How Does a Library Respond to a Global Health Crisis?

Coronavirus image from NIH

Around the world, scientists, public health officials, medical professionals, and others are working to address the coronavirus pandemic.

At NLM, we’ve been working on multiple fronts to improve researchers’ understanding of SARS-CoV-2 (the virus that causes the novel coronavirus) and aid in the response to COVID-19 (the disease caused by the novel coronavirus). By enhancing access to relevant data and information, NLM is demonstrating how libraries can contribute in real time to research and response efforts during this crisis.

Harnessing the Power of PubMed Central® to Enable Data Science Research

With new initiatives launched in the past two weeks, NLM is using PubMed Central®, our digital archive of peer-reviewed biomedical and life sciences journal literature, to expand access to full-text articles related to coronavirus. These activities build on recent requests from the White House Office of Science and Technology Policy (OSTP) and science policy leaders of other nations calling on the global publishing community to make all COVID-19-related research publications and data immediately available to the public in forms that support automated text-mining.  

NLM has stepped up its collaboration with publishers and scholarly societies to increase the number of coronavirus-related journal articles in PMC, along with the available data supporting them. NLM is adapting its standard procedures for depositing articles into PMC to make it easier and faster to submit articles in machine-readable formats. We’re also engaging with journals and publishers that do not participate in PMC but whose publications are within the scope of the Library’s collection. A growing number of publishers and societies are taking advantage of these flexibilities.

Submitted publications are being made available as quickly as possible after publication for discovery in PMC and through the PMC Text Mining Collections for machine analysis,  secondary analysis, and other types of reuse.

This enhanced collection of text-minable content enables AI and machine-learning researchers to develop and apply novel text-mining approaches that can help answer some of the many questions about coronavirus.

Along these lines, NLM and leaders across the technology sector and academia joined OSTP on Monday, March 16 to announce the COVID-19 Open Research Dataset (CORD-19). Hosted by the Allen Institute for AI, CORD-19 is a free and growing resource that was launched with more than 29,000 scholarly articles about COVID-19 and the coronavirus family of viruses.  CORD-19 represents the most extensive machine-readable coronavirus literature collection available for text mining to date. This dataset enables researchers to apply novel AI and machine learning strategies to identify new knowledge to help end the pandemic. Researchers can submit text and data mining tools to be applied to the dataset via the Kaggle platform.

Providing Other Resources

NLM’s efforts to support coronavirus-related research and response efforts are not limited to PMC. Key among the Library’s other important resources are:  

  • NLM’s GenBank Sequence Database — NLM created the Severe acute respiratory syndrome coronavirus 2 data hub, where people can search for, retrieve, and analyze sequences of the virus that have been submitted to GenBank. Our GenBank team is expediting the processing of all SARS-associated coronavirus sequences. Depending on the quality of submitted sequences, they are being annotated and released to the public as fast as 20 minutes after receipt and, in almost all cases, within 24 hours of receipt.
  • NLM’s Sequence Read Archive (SRA) — NLM’s SRA is the world’s largest publicly available repository of unprocessed sequence data which can be mined for previously unrecognized pathogen sequence. For example, a team from Stanford University recently reported that in a search of certain metagenomic datasets in the SRA, they identified a 2019-nCoV-like coronavirus in pangolins (a long-snouted mammal). This type of genetic sequence research can play an important role in understanding how the virus originated and is spreading.

NLM has also made the SRA available through commercial cloud providers participating in the National Institutes of Health’s Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) Initiative. Researchers may now compute across the full SRA dataset for metagenomic research on the new coronavirus in ways not previously possible.

  • NLM Intramural Research Contributions —NLM has a multidisciplinary group of researchers comprised of molecular biologists, biochemists, computer scientists, mathematicians and others working on a variety of problems, including some that relate to SARS-CoV-2/COVID-19. One such project is LitCovid, a resource that tracks COVID-19 specific literature published since the outbreak. This resource builds on NLM research to develop new approaches to locating and indexing the literature related to COVID-19 including a text classification algorithm for screening and ranking relevant documents, topic modeling for suggesting relevant research categories, and information extraction for obtaining geographic location(s) found in the abstract.

NLM is also providing targeted searches within several of its other information resources to help users find data and information relevant to COVID-19. These searches, available through the NLM home page, include information on clinical studies related to COVID-19 listed in ClinicalTrials.gov, and articles related to the SARS-CoV-2/COVID-19 in PubMed, NLM’s database of citations and abstracts to more than 30 million journal articles and online books.

These resources are already proving to be useful to the scientific community and others working together to address this public health threat.

We continue to seek new ways to support these efforts and demonstrate how libraries can best contribute. Please send us your ideas of how NLM can help you respond to the global health crisis or how your library is contributing.

Author: Patti Brennan

Director, US National Library of Medicine

12 thoughts on “How Does a Library Respond to a Global Health Crisis?”

    1. Hi Linda,

      We have stepped up our collaboration with publishers and scholarly societies to increase the number of coronavirus-related journal articles in PubMed Central (PMC), along with available data supporting them. Deposited publications are made available in PMC as quickly as possible after receipt, in formats and with needed permissions to support text mining. PMC has received articles as far back as the 1960s related to coronaviruses under the COVID-19 Initiative. You can find additional information about this on our Public Health Emergency COVID-19 Initiative webpage – https://www.ncbi.nlm.nih.gov/pmc/about/covid-19/.

      Our staff is fulfilling interlibrary loan requests from electronic resources, which accounts for more than 80% of the requests we have received since March 13, 2020. Because it is housed at the NIH, our print collection is currently unavailable given the need for our staff to follow COVID-19 guidance from the Office of Personnel Management and recommendations from the CDC prohibiting access to the campus.

      Patti

      Like

  1. As a medical librarian I have some lines by seeing the present situation of the entire world. During this pandemic situation its very essential to provide the library services for the users of the medical library. Library e-resources should be provided for all the users through remote login facility so that users can utilize maximum library services. As social distancing is the main factor for saving our live from the pandemic COVID-19 and equally we must need to provide the library services also. So in this time I must say that emerging ICT can help to provide the best practices for the medical library and medical librarian also. Medical librarian is the most challenging job for disseminating the current and upcoming new information to the health professionals to keep abreast themselves related to the present situation of the entire world. Definitely we must say that impact of ICT is very effective in this crucial period.

    Like

    1. Dear Hira,

      The use of information and communication technologies (ICT), particularly during this time of COVID-19, is of great importance as it enables researchers, clinicians, and the public to have access to biomedical data and information to promote public health and save lives. Indeed, the entire NLM workforce is on full telework and ICT is the key platform for keeping operations running!

      Thank you for your feedback.

      Patti

      Like

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