Update: August 3, 2021

COVID-TIB Virus-Drug Pair Data

A dataset containing results from all documents processed through July 6, 2021 is now available for download. This includes virus-drug pairs identified in documents, assignments of documents to research stages, and some additional information. The data description file also contains precision and recall statistics. Please click the “Data” tab in the navigation bar to the left to access this dataset.

About the COVID-19 Therapeutic Information Browser (COVID-TIB)

Welcome! This site provides browsable therapeutic and vaccine-related information about SARS-CoV-2 (COVID-19) and other viruses. This information was extracted via natural language processing (NLP) of more than 200k PubMed, MedRxiv, and BioRxiv abstracts and clinicaltrials.gov summaries1. The summary tables show the number of documents with information about a given virus and drug (Viral Therapeutics page) or vaccine type (Vaccine Type page). The numbers of papers are arranged by selected research stages, e.g. clinical studies. Metadata about the papers, as well as a link to figures and tables about COVID-19 and a selected drug, are available below. This site also enables keyword full-text search for a subset of papers that are open access.

For information on how to use this site, please see the demo briefing available in the navigation bar on the left. For more information about the NLP pipeline, please see the briefing and description of data available for download in the navigation bar. For more information about term definitions, see the tabs under the “About” menu in the navigation bar. Full text search is powered by xDD and COSMOS from the University of Wisconsin-Madison.

Caveat: Machines are now great at processing documents at-scale but currently are not nearly as accurate as human subject matter experts. Consequently, you will see mistakes in raw machine-extracted information posted here.

Browser recommendation: Internet Explorer is not supported by this application. Please consider using an updated version of Chrome, Edge, Firefox, or Safari.

This is a beta version prototype. Your feedback is welcome. Please send comments, suggestions, or bug reports to covid-browser@groups.mitre.org.

[1]: The natural language processing (NLP) uses REACH reading software developed by the University of Arizona (M. Valenzuela-Escárcega et al, Large-scale automated machine reading discovers new cancer-driving mechanisms, Database, Volume 2018, 2018, bay098) that was adapted for virus-related information by MITRE. Data sources include: NCBI, clinicaltrials.gov, the CORD-19 Open Research Dataset, UniProt, and DrugBank.

Curation's Role

Our approach integrates natural language processing (NLP) with expert curation to improve the accuracy of the information presented. Our NLP pipeline generates results about viruses, drugs, vaccine types, entry receptors, and research stages. These results are sent to a MITRE-developed curation user interface, where subject matter expert curators can easily review the extracted information with text evidence. Curators determine whether a paper is about the virus and drug/vaccine type/entry receptor identified by NLP. If the curator determines that it is, the curator selects supporting sentence(s) of interest from the abstract to show in the Information Browser and the paper is marked as curated. When a curator determines that a paper is not about the extracted virus and drug/vaccine type/entry receptor, the paper is no longer shown for that result in the Information Browser.

Our NLP system identifies the research stages; human curators can also curate this information. Papers with research stage information from NLP only are marked “Machine-only” while papers with research stage information that has been reviewed or added by curators are marked “Curated”.

All the information about reported drug efficacy is added by curators. This added information is solely an assessment of what the abstract states or claims about the drug's efficacy in the study. Our curators do not assess the scientific merits of these results and conclusions.

Term Definitions

Research Stages

Only one research stage is listed for a virus and drug or vaccine per paper and the most advanced research stage reported in the abstract is preferentially selected. Research stages are listed below in ascending order from least to most advanced.

  • AI/in silico: Drug or vaccine has been designed, modeled, or predicted for activity against the virus using AI/in silico methods.
  • In vitro: Drug or vaccine has been studied/tested with purified proteins/enzymes/components and not in cells.
  • Cell line: Drug or vaccine has been screened/tested for activity against the virus in a cultured cell line(s).
  • Small animal: Drug or vaccine has been screened/tested for safety and prophylactic or therapeutic activity against the virus- in vivo in a small animal model(s) such as mice, ferrets, rabbits.
  • Nonhuman primate: Drug or vaccine has been screened/tested for safety and prophylactic or therapeutic activity against the virus in vivo in a non-human primate (NHP) model(s).
  • Emergency use or case report: Reported use of a drug or vaccine for prophylactic or therapeutic treatment against the virus in vivo in humans.
  • Clinical study: Drug or vaccine has been or is currently undergoing evaluation for safety and efficacy in humans in controlled, randomized Phase 1 – 4 clinical trials. Also includes observational studies, retrospective studies, and clinical meta-analyses where the drug plays a prominent role.
  • Review: Drug or vaccine research or testing progress is summarized in a review article where multiple research stages may be described (e.g., small animal, non-human primate, and clinical trials).

Vaccine Types

  • Inactivated: Includes vaccines where the virus has been inactivated by heat, chemical or radiation methods.
  • Live attenuated: Includes vaccines where the targeted virus has been attenuated by passage, genetic modification, or natural reassortment with a non-pathogenic virus (in vivo or in vitro). This category does not include vaccines where select virus antigens are engineered for expression in a different virus backbone (see viral vector category below); these can be referred to as “live, attenuated chimeric” vaccines in literature but should be categorized as viral vector vaccine.
  • Protein subunit: Includes any vaccines that use select virus proteins as an antigen including purified proteins from a virus; recombinant proteins; recombinant epitopes; and virus-like particles (VLP) or nanoparticles.
  • Virus-like particles (VLP)/nanoparticles: include 1) when discreet protein(s) self-assemble or are encouraged to assemble into particles; and 2) virosomes. This technology involves purification or expression of discreet virus proteins that are reassembled with phospholipids to form a VLP that resembles a virus particle without genomic material. The protein subunit category excludes vaccine that used target virus proteins expressed in a viral vector.
  • Viral vector: Includes any vaccine engineered so that selected antigens from the target virus are expressed with the backbone of a different virus; both standard virus vectored vaccines as well as engineered chimeric viruses (can be referred to as “live attenuated chimeric”) are included in this category.
  • DNA vaccine: Includes DNA constructs engineered to express selected virus antigens.
  • RNA vaccine: Includes RNA constructs engineered to express selected virus antigens.
  • Vaccine type not identified: Indicates a paper is about vaccine research but is either not about a particular vaccine type or NLP did not identify a particular vaccine type. This includes early vaccine-related research, such as research on epitopes.

This figure shows the numbers of papers found with information about pairs of drugs and viruses, sorted by research stage. Click on a number in the figure to see the papers below the figure. Click on the numbers between Previous and Next to see additional drugs and papers. Type in a drug name in the search box below Therapeutic to find a particular drug.

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Enter terms or phrases separated by commas (e.g., alpha variant,B.1.1.7).

Type in term(s) to search for in full text journal papers. Multiple terms must be comma-separated. This search will reduce the paper counts shown above to those that contain the term(s). Click on a number to show the set filtered for the given term(s) in the paper table below. In the paper table below, click on a link in the Snippets column to see text snippets with the search term(s) from a paper.

Note: results are limited to papers published by participating publishers.

This figure shows the numbers of papers found with information about types of vaccines and viruses, sorted by research stage. Click on a number in the figure to see the papers below the figure.

Loading...

Enter terms or phrases separated by commas (e.g., alpha variant,B.1.1.7).

Type in term(s) to search for in full text journal papers. Multiple terms must be comma-separated. This search will reduce the paper counts shown above to those that contain the term(s). Click on a number to show the set filtered for the given term(s) in the paper table below. In the paper table below, click on a link in the Snippets column to see text snippets with the search term(s) from a paper.

Note: results are limited to papers published by participating publishers.

Dataset and Data Description

A dataset containing results from all documents processed through July 6, 2021 is now available for download. This includes virus-drug pairs identified in documents, assignments of documents to research stages, and some additional information. The data description file also contains precision and recall statistics.

Download the Dataset and Data Description

Briefing

A briefing to the NIH NIAID Data Science Seminar Series presenting an analysis of published COVID-19 drug research and additional information about the NLP methods is available for download.

Download the Briefing

COVID-TIB Demo Briefing

For information on how to use this site, please see the demo briefing available for download below.

Download the Demo