Create Basic Dataset

Introduction

In this project’s initial phase, potential sources for the intended dataset were gathered and assessed in terms of comprehensiveness and accessibility. The decision was made for Dimensions as the dataset’s core source, due to its straightforward and for research purposes free accessibility, as well as its comparatively rich amount of preprint-related data

Login

Please check Dimensions’ Getting Started Checklist for details about installing the Dimcli library and using it to authenticate against the API of Dimension.

Code

dimcli.login()
dsl = dimcli.Dsl()

Query for COVID-19 related preprints publishd in 2020

This is the same query that is used by the COVID-19 webapp provided by Dimensions as part of their COVID-19 resources.

Query-Strings für COVID19-Preprints

covid19_search = """"2019-nCoV" OR "COVID-19" OR “SARS-CoV-2” OR "HCoV-2019" OR "hcov" OR "NCOVID-19" OR "severe acute respiratory syndrome coronavirus 2" OR "severe acute respiratory syndrome corona virus 2" OR “coronavirus disease 2019” OR (("coronavirus" OR "corona virus") AND (Wuhan OR China OR novel))""".replace("“", "\"").replace("”", "\"").replace("\"", '\\"')

query_P_test = f"""search publications for "{covid19_search}" where year in [2020] and type="preprint" return publications [id + doi + title + year + journal + resulting_publication_doi + altmetric + times_cited + recent_citations + type + issn + linkout + abstract + date] limit 1000"""
query_P_full = f"""search publications for "{covid19_search}" where year in [2020] and type="preprint" return publications [id + doi + title + year + journal + resulting_publication_doi + altmetric + times_cited + recent_citations + type + issn + linkout + abstract + date]"""

This may take a few minutes …

Code

P = %dslloopdf $query_P_full
#P = %dsldf $query_P_test

Code

P.head().T

	0	1	2	3	4
id	pub.1139066291	pub.1134469293	pub.1134363910	pub.1134331013	pub.1134331012
title	The kidnapping of mitochondrial function assoc...	Hypothesis of Potential Evolution of SARS-CoV-...	Networks of Necessity: Simulating COVID-19 Mit...	Twitter Users Display Desensitization to Bad H...	COVID-19 Vaccine Hesitancy in Canada: Content ...
abstract	<p>Severe Acute Respiratory Syndrome Coronavir...	Abstract Background Discovery of the or...	A major strategy to prevent the spread of COVI...	<sec> BACKGROUND <p>Among the countries affect...	<sec> BACKGROUND <p>With the approval of two C...
date	2020-12-31	2020-12-31	2020-12-31	2020-12-31	2020-12-31
doi	10.21203/rs.3.rs-137853/v1	10.14293/s2199-1006.1.sor-.ppdo2zu.v1	10.48550/arxiv.2101.00060	10.2196/preprints.26876	10.2196/preprints.26874
linkout	https://www.researchsquare.com/article/rs-1378...	https://www.scienceopen.com/document_file/1ad6...	NaN	http://dx.doi.org/10.2196/preprints.26876	https://www.jmir.org/2021/4/e26874/PDF
recent_citations	1	1	0	0	2
resulting_publication_doi	10.14670/hh-18-354	NaN	NaN	NaN	10.2196/26874
times_cited	1	1	0	0	2
type	preprint	preprint	preprint	preprint	preprint
year	2020	2020	2020	2020	2020
journal.id	jour.1380788	jour.1381049	jour.1371339	jour.1345647	jour.1345647
journal.title	Research Square	ScienceOpen Preprints	arXiv	JMIR Preprints	JMIR Preprints
altmetric	NaN	1.0	11.0	NaN	NaN
issn	NaN	NaN	NaN	NaN	NaN

Save dataset

P.to_csv("../data/covid_preprints_basic.csv", index=None)