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corona

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

corona literature and study reports

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

https://www.who.int/emergencies/diseases/novel-coronavirus-2019/global-research-on-novel-coronavirus-2019-ncov

CORD-19 dataset (biorxiv, medrxiv, Elsevier and other sources)

https://pages.semanticscholar.org/coronavirus-research

Wiley

https://novel-coronavirus.onlinelibrary.wiley.com/

Curated sets and databases

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

https://docs.google.com/spreadsheets/d/1c6M0XmvSaRfA56AtgUc1j6ECXD-B2bva4vON7JD18ho/edit#gid=1440796014

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

Lists of publishers which make their content available

http://libguides.lub.lu.se/c.php?g=297899&p=4838427

https://coronavirustechhandbook.com/self-reporting

https://github.com/Co-Epi

Clinical trials and pharmacovigilance

EU Clinical Trials Register - trials related to COVID-19

https://www.clinicaltrialsregister.eu/ctr-search/search?query=covid-19&page=2

Clinicaltrial.gov

https://clinicaltrials.gov/

Cochrane Central Register of Controlled Trials (CENTRAL)

https://leoss.net/statistics/

International Clinical Trials Registry Portal

lists COVID-19 trials

http://apps.who.int/trialsearch/AdvSearch.aspx?SearchTermStat=117&ReturnUrl=~/ListBy.aspx?TypeListing=0

The European Union electronic Register of Post-Authorisation Studies (EU PAS Register)

http://www.encepp.eu/encepp/studiesDatabase.jsp

https://lif.se/forskningsoversikt-coronavirus/

https://www.covid-trials.org/

knowledge graphs

COVID graph

https://covidgraph.org/

https://github.com/covidgraph/documentation/wiki

KG-COVID-19

https://github.com/Knowledge-Graph-Hub/kg-covid-19/wiki

corona data, tools and other resources

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

https://www.who.int/emergencies/diseases/novel-coronavirus-2019/global-research-on-novel-coronavirus-2019-ncov

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

https://www.covid.is/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

https://www.kaggle.com/

COVID19 data on Harvard Dataverse

https://dataverse.harvard.edu/dataverse/covid19

Dimensions COIVD-19 database

lists publications, clinical trials, datasets

https://docs.google.com/spreadsheets/d/1-kTZJZ1GAhJ2m4GAIhw1ZdlgO46JpvX0ZQa232VWRmw/edit#gid=2034285255

Microsoft COVID-19 resources

https://www.microsoft.com/en-us/research/project/academic/articles/microsoft-academic-resources-and-their-application-to-covid-19-research/

https://www.lif.se/forskningsoversikt-coronavirus/

https://github.com/Co-Epi

EMBL-EBI COVID-19 portal

https://www.ebi.ac.uk/covid-19

Miso question answering literture search

https://covid19.askmiso.com/

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

mobility data

https://www.apple.com/covid19/mobility

genomic data

Nextstain.org visualization tool

https://nextstrain.org/ncov

https://www.gisaid.org/

Graphen genomic data

http://www.graphen.ai/covid.html

http://www.graphen.ai/covid/types.html

https://artic.network/hCoV-19-viz

clinical data and patient registries

COVID-19 chest CT and x-rays

https://github.com/ieee8023/covid-chestxray-dataset/blob/master/README.md?fbclid=IwAR30yTGBr55WXdCngCoICDENHycmdL2bGwlvl1ckdZM-ucjGH10Uakz7khk

Stanford data on clinical notes

https://medium.com/@nigam/an-ehr-derived-summary-of-the-presenting-symptoms-of-patients-screened-for-sars-cov-2-910ceb1b22b9

https://docs.google.com/spreadsheets/d/1iZZvbv94fpZdC6XaiPosiniMOh18etSPliAXVlLLr1w/edit#gid=344371264

ASH RC COVID-19 Registry

https://www.ashresearchcollaborative.org/s/covid-19-registry-data-summaries

COVID-19 Registry for Hematology

COVID-Hep.net

https://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

https://leoss.net/

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

https://sccmcovid19.org/

Register of current ICU and hospital care patients

symptom tracker websites, fitness bands and apps for self-reporting

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://corona.sll.se/

https://www.coronaviruscensuscollective.org/

https://quantifiedflu.org/

Link lists to many resources

https://dataverse.harvard.edu/dataverse/covid19

https://www.who.int/emergencies/diseases/novel-coronavirus-2019/global-research-on-novel-coronavirus-2019-ncov

https://github.com/virtual-biohackathons/covid-19-bh20/blob/master/datasets_and_tools.md

https://discourse.data-against-covid.org/t/community-wiki-resources-on-data-science-and-friends-vs-covid-19/731

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

hackathons and citizen science

https://euvsvirus.org/

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://callforcode.org/

https://covid.postera.ai/covid

https://accelerateestonia.ee/en/hack-the-crisis/?fbclid=IwAR3F_HzMfa-YF5ZpwbrCp6Yh6lmDGuH7JEH9Pcgzw7qTzlPGhGj9aaASnvg

https://garage48.org/hackthecrisis?fbclid=IwAR2cokE5K3QUbJxMFriaY6KhUwRXde8wR-8LwrCOXgLoSbwpjhXgc5ac3WA

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

structural biology

SARS-CoV2 structure predictions

https://deepmind.com/research/open-source/computational-predictions-of-protein-structures-associated-with-COVID-19

systems biology, proteomics, drug targets

https://covid.pages.uni.lu/

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

3D printing

http://3dskane.se/doku.php

https://3dprintingindustry.com/news/3d-printing-community-responds-to-covid-19-and-coronavirus-resources-169143/

discussion groups and platforms connecting researchers and volunteers

https://www.coronawhy.org/

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://forum.scilifelab.se/

videos

https://ellis.eu/covid-19

research funding and infrastructure support

https://coronavirus.frontiersin.org/covid-19-research-funding-monitor

https://www.xsede.org/covid19-hpc-consortium

https://prace-ri.eu/

COVID-19 AI articles

https://www.nature.com/articles/s41591-020-0931-3

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