An Innovative User-friendly Platform for Covid-19 Pandemic Databases and Resources

Abstract

Background
COVID-19 is a global outbreak of a disease from a new virus, occurred in Wuhan China in December 2019. Several databases have been published on this pandemic, but the research community still needs an easy way to get comprehensive information on COVID-19.

Objectives
COVID-19 pandemic database (CO-19 PDB) aims to provide wonderful insights for COVID-19 researchers with the well-gathered of all the COVID-19 data to one platform, which is a global challenge for the research community these days.

Methods
We gathered 59 updated databases since December-2019 until May 2021 and divided them into six categories: digital image database, genomic database, literature database, visualization tools database, chemical structure database, and social science database. These categories focus on taking number of functions from the images, information from gene sequences, updates from relevant papers, essays, reports, articles, and books, the data or information in the form of maps, graphs, and charts, information of bonds between atoms, and updates about events of the physical and social environment, respectively.

Results
Users can search the information of interest in two ways including typing the name of the database in the search bar or by clicking the right category directly. Computer languages such as CSS, PHP, HTML, Java, etc. are utilized to construct CO-19 PDB.

Full text

Since January 2020 Elsevier has created a COVID-19 resource centre with
free information in English and Mandarin on the novel coronavirus COVID-
19. The COVID-19 resource centre is hosted on Elsevier Connect, the
company's public news and information website.
Elsevier hereby grants permission to make all its COVID-19-related
research that is available on the COVID-19 resource centre - including this
research content - immediately available in PubMed Central and other
publicly funded repositories, such as the WHO COVID database with rights
for unrestricted research re-use and analyses in any form or by any means
with acknowledgement of the original source. These permissions are
granted for free by Elsevier for as long as the COVID-19 resource centre
remains active.

Computer Methods and Programs in Biomedicine Update 1 (2021) 100031
Available online 26 September 2021
2666-9900/© 2021 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license
(http://creativecommons.org/licenses/by-nc-nd/4.0/).
An innovative user-friendly platform for Covid-19 pandemic databases
and resources
Shahid Ullah
b
,
*
, Anees Ullah
d
, Wajeeha Rahman
b
, Farhan Ullah
b
, Sher Bahadar Khan
c
,
Gulzar Ahmad
b
, Muhammad Ijaz
b
, Tianshun Gao
a
,
**
a
Research Center, The Seventh Afliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
b
S Khan Lab Mardan, Khyber Pakhtunkhwa, Pakistan
c
Department of Animal Health, The University of Agriculture, Peshawar, Pakistan
d
Kyrgyz State Medical Academy (KSMA), Kyrgyzstan
ARTICLE INFO
Keywords:
CO-19 PDB
COVID-19
Digital image
Genomic
Chemical structure
ABSTRACT
Background: The current coronavirus disease-19 (COVID-19) is caused by severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) is a global outbreak of a disease from a new coronavirus. Several databases have
been published on this pandemic, but the research community still needs an easy way to get comprehensive
information on COVID-19.
Objectives: COVID-19 pandemic database (CO-19 PDB) aims to provide wonderful insights for COVID-19 re-
searchers with the well-gathered of all the COVID-19 data to one platform, which is a global challenge for the
research community these days.
Methods: We gathered 59 updated databases since December-2019 until May 2021 and divided them into six
categories: digital image database, genomic database, literature database, visualization tools database, chemical
structure database, and social science database. These categories focus on taking number of functions from the
images, information from gene sequences, updates from relevant papers, essays, reports, articles, and books, the
data or information in the form of maps, graphs, and charts, information of bonds between atoms, and updates
about events of the physical and social environment, respectively.
Results: Users can search the information of interest in two ways including typing the name of the database in the
search bar or by clicking the right category directly. Computer languages such as CSS, PHP, HTML, Java, etc. are
utilized to construct CO-19 PDB.
Conclusion: This article attempts to compile up-to-date appropriate COVID-19 datasets and resources that have
not been compiled and given in such an accessible and user-friendly manner. As a result, the CO-19 PDB offers
extensive open data sharing for both worldwide research communities and local people. Further, we have
planned future development of new features, that will be awesome for future study.
Introduction
Background
COVID-19 pandemic broke out in the end of the year 2019 [1], and
spread to 211 countries quickly [2,3]. It is caused by a novel virus
known as severe acute respiratory syndrome coronavirus 2. (SAR-
S-CoV-2) [4], which is responsible for the violent (COVID-19) pandemic
[5]. Researchers recently clearly stated that COVID-19 patients getting
angiotensin-converting-enzyme inhibitors (ACEI) could experience
better health [5,6]. The COVID-19 vaccine, considered to be an impor-
tant prophylactic safety and prevention technique, is being
* Corresponding author at: S Khan Lab, Mardan, KPK, Pakistan, PhD From Huazhong University of Science and technology, Wuhan, China. Postdoctoral. Chinese
academy of Science & Shenzhen University Institute of Low-dimensional Materials Genome Initiative, College of Chemistry and Environmental Engineering,
Shenzhen, Guangdong 518060, P. R. China
** Corresponding author at: Currently working as an associate Prof in. Research Center, The Seventh Afliated Hospital of Sun Yat-sen University, Shenzhen,
Guangdong, China PhD: Department of Bioinformatics & Systems Biology, Collage of life science and technology Huazhong University of Science and Technology
(HUST) Wuhan 430074, China
E-mail addresses: dridechina@gmail.com, drsbioch@yahoo.com, drskbioch@gmail.com (S. Ullah).
Contents lists available at ScienceDirect
Computer Methods and Programs in Biomedicine Update
journal homepage: www.sciencedirect.com/journal/computer-methods-
and-programs-in-biomedicine-update
https://doi.org/10.1016/j.cmpbup.2021.100031
Received 18 May 2021; Received in revised form 18 September 2021; Accepted 24 September 2021

Computer Methods and Programs in Biomedicine Update 1 (2021) 100031
2
manufactured in about 90 institutions around the world [2]. Previously
we have published several databases on different research areas in
well-cited international journals, such as, databases on phosphorylation
animal and fungi (DBPAF), in Scientic Report journal [7], a database of
circadian genes in eukaryotes (CGDB), in Nucleic Acids Research journal
[8], database for protein phosphorylation sites in prokaryotes (dbPSP),
in Oxford Database journal [9], Emergency Data Base of COVID-19
(EDBCO-19) [10], Database of plant Research (DBPR) [11] and so on.
Taken together, we have provided a huge platform named HABDSK to
scientic community in the form of eleven databases of a different
research eld that can be freely accessed [12] with timely updates.
Aim of the study
This article attempts to gather all the knowledge needed for the
COVID-19 pandemic worldwide by analyzing papers and databases that
have been published by a recent global scientists, Like the regular
publishing of articles reported in the Centers for Disease Control and
Prevention (CDC) database [13], statistics are reported by World Health
Organization (WHO) [14], and several other databases have been online
on the COVID-19 pandemic in various study areas and facets of
COVID-19, each and every one has its own information and importance,
however, in this crucial time, we have gathered all this data on a friendly
and faster-nding platform for the global scientic community, and
have grouped them into 6 categories so researchers can query for the
knowledge they need in a short time. In short, we have provided a new
way of searching in the form of a new feature (Fig. 2A), and will be
useful for future research.
Materials and methods
Construction of database
CO-19 PDB, data is collected and constructed on the friendly nding
way (Fig. 1), many keywords have been used for searching the data such
as; COVID-19 database, Corona database, Virus database, etc. in several
searching engines like Google, Google Scholar and especially PubMed.
Computer programming platforms have been used in the construction of
the database. Finally, CO-19 PDB is available for researchers to be
operated easily.
Use of the CO-19 PDB
Our database offers two ways to search. Users can search by clicking
on the categories that lead to the proper table of the categories with
small description which is shown in the (Fig. 2A). Further clicking will
lead to the ofcial link with a small description of the needed query,
shown in (Fig. 2B), furthermore clicking will give the new window of
needed database which we have placed the tickmark sign as an example.
In addition, insert the required database name in the search bar that is
mentioned at the top of the main page and has been highlighted in the
(Fig. 2C).
Results
Statistic of the database
In this work, we have focused on COVID-19 databases, and have
Fig. 1. The data collection and construction procedure of the CO-19 PDB.
S. Ullah et al.

Computer Methods and Programs in Biomedicine Update 1 (2021) 100031
3
collected all the database from December 2019 till May 2021, (Fig. 3A)
is the growth of monthly wise databases, which show the tremendous
growth with the passage of time, while (Fig. 3B) is the category wise
growth of databases, in which, the literature category shown the highest
value, due to vast amount of globally published literature in COVID-19
pandemic, in (Fig. 3C) the clear percentile of the data is shown, which
can be of great help to further researchers, (Fig. 3D) depicts the overall
number of new cases, while (Fig. 3E) depicts the overall number of
deaths from December 2019 till 5 May 2021, in which the United States
and India are at the top, and (Fig. 3F) depicts the top 6 conrmed cases
by area, with America and Europe at the top. For more updated infor-
mation and research we have provided this separate platform. It is to be
noted, that all the redundant, disabled, and non-assessable database
links have been updated or removed and provided new and updated
COVID-19 databases which are in the form of database and table,
(Table S1).
Previous published work and development of new features
Previously many articles have been published in well-known jour-
nals [15–18](Tab: 1), which have collected the databases of different
organisms and different research area, e.g. Biological databases for
human research [19] which have collected 74 human databases, “Online
Databases for Taxonomy and Identication of Pathogenic Fungi and
Proposal for a Cloud-Based Dynamic Data Network Platform [20]” have
collected 24 fungi databases, so that a well comprehensive COVID-19
database is also needed for the research community to sort and save
all the COVID-19 data for future researchers [21], because nowadays
database of COVID-19 has been an integral part of modern biology.
Further, published work has collected the databases and has presented
them in the form of a Table, while in our work we have provided the
table as well as the database of the databases, named COVID-19 PD, the
Comparison is given in (Table 1). Furthermore, to make easier and
clearer, we have categorized the databases on the basis of their prop-
erties such as, digital image database, genomic database, literature
database, visualization tools database, chemical structure database, and
social science database, and have planned future development of new
features, which are shown in (Fig. 2A). that have not been provided
before.
Fig. 2. The usage and statistic of CO-19 PDB, (A) Searching by clicking the name of the category. (B) Can search the name of needed database. (C) The percentage of
the collected data.
S. Ullah et al.

Computer Methods and Programs in Biomedicine Update 1 (2021) 100031
4
Discussion
CO-19 PDB classication
The classication of various viruses is based on the selection and
contrast displayed by the viruses, them to distinguish [23] based on
sequence similarity [24], the molecular structure of the genome [25],
pathogenicity [26], structural similarities [27,28] and host range [29].
Huge research has been done on different viruses and has been saved in
the form of published literature or databases, for an easy access and
using this huge data, several databases have been released previously
such as NIH, COVID-19 Data Portal and EDBCO-19. Currently on
COVID-19 Pandemic, number of databases have been published, but a
simplied and easier-to-use research is still needed for the conformant of
the scientic community, so we have gathered revised datasets and
grouped them into several categories based on their external and in-
ternal structure and function as described below, that can be access
through this link https://www.habdsk.org/co-19pdb.php
Fig. 3. The statistic of CO-19 PDB, (A) Monthly wise growth, (B) Category-wise growth, (C) The percentage of the collected data, (D) Total new cases, (E) Total
death, (F) Top 6 conrmed cases by region.
S. Ullah et al.

Computer Methods and Programs in Biomedicine Update 1 (2021) 100031
5
Table 1
Comparison of CO-19 PDB with other published work.
Authors Year Category Form of DB. No Journal name Ref.
Our current work 2021 COVID-19 DB+Table 59 ……. ….
Rigden and Fern´
andez 2021 2021 Covid+other Table 89 Nucleic Acids Res. [22]
Rigden and Fern´
andez 2020 2020 Nucleic acid Table 70 Nucleic Acids Res. [18]
Xu 2012 2012 Protein Table 121 Curr. Protoc. Mol. Biol. [15]
Zou, Ma et al. 2015 2015 Human Table 74 Genomics, Proteomics Bioinf. [19]
Harper 1994 1994 DNA+Protein Table 50 Curr. Opin. Biotechnol. [17]
Fig. 4. The main pages of some common using databases in COVID-19 pandemic.
S. Ullah et al.

Computer Methods and Programs in Biomedicine Update 1 (2021) 100031
6
Chemical structure database
A chemical database contains information about the arrangement of
chemical bonds between atoms in a molecule, ion, or radical with
several atoms, specically which atoms are chemically bonded to other
atoms in what kind of chemical bond [30].There is a variety of useful
chemical knowledge and freely accessible libraries for the usage of
research scientists. Such as knowledge related to the chemical structure
[31] (Fig. 4A) shown COV3D is a weekly modied database that pro-
vides a detailed annotated collection of coronavirus protein structures
and their identication by antibodies and other molecules.
Visualization tools database
Visualization tool database contains a graphical representation of
any data or information. Visual elements such as maps, graphs, and
charts are some of the few data visualization tools that provide the
audience with an easy and accessible way of understanding the repre-
sented information. Using Visualization tools, the COVID-19 data and
information can be read and generated easily and quickly [32].(Fig. 4B)
shown MIDAS is a global network of scientists who developed and
applied theoretical, methodological, and mathematical models to help
explain the complexities of infectious diseases in terms of pathogenesis,
dissemination, efcient management methods, and forecasting.
Genomic database
Genomics is an interdisciplinary biological eld that focuses on the
structure, work, development, and edition of the genome. It is a com-
plete set of DNA of an organism including all its genes [33]. Mostly it
includes gene sequencing and analysis by using high-volume DNA
sequencing and bioinformatics to evaluate the role and composition of
whole genomes [34]. (Fig. 4C) shown COVID-19 genomic sequence
database is a consolidated sequence database for all records containing
sequences associated with the novel corona virus (SARS-CoV-2) that
have been sent to the Sequence Read Archive (SRA) at the National
Center for Biotechnology Information.
Social science database
Social science is the study of the physical and modern sphere. It is
basically an analysis of international relations or the scientic study of
human culture. Simply, it deals with the humans-their development,
behavior, relationship, and resources they use and many kinds of or-
ganizations such as family, school, workplace, etc. it has brought
awareness among the people about our environments and the incidents
that happened in the past [35]. (Fig. 4D) shown main page named
“Outbreak.info” is a web initiative that seeks to collect COVID-19 and
SARS-CoV-2 epidemiology and genomic evidence, as well as published
research and other materials.
Digital image database
A digital picture is consisting of graphic components, also known as
pixels, each with a limited, distinct quantity of numerical representation
due to its strength or gray color from its two-dimensional functions [36].
A digital image has the potential to improve a number of functions, such
as the understanding of information for low-contrast lms, the elec-
tronic transfer of images to remote installations, and the storage space
requirements for archiving once treatment has been completed [37].
(Fig. 4E) shown, the cancer image archive (TCIA) is a service that
de-identies and hosts a large archive of medical image of cancer, that
plays an important role in Covid-19 pandemic.
Literature database
The scientic literature contains publications that report a novel,
experimental and theoretical work in the natural and social sciences,
and is often abbreviated as literature within a scientic eld [38].
Literature Database is an on-line, searchable bibliographic database of
selected papers, essays, report, articles, and books relevant to the study
of arts and cultural policy [39]. (Fig. 4F) shown “LitCovid” is a curated
literature hub for monitoring up-to-date research knowledge about the
newly discovered Corona virus in 2019. It is the most extensive resource
on the topic, providing unied access to 125674 related PubMed
articles.
Conclusion
People around the world are widely infected with COVID-19. Global
scientists are working on COVID-19 and nearly 90 well-known research
institutions are on record. Computational work has been done, and
many datasets have been released and updated on a regular basis.
Therefore, we have created a database of databases that contains all
updated COVID-19 data on an easy platform and is accessible to all
global researchers to aid in their research and study. To prevent wastage
of time and to make it easier to nd, we have classied the updated data
into six categories according to their physical and chemical properties
and have two ways of accessing to it, users can search by clicking on the
category or enter the name of the database they need in the search bar.
In short, the goal of this article is to put together up-to-date applicable
COVID-19 datasets and resources that have not been gathered and
provided before in such an easy and friendly nding ways. As a result,
CO-19 PDB provides wide-ranging open data sharing for both global
research communities and local people.
Author’s contribution
Dr. Shahid Ullah and Prof. Tianshun Gao supervised the project. Dr.
Anees Ullah, Ms. Wajeeha Rahman, Mr. Farhan Ullah, Dr. Sher Bahadar
Khan, Mr. Gulzar Ahmad, and Mr. Muhammad Ijaz collected and veri-
ed the data carefully, all authors reviewed the manuscript and agreed
to submit.
Declaration of Competing Interest
To avoid future conict, Co-19PDB database is uploaded on (http:
//www.habdsk.org/co-19pdb.php) so that we have provided some
content in this article.
Acknowledgment
To avoid future conict, CO-19 PDB database is uploaded on (http:
//www.habdsk.org/co-19pdb.php) so that we have provided some
content in this article. This project is supported by National Natural
Science Foundation of China [32100434] and Shenzhen’s introduction
of talents and research start-up [392020].
Supplementary materials
Supplementary material associated with this article can be found, in
the online version, at doi:10.1016/j.cmpbup.2021.100031.
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Anees Ullah: Bachelor in medicine: Kyrgyz state medical University, Email: anes-
ullah923@gmail.com
Wajeeha Rahman: done Master: now working as a researcher in S-Khan Lab Mardan KPK,
Pakistan http://www.habdsk.org/students.php, Email: wajeeharehman7464@gmail.com
Farhan Ullah: done Master: now working as a researcher in S-Khan Lab Mardan KPK,
Pakistan http://www.habdsk.org/students.php, Email: Farhanu686@gmail.com
Sher Bahadr khan: Assistant professor: Department of Animal Health, The University of
Agriculture, Peshawar, Pakistan, Email: drsher@aup.edu.pk
Gulzar Ahmad: done Master: now working as a researcher in S-Khan Lab Mardan KPK,
Pakistan http://www.habdsk.org/students.php, Email: gulzarbiotech@gmail.com
Muhammad Ijaz: done Master: now working as a researcher in S-Khan Lab Mardan KPK,
Pakistan http://www.habdsk.org/students.php, Email: m.ijaz.biotech@gmail.com
S. Ullah et al.