a repository with an NLP toolbox (in manuscript folder) and other resources for SARS-CoV-2/COVID-19 research.
If you use our NLP tools please cite our manuscript: "English dictionaries, gold and silver standard corpora for biomedical natural language processing related to SARS-CoV-2 and COVID-19" by Salma Kazemi Rashed, Johan Frid, Sonja Aits (https://arxiv.org/abs/2003.09865, cite as arXiv:2003.09865 [q-bio.OT]). Additional licence conditions are in the license file.
This repo is hopefully useful for everyone participating in the COVID-19 Open Research Dataset Challenge (CORD-19) or other COVID-19 hackathons: https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge
COVID-19 SARS-CoV-2 preprints from medRxiv and bioRxiv (json file)
https://connect.medrxiv.org/relate/content/181
Elsevier articles (xml or pdf file)
https://www.elsevier.com/connect/coronavirus-information-center
WHO database of COVID-19 publications
CORD-19 dataset (biorxiv, medrxiv, Elsevier and other sources)
https://pages.semanticscholar.org/coronavirus-research
Wiley
https://novel-coronavirus.onlinelibrary.wiley.com/
OpenAIRE COVID-19 gateway
Covid-19 publications, datasets, software and projects metadata
Cochrane
https://covid-19.cochrane.org/
CORD-19 data set
over 50000 scholarly articles, many with full text, about COVID-19, SARS-CoV-2, and related coronaviruses
https://pages.semanticscholar.org/coronavirus-research
CORD-19 Annotations
https://github.com/SciBiteLabs/CORD19
https://github.com/fhircat/CORD-19-on-FHIR
https://github.com/fhircat/CORD-19-on-FHIR/wiki/CORD-19-Semantic-Annotation-Projects
Miso COVID-19 paper set
LitCOVID
Curated database of COVID-19 literature from NIH
https://www.ncbi.nlm.nih.gov/research/coronavirus/
https://asm.org/COVID/COVID-19-Research-Registry/Home
Twitter datasets
https://zenodo.org/record/3738018#.Xp7jQyNS-Mo
https://www.kaggle.com/smid80/coronavirus-covid19-tweets
https://github.com/echen102/COVID-19-TweetIDs
http://libguides.lub.lu.se/c.php?g=297899&p=4838427
https://coronavirustechhandbook.com/self-reporting
EU Clinical Trials Register - trials related to COVID-19
https://www.clinicaltrialsregister.eu/ctr-search/search?query=covid-19&page=2
Clinicaltrial.gov
Cochrane Central Register of Controlled Trials (CENTRAL)
International Clinical Trials Registry Portal
lists COVID-19 trials
The European Union electronic Register of Post-Authorisation Studies (EU PAS Register)
http://www.encepp.eu/encepp/studiesDatabase.jsp
https://lif.se/forskningsoversikt-coronavirus/
COVID graph
https://github.com/covidgraph/documentation/wiki
KG-COVID-19
https://github.com/Knowledge-Graph-Hub/kg-covid-19/wiki
Ourworldindata
https://ourworldindata.org/coronavirus
ELIXIR Covid-19 portal
https://www.covid19dataportal.org/
CDC Research Guide on COVID-19
https://www.cdc.gov/library/researchguides/2019NovelCoronavirus.html
Johns Hopkins dashboard of COVID-19 cases
https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6
Johns Hopkins dataset of global COVID-19 cases
https://github.com/CSSEGISandData/COVID-19 and https://www.kaggle.com/sudalairajkumar/novel-corona-virus-2019-dataset
ECDC dataset of global COVID-19 cases
https://www.ecdc.europa.eu/en/publications-data
WHO COVID-19 database
Italy's data
https://github.com/pcm-dpc/COVID-19
Swedish intensive care register
https://www.icuregswe.org/data--resultat/covid-19-i-svensk-intensivvard/
Iceland data
Elsevier corona virus page
https://www.elsevier.com/connect/coronavirus-information-center
https://covid19.healthdata.org/
Kaggle
has lots of COVID-19 related datasets, notebooks, discussions
COVID19 data on Harvard Dataverse
https://dataverse.harvard.edu/dataverse/covid19
Dimensions COIVD-19 database
lists publications, clinical trials, datasets
Microsoft COVID-19 resources
https://www.lif.se/forskningsoversikt-coronavirus/
EMBL-EBI COVID-19 portal
https://www.ebi.ac.uk/covid-19
Miso question answering literture search
BERT base model finetuned on CORD-19 data
https://huggingface.co/deepset/covid_bert_base
COVID-19 embeddings
https://www.kaggle.com/jonathanbesomi/covid19-word-embeddings
https://www.kaggle.com/jonathanbesomi/cord-19-embeddings-from-abstracts-with-spacy
https://www.kaggle.com/fmitchell259/creating-a-doc2vec-model
https://tfhub.dev/tensorflow/cord-19/swivel-128d/2
https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge/discussion/138159
https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge/discussion/138050
CORD-19 annotations
https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge/discussion/138219
https://github.com/fhircat/CORD-19-on-FHIR
List of tools
https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge/discussion/137256
https://docs.google.com/spreadsheets/d/13vO8jZ4mrYD1U86U8r1qolY2HV552D7e5Fmko3c6Vrg/edit#gid=0
Notebooks
quick setup and downloading the COVID-19 dataset (by Aymeric Alixe)
https://colab.research.google.com/drive/1Qw74IpbvO105J2fTExqKURnrZuT0NW7X
scispacy BioNER
https://github.com/nasa-jpl-cord-19/Biomolecular-Named-Entities/blob/master/SciSpacy%20NER.ipynb
Coronavirus Tech Handbook
https://coronavirustechhandbook.com/home
https://www.apple.com/covid19/mobility
Nextstain.org visualization tool
Graphen genomic data
http://www.graphen.ai/covid.html
http://www.graphen.ai/covid/types.html
https://artic.network/hCoV-19-viz
COVID-19 chest CT and x-rays
Stanford data on clinical notes
ASH RC COVID-19 Registry
https://www.ashresearchcollaborative.org/s/covid-19-registry-data-summaries
COVID-19 Registry for Hematology
COVID-Hep.net
Coronavirus (COVID-19) in liver disease reporting registry
ELSO registry
https://www.elso.org/Registry/FullCOVID19RegistryDashboard.aspx
COVID-19 patients on ECMO
EUROELSO
https://www.euroelso.net/covid-19/covid-19-survey/
ECMO use in adult COVID-19 patients in Europe
LEOSS register
IntubateCOVID
https://www.intubatecovid.org/dashboards
COVID-10 Intubation registry
Pediatric COVID-19 U.S. Registry
https://www.pedscovid19registry.com/current-data.html
PSOProtect
https://psoprotect.org/current-data/
Psoriasis Registry for Outcomes, Therapy and Epidemiology of COVID-19 Infection
SECURE-Cirrhosis
https://covidcirrhosis.web.unc.edu/updates-and-data/
Reporting Registry for COVID-19 in liver disease
SECURE-IBD
https://covidibd.org/current-data/
COVID-19 and Inflammatory Bowel Disease (IBD) Reporting Registry
SECURE-SCD
https://covidsicklecell.org/updates-data/
COVID-19 and Sickle Cell Disease Registry
The COVID-19 Global Rheumatology Alliance Global Registry
https://rheum-covid.org/updates/combined-data.html
Registers with data provided by providers and patients
VIRUS COVID-19 Registry
Register of current ICU and hospital care patients
COVID19 Symptom Study (Swedish self-reporting app from Lund and Uppsala Universities)
https://csss-resultat.shinyapps.io/csss_dashboard/
https://barrel.ai/covid19_symptoms_tracker/
https://www.coronaviruscensuscollective.org/
Large-scale COVID-19 Twitter chatter dataset
https://zenodo.org/record/7497980#.Y7MgQxXMJEY
https://dataverse.harvard.edu/dataverse/covid19
https://github.com/virtual-biohackathons/covid-19-bh20/blob/master/datasets_and_tools.md
https://swelife.se/verktyg/covid-19/
https://vgrblogg.se/utveckling/2020/03/31/covid19-resurser-for-dig-som-vill-hacka-krisen/
https://www.hackthecrisis.se/inspiration
http://open-source-covid-19.weileizeng.com/index
https://www.producthunt.com/@chrismessina/collections/coronavirus
https://covid-global-hackathon.devpost.com/submissions
https://wirvsvirushackathon.org/
https://www.youtube.com/channel/UCPv_kdljMHmt4kLNB7QGn0g
https://www.guaana.com/challenges/dSvc4QnSmsSvmDG5k/results/4fTtLGpD2CRytd9Gy
https://covid.postera.ai/covid
https://github.com/virtual-biohackathons/covid-19-bh20
https://codevscovid19.devpost.com/submissions
http://eu-citizen.science/citizen-science-resources-related-to-the-covid19-pandemic/
https://github.com/virtual-biohackathons/covid-19-bh20
SARS-CoV2 structure predictions
https://www.nature.com/articles/s41586-020-2286-9
https://www.biorxiv.org/content/10.1101/2020.03.22.002386v3
https://www.researchsquare.com/article/rs-17218/v1
https://www.covid19cellatlas.org/
https://covid.barabasilab.com/2020/04/network-based-embedding-of-all-human.html
https://www.nature.com/articles/s41586-020-2286-9
https://trello.com/b/y4odX7yZ/covid-19-global-team
https://discourse.data-against-covid.org/
https://groups.google.com/forum/#!forum/virtual-biohackathon
https://crowdfightcovid19.org/
https://www.facebook.com/groups/494650038080423/about/
https://coronavirus.frontiersin.org/covid-19-research-funding-monitor