Repurposing Biomedical Informaticians for COVID-19.
Identifieur interne : 000031 ( Main/Exploration ); précédent : 000030; suivant : 000032Repurposing Biomedical Informaticians for COVID-19.
Auteurs : Daniel N. Sosa [États-Unis] ; Binbin Chen [États-Unis] ; Amit Kaushal [États-Unis] ; Adam Lavertu [États-Unis] ; Jake Lever [États-Unis] ; Stefano Rensi [États-Unis] ; Russ Altman [États-Unis]Source :
- Journal of biomedical informatics [ 1532-0480 ] ; 2021.
Abstract
The COVID-19 pandemic is an unprecedented challenge to the biomedical research community at the intersection of great uncertainty due to the novelty of the virus and extremely high stakes due to the large global death count. The global quarantine shut-downs complicated scientific matters because many laboratories were closed down unless they were actively doing COVID-19 related research, making repurposing of activities difficult for many biomedical researchers. Biomedical informaticians, who have been primarily able to continue their research through remote work and video conferencing, have been able to maintain normal activities. In addition to continuing ongoing studies, there has been great grass roots interest in helping in the fight against COVID-19. In this commentary, we describe several projects that arose from this desire to help, and the lessons that the authors learned along the way. We then offer some insights into how these lessons might be applied to make scientific progress be more efficient in future crisis scenarios.
DOI: 10.1016/j.jbi.2021.103673
PubMed: 33486067
PubMed Central: PMC7825863
Affiliations:
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Sosa</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Data Science, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Stanford (Californie)</settlement></placeName><orgName type="university">Université Stanford</orgName></affiliation></author><author><name sortKey="Chen, Binbin" sort="Chen, Binbin" uniqKey="Chen B" first="Binbin" last="Chen">Binbin Chen</name><affiliation wicri:level="4"><nlm:affiliation>Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Stanford (Californie)</settlement></placeName><orgName type="university">Université Stanford</orgName></affiliation></author><author><name sortKey="Kaushal, Amit" sort="Kaushal, Amit" uniqKey="Kaushal A" first="Amit" last="Kaushal">Amit Kaushal</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Stanford (Californie)</settlement></placeName><orgName type="university">Université Stanford</orgName></affiliation></author><author><name sortKey="Lavertu, Adam" sort="Lavertu, Adam" uniqKey="Lavertu A" first="Adam" last="Lavertu">Adam Lavertu</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Data Science, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Stanford (Californie)</settlement></placeName><orgName type="university">Université Stanford</orgName></affiliation></author><author><name sortKey="Lever, Jake" sort="Lever, Jake" uniqKey="Lever J" first="Jake" last="Lever">Jake Lever</name><affiliation wicri:level="4"><nlm:affiliation>Deprtment of Bioengineering, Stanford University, Stanford, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Deprtment of Bioengineering, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Stanford (Californie)</settlement></placeName><orgName type="university">Université Stanford</orgName></affiliation></author><author><name sortKey="Rensi, Stefano" sort="Rensi, Stefano" uniqKey="Rensi S" first="Stefano" last="Rensi">Stefano Rensi</name><affiliation wicri:level="4"><nlm:affiliation>Deprtment of Bioengineering, Stanford University, Stanford, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Deprtment of Bioengineering, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Stanford (Californie)</settlement></placeName><orgName type="university">Université Stanford</orgName></affiliation></author><author><name sortKey="Altman, Russ" sort="Altman, Russ" uniqKey="Altman R" first="Russ" last="Altman">Russ Altman</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA; Deprtment of Bioengineering, Stanford University, Stanford, CA, USA. 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Sosa</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Data Science, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Stanford (Californie)</settlement></placeName><orgName type="university">Université Stanford</orgName></affiliation></author><author><name sortKey="Chen, Binbin" sort="Chen, Binbin" uniqKey="Chen B" first="Binbin" last="Chen">Binbin Chen</name><affiliation wicri:level="4"><nlm:affiliation>Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Stanford (Californie)</settlement></placeName><orgName type="university">Université Stanford</orgName></affiliation></author><author><name sortKey="Kaushal, Amit" sort="Kaushal, Amit" uniqKey="Kaushal A" first="Amit" last="Kaushal">Amit Kaushal</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Stanford (Californie)</settlement></placeName><orgName type="university">Université Stanford</orgName></affiliation></author><author><name sortKey="Lavertu, Adam" sort="Lavertu, Adam" uniqKey="Lavertu A" first="Adam" last="Lavertu">Adam Lavertu</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Data Science, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Stanford (Californie)</settlement></placeName><orgName type="university">Université Stanford</orgName></affiliation></author><author><name sortKey="Lever, Jake" sort="Lever, Jake" uniqKey="Lever J" first="Jake" last="Lever">Jake Lever</name><affiliation wicri:level="4"><nlm:affiliation>Deprtment of Bioengineering, Stanford University, Stanford, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Deprtment of Bioengineering, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Stanford (Californie)</settlement></placeName><orgName type="university">Université Stanford</orgName></affiliation></author><author><name sortKey="Rensi, Stefano" sort="Rensi, Stefano" uniqKey="Rensi S" first="Stefano" last="Rensi">Stefano Rensi</name><affiliation wicri:level="4"><nlm:affiliation>Deprtment of Bioengineering, Stanford University, Stanford, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Deprtment of Bioengineering, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Stanford (Californie)</settlement></placeName><orgName type="university">Université Stanford</orgName></affiliation></author><author><name sortKey="Altman, Russ" sort="Altman, Russ" uniqKey="Altman R" first="Russ" last="Altman">Russ Altman</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA; Deprtment of Bioengineering, Stanford University, Stanford, CA, USA. Electronic address: Russ.Altman@stanford.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA; Deprtment of Bioengineering, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region><settlement type="city">Stanford (Californie)</settlement></placeName><orgName type="university">Université Stanford</orgName></affiliation></author></analytic><series><title level="j">Journal of biomedical informatics</title><idno type="eISSN">1532-0480</idno><imprint><date when="2021" type="published">2021</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The COVID-19 pandemic is an unprecedented challenge to the biomedical research community at the intersection of great uncertainty due to the novelty of the virus and extremely high stakes due to the large global death count. The global quarantine shut-downs complicated scientific matters because many laboratories were closed down unless they were actively doing COVID-19 related research, making repurposing of activities difficult for many biomedical researchers. Biomedical informaticians, who have been primarily able to continue their research through remote work and video conferencing, have been able to maintain normal activities. In addition to continuing ongoing studies, there has been great grass roots interest in helping in the fight against COVID-19. In this commentary, we describe several projects that arose from this desire to help, and the lessons that the authors learned along the way. We then offer some insights into how these lessons might be applied to make scientific progress be more efficient in future crisis scenarios.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">33486067</PMID><DateRevised><Year>2021</Year><Month>01</Month><Day>27</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1532-0480</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2021</Year><Month>Jan</Month><Day>21</Day></PubDate></JournalIssue><Title>Journal of biomedical informatics</Title><ISOAbbreviation>J Biomed Inform</ISOAbbreviation></Journal><ArticleTitle>Repurposing Biomedical Informaticians for COVID-19.</ArticleTitle><Pagination><MedlinePgn>103673</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S1532-0464(21)00002-2</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jbi.2021.103673</ELocationID><Abstract><AbstractText>The COVID-19 pandemic is an unprecedented challenge to the biomedical research community at the intersection of great uncertainty due to the novelty of the virus and extremely high stakes due to the large global death count. The global quarantine shut-downs complicated scientific matters because many laboratories were closed down unless they were actively doing COVID-19 related research, making repurposing of activities difficult for many biomedical researchers. Biomedical informaticians, who have been primarily able to continue their research through remote work and video conferencing, have been able to maintain normal activities. In addition to continuing ongoing studies, there has been great grass roots interest in helping in the fight against COVID-19. In this commentary, we describe several projects that arose from this desire to help, and the lessons that the authors learned along the way. We then offer some insights into how these lessons might be applied to make scientific progress be more efficient in future crisis scenarios.</AbstractText><CopyrightInformation>Copyright © 2021 Elsevier Inc. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sosa</LastName><ForeName>Daniel N</ForeName><Initials>DN</Initials><AffiliationInfo><Affiliation>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Binbin</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kaushal</LastName><ForeName>Amit</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lavertu</LastName><ForeName>Adam</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lever</LastName><ForeName>Jake</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Deprtment of Bioengineering, Stanford University, Stanford, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rensi</LastName><ForeName>Stefano</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Deprtment of Bioengineering, Stanford University, Stanford, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Altman</LastName><ForeName>Russ</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Biomedical Data Science, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA; Deprtment of Bioengineering, Stanford University, Stanford, CA, USA. Electronic address: Russ.Altman@stanford.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2021</Year><Month>01</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Biomed Inform</MedlineTA><NlmUniqueID>100970413</NlmUniqueID><ISSNLinking>1532-0464</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Biomedical Literature</Keyword><Keyword MajorTopicYN="N">COVID-19</Keyword><Keyword MajorTopicYN="N">Structural Bioinformatics</Keyword><Keyword MajorTopicYN="N">Translational Research</Keyword></KeywordList><CoiStatement>Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>10</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>12</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2021</Year><Month>01</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2021</Year><Month>1</Month><Day>24</Day><Hour>20</Hour><Minute>34</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2021</Year><Month>1</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2021</Year><Month>1</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">33486067</ArticleId><ArticleId IdType="pii">S1532-0464(21)00002-2</ArticleId><ArticleId IdType="doi">10.1016/j.jbi.2021.103673</ArticleId><ArticleId IdType="pmc">PMC7825863</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li></region><settlement><li>Stanford (Californie)</li></settlement><orgName><li>Université Stanford</li></orgName></list><tree><country name="États-Unis"><region name="Californie"><name sortKey="Sosa, Daniel N" sort="Sosa, Daniel N" uniqKey="Sosa D" first="Daniel N" last="Sosa">Daniel N. Sosa</name></region><name sortKey="Altman, Russ" sort="Altman, Russ" uniqKey="Altman R" first="Russ" last="Altman">Russ Altman</name><name sortKey="Chen, Binbin" sort="Chen, Binbin" uniqKey="Chen B" first="Binbin" last="Chen">Binbin Chen</name><name sortKey="Kaushal, Amit" sort="Kaushal, Amit" uniqKey="Kaushal A" first="Amit" last="Kaushal">Amit Kaushal</name><name sortKey="Lavertu, Adam" sort="Lavertu, Adam" uniqKey="Lavertu A" first="Adam" last="Lavertu">Adam Lavertu</name><name sortKey="Lever, Jake" sort="Lever, Jake" uniqKey="Lever J" first="Jake" last="Lever">Jake Lever</name><name sortKey="Rensi, Stefano" sort="Rensi, Stefano" uniqKey="Rensi S" first="Stefano" last="Rensi">Stefano Rensi</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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