data on diseases that pose a threat to public health.
REACTOME
REACTOME
A graphical map of known biological processes and pathways. Provides tools to visualise, interpret, and analyse pathways to support research. Used for genome analysis, modelling, and systems biology.
Registers in Sweden
Registers in Sweden
A list of Swedish registry-based data sources, maintained by the Swedish Research Council. Users can link data from multiple registers, including healthcare records, biobanks, and research data.
Researchdata.se
Researchdata.se
Researchdata.se is a national web portal where you can find, share, and reuse research data from a wide range of research fields. You can also find helpful advice and recommendations on managing research data.
SILVA
SILVA
A comprehensive online resource for quality-checked ribosomal RNA (rRNA) data. Includes aligned small and large subunits of rRNA from all three domains of life (archea, bacteria, eukarya).
Statistics Swede
Statistics Swede
Statistics Sweden has a large amount of data available for everyone to use free of charge under open licences. It includes geodata, public data, and data from different sectors.
STRING
STRING
Database of known and predicted protein-protein interactions, including both direct and indirect associations. Data is aggregated from multiple sources, e.g. existing databases and computer modelling.
SubCellBarCode
SubCellBarCode
A collection of resources centred around the subcellular localisation of proteins
Sveriges Dataportal
Sveriges Dataportal
Organisations can share and download data related to data-driven development and innovation. It is created by Myndigheten for Digital Förvaltning (DIGG). Multiple types of data are available.
SweFreq
SweFreq
A website developed to make genomic datasets more findable and accessible.
SWISS-MODEL
SWISS-MODEL
An automated protein structure homology server. Protein sequences for 13 core species are modelled weekly. The aim of this database is to make protein modelling is accessible to researchers worldwide.
UK Biobank
UK Biobank
A large-scale biomedical database including biological and clinical data from 500K participants in the UK. Applications to access the data are welcomed from researchers anywhere in the world.
VEuPathoDB
VEuPathoDB
Aggregation of data from multiple genomic and other large datasets related to eukaryotic pathogens and invertebrate disease vectors. Includes data on many emerging and re-emerging infectious disease.
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