An innovative user-friendly platform for Covid-19 pandemic databases and resources

Ullah, Shahid; Ullah, Anees; Rahman, Wajeeha; Ullah, Farhan; Khan, Sher Bahadar; Ahmad, Gulzar; Ijaz, Muhammad; Gao, Tianshun

doi:10.1016/j.cmpbup.2021.100031

Cited by 10 publications

(4 citation statements)

References 35 publications

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“…A user-friendly platform (CO-19 PDB; COVID-19 Pandemic Data Base) for COVID-19 research was developed by Ullah et al ( 8 ). A total of 59 databases were gathered into the CO-19 PDB database between December 2019 and May 2021 and the data was organized into six different categories, namely databases for (a) digital images, (b) genomic information, (c) literature collection, (d) visualization tools, (e) chemical structure, and (f) social science-related information.…”

Section: Introductionmentioning

confidence: 99%

COVID-19Base v3: Update of the knowledgebase for drugs and biomedical entities linked to COVID-19

Basit

Qureshi

Musleh

et al. 2023

Front. Public Health

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COVID-19 has taken a huge toll on our lives over the last 3 years. Global initiatives put forward by all stakeholders are still in place to combat this pandemic and help us learn lessons for future ones. While the vaccine rollout was not able to curb the spread of the disease for all strains, the research community is still trying to develop effective therapeutics for COVID-19. Although Paxlovid and remdesivir have been approved by the FDA against COVID-19, they are not free of side effects. Therefore, the search for a therapeutic solution with high efficacy continues in the research community. To support this effort, in this latest version (v3) of COVID-19Base, we have summarized the biomedical entities linked to COVID-19 that have been highlighted in the scientific literature after the vaccine rollout. Eight different topic-specific dictionaries, i.e., gene, miRNA, lncRNA, PDB entries, disease, alternative medicines registered under clinical trials, drugs, and the side effects of drugs, were used to build this knowledgebase. We have introduced a BLSTM-based deep-learning model to predict the drug-disease associations that outperforms the existing model for the same purpose proposed in the earlier version of COVID-19Base. For the very first time, we have incorporated disease-gene, disease-miRNA, disease-lncRNA, and drug-PDB associations covering the largest number of biomedical entities related to COVID-19. We have provided examples of and insights into different biomedical entities covered in COVID-19Base to support the research community by incorporating all of these entities under a single platform to provide evidence-based support from the literature. COVID-19Base v3 can be accessed from: https://covidbase-v3.vercel.app/. The GitHub repository for the source code and data dictionaries is available to the community from: https://github.com/91Abdullah/covidbasev3.0.

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Section: Introductionmentioning

confidence: 99%

COVID-19Base v3: Update of the knowledgebase for drugs and biomedical entities linked to COVID-19

Basit

Qureshi

Musleh

et al. 2023

Front. Public Health

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“…Because of the effects of antineoplastic therapy, supportive drugs including steroids, and the immunosuppressive qualities of cancer, people with cancer could be immunocompromised [ 5 ]. The advancement of modern genomic technology—such as microarrays, proteomics, transcriptomics, and gene sequencing—and the serious situation resulting from the COVID-19 pandemic have resulted in the generation of a huge amount of data [ 9 , 10 ]; therefore, the first challenge of these multi-omics cancer and COVID-19 data was the design and usage of electronic databases to store and manage the large amount of knowledge [ 11 ]. A number of databases have been published in this research area, which have explained the wide-ranging information about cancer research and COVID-19 [ 10 , 12 - 16 ], such as The Cancer Genome Atlas (TCGA), RespCanDB, cBioPortal, Co-19PDB, and ICGC, these databases have been exploring, analyzing, and visualizing multidisciplinary genomics data.…”

Section: Introductionmentioning

confidence: 99%

“…The advancement of modern genomic technology—such as microarrays, proteomics, transcriptomics, and gene sequencing—and the serious situation resulting from the COVID-19 pandemic have resulted in the generation of a huge amount of data [ 9 , 10 ]; therefore, the first challenge of these multi-omics cancer and COVID-19 data was the design and usage of electronic databases to store and manage the large amount of knowledge [ 11 ]. A number of databases have been published in this research area, which have explained the wide-ranging information about cancer research and COVID-19 [ 10 , 12 - 16 ], such as The Cancer Genome Atlas (TCGA), RespCanDB, cBioPortal, Co-19PDB, and ICGC, these databases have been exploring, analyzing, and visualizing multidisciplinary genomics data. Further, we have presented a comparison table with previously published work, in which we have noticed a considerable growth in the number of databases, and we have provided the list of all the cancer databases and have built a database of the databases named the Cancer Research Database (CRDB), with the improvement highlighted in Table 1 .…”

Section: Introductionmentioning

confidence: 99%

“…Previously, we have published several articles in well-known journals, such as the database of Phospho-sites in Animals and Fungi [ 23 ] in Scientific Reports , the Circadian Gene Database [ 24 ] in Nucleic Acids Research , Co-19PDB [ 10 ] in Computer Methods and Programs in Biomedicine Update , DataBases relevant to Human Research [ 25 ] in Future Science and DataBase of Plant Research [ 26 ]; we have provided 15 databases to the scientific community during the COVID-19 pandemic, which can be accessed on the internet [ 27 ].…”

Section: Introductionmentioning

confidence: 99%

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The Cancer Research Database (CRDB): Integrated Platform to Gain Statistical Insight Into the Correlation Between Cancer and COVID-19

Ullah¹,

Ullah²,

Karras³

et al. 2022

JMIR Cancer

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Background The advancement of cancer research has been facilitated through freely available cancer literature, databases, and tools. The age of genomics and big data has given rise to the need for cooperation and data sharing in order to make efficient use of this new information in the COVID-19 pandemic. Although there are many databases for cancer research, their access is not easy owing to different ways of processing and managing the data. There is an absence of a unified platform to manage all of them in a transparent and more comprehensible way. Objective In this study, an improved integrated cancer research database and platform is provided to facilitate a deeper statistical insight into the correlation between cancer and the COVID-19 pandemic, unifying the collection of almost all previous published cancer databases and defining a model web database for cancer research, and scoring databases on the basis of the variety types of cancer, sample size, completeness of omics results, and user interface. Methods Databases examined and integrated include the Data Portal database, Genomic database, Proteomic database, Expression database, Gene database, and Mutation database; and it is expected that this launch will sort, save, advance the understanding and encourage the use of these resources in the cancer research environment. Results To make it easy to search valuable information, 85 cancer databases are provided in the form of a table, and a database of databases named the Cancer Research Database (CRDB) has been built and presented herein. Furthermore, the CRDB has been herein equipped with unique navigation tools in order to be explored by three methods; that is, any single database can be browsed by typing the name in the given search bar, while all categories can be browsed by clicking on the name of the category or image expression icon, thus serving as a facility that could provide all the category databases on a single click. Conclusions The computational platform (PHP, HTML, CSS, and MySQL) used to build CRDB for the cancer scientific community can be freely investigated and browsed on the internet and is planned to be updated in a timely manner. In addition, based on the proposed platform, the status and diagnoses statistics of cancer during the COVID-19 pandemic have been thoroughly investigated herein using CRDB, thus providing an easy-to-manage, understandable framework that mines knowledge for future researchers.

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The HABD: Home of All Biological Databases Empowering Biological Research With Cutting‐Edge Database Systems

Ullah,

Rahman,

Ullah

et al. 2024

Current Protocols

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The emergence of computer technologies and computing power has led to the development of several database systems that provide standardized access to vast quantities of data, making it possible to collect, search, index, evaluate, and extract useful knowledge across various fields. The Home of All Biological Databases (HABD) has been established as a continually expanding platform that aims to store, organize, and distribute biological data in a searchable manner, removing all dead and non‐accessible data. The platform meticulously categorizes data into various categories, such as COVID‐19 Pandemic Database (CO‐19PDB), Database relevant to Human Research (DBHR), Cancer Research Database (CRDB), Latest Database of Protein Research (LDBPR), Fungi Databases Collection (FDBC), and many other databases that are categorized based on biological phenomena. It currently provides a total of 22 databases, including 6 published, 5 submitted, and the remaining in various stages of development. These databases encompass a range of areas, including phytochemical‐specific and plastic biodegradation databases. HABD is equipped with search engine optimization (SEO) analyzer and Neil Patel tools, which ensure excellent SEO and high‐speed value. With timely updates, HABD aims to facilitate the processing and visualization of data for scientists, providing a one‐stop‐shop for all biological databases. Computer platforms, such as PhP, html, CSS, Java script and Biopython, are used to build all the databases. © 2024 Wiley Periodicals LLC.

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An innovative user-friendly platform for Covid-19 pandemic databases and resources

Cited by 10 publications

References 35 publications

COVID-19Base v3: Update of the knowledgebase for drugs and biomedical entities linked to COVID-19

COVID-19Base v3: Update of the knowledgebase for drugs and biomedical entities linked to COVID-19

The Cancer Research Database (CRDB): Integrated Platform to Gain Statistical Insight Into the Correlation Between Cancer and COVID-19

The HABD: Home of All Biological Databases Empowering Biological Research With Cutting‐Edge Database Systems

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