Open Access COVID-19 Research for Analysis

Open Access COVID-19 Research Available for Analysis-Updated Biweekly

Announcement also available in Portuguese

The U.S. Government is helping to provide access to research related to Covid-19.1 The VPInstitute along with TechMining for Global Good hopes to support and accelerate global knowledge sharing of insights and intelligence embedded in the growing body of open access COVID-19 related research, clinical trials, and intellectual property. Below are:

  1. A cleaned/refined PubMed coronavirus data-set ready for analysis in VantagePoint text-mining software. (UPDATED JUNE 17, 2020). Leave a Reply in the comment field below to offer suggestions, requests, etc. You may also wish to view the accompanying PDF profile of the search results, Corona Virus Research Publications from PUBMED search June172020, also updated bi-weekly. We will keep past PDF research profiles from prior searches available, should you want to revisit.

DOWNLOAD “Pubmed_coronavirus-6-17-2020 43254.vpt” HERE

Series of Bi-weekly searches:

  • March 25, 2020: Initial dataset – 19,538 records.
  • April 8, 2020: Update yielded 21,314 records.
  • April 22, 2020: Update yielded 24,479 records.
  • May 6, 2020: Update yielded 28,264 records.
  • May 21, 2020: Update yielded 34,181
  • June 3, 2020:  Update yielded 38,183
  • June 17, 2020: Update yielded 43,254

Explosive growth in COVID-19 research publication this year!

We apply the search query, but apply it to the legacy version of the PubMed database [by shifting from “PMC’ via pull-down to “PubMed”]

  • “COVID-19” OR Coronavirus OR “Corona virus” OR “2019-nCoV” OR “SARS-CoV” OR “MERS-CoV” OR “Severe Acute Respiratory Syndrome” OR “Middle East Respiratory Syndrome”[1]

Starting with May 20, we encountered limitations in PubMed downloading.  The interface now limits downloads to the first 10,000 records, so we ran a combination of partial searches to recombine in VantagePoint on desktop. Did so using 5 separate searches this time, for select year sets (the interface gives a slider to choose years).

Download by — Save; Selection: all results; Format: PubMed; Create File [downloads to my computer]

  • (“COVID-19” OR “Corona virus” OR “2019-nCoV” OR “SARS-CoV” OR “MERS-CoV” OR “Severe Acute Respiratory Syndrome” OR “Middle East Respiratory Syndrome”) – restricted to
  • 2007-2018 =     9082 saved
  • 1949-2006 =     9524 saved
  • 2020 =              24812
      • [search query as above] AND coronavirus = 14324
        • AND clinical =  5504 saved
        • NOT clinical =  8820 saved
      • [search query as above] NOT coronavirus = 10488
        • AND viral = 654 saved
        • NOT viral = 9834 saved
  • Imported using PubMed configuration file and thereby consolidated these in one VantagePoint file; removed duplicates = 43,254 records.

[1] In MEDLINE detail:  “COVID-19″[All Fields] OR (“coronavirus”[MeSH Terms] OR “coronavirus”[All Fields]) OR “Corona virus”[All Fields] OR “2019-nCoV”[All Fields] OR “SARS-CoV”[All Fields] OR “MERS-CoV”[All Fields] OR “Severe Acute Respiratory Syndrome”[All Fields] OR “Middle East Respiratory Syndrome”[All Fields].

2. A cleaned/refined ClinicalTrials.gov dataset ready for analysis in VantagePoint text-mining software. Leave a Reply in the comment field below to offer suggestions, requests, etc. (UPDATED JUNE 8, 2020)

Data Source: https://clinicaltrials.gov/ct2/results?cond=COVID-19
File type: .vpt (XML format imported into VantagePoint; Refined to extract Country field; list cleanup routines tuned to “conditions”. Detailed tuning by humans was not done.)

DOWNLOAD “ClinicalTrials1982.vpt” HERE

NOTES:
1 Resources include:
a. https://www.whitehouse.gov/briefings-statements/call-action-tech-community-new-machine-readable-covid-19-dataset/

b. Follow the link to here: https://pages.semanticscholar.org/coronavirus-research

Researchers without a subscription to VantagePoint text-mining software may request 60 days free access

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