Virus world database (VWdb), an API-enabled database of virus taxonomy
LETTER
The number of viruses that are being identified and characterized is growing by the day. However, it is not easy to gather information on the taxonomy of these viruses as the related data at NCBI (https://www.ncbi.nlm.nih.gov/) (1) are too large (hundreds of thousands of lines) and loaded into a single webpage or not up to date at the ICTV (https://ictv.global/) (2). Hence, there is a gap in knowledge and the need for easy access to the taxonomy information in a user-friendly manner.
In this work, we created an easy-to-use web interface, entitled Virus World database (VWdb), accessed from the URL: https://viperdb.org/vw, that can be utilized to select viruses according to various aspects of taxonomy and the related information available in other relevant databases: UniProtKB (3), PDB (4), VIPERdb (5, 6), and EMDB (7). In addition, we created an API (Application Programming Interface) that can be used for programmatic access of the metadata available in VWdb.
We downloaded all the taxonomy data available in the new format (https://ncbiinsights.ncbi.nlm.nih.gov/2018/02/22/new-taxonomy-files-available-with-lineage-type-and-host-information/) on all the kingdoms (e.g., bacteria, invertebrates, and viruses) from NCBI. We then parsed and stored all the taxonomy data into a temporary MySQL database (Taxo), followed by searching, extracting, and uploading virus-specific information into a virus entry-specific database, VWdb. This was followed by searching and storing virus-related data from various databases (e.g., UniProtKB, PDB, EMDB, AlphaFoldDB), which involved accessing various APIs via Python scripts with multi-threading on to speed up the search significantly. We have used the taxonomy-ID as the primary key in VWdb and to connect to relevant databases. Additionally, we included the information on Baltimore classification system of genomes for virus families available at ViralZone web resource (8). The details of VWdb schema are given in the Supplementary Information (Fig. S1). We then created multiple PHP web services to query and access data from a web interface to select and display the taxonomy data associated with each virus genome/family/genus in a table form. A flow chart depicting the various steps involved in data acquisition and setting up the MySQL database at VWdb is shown in Fig. S2. Furthermore, we have included a table comprising a glossary of technical terms (e.g., JSON, MySQL) and the description of their intended function (Table 1).
TABLE 1
| Term | Description |
|---|---|
| API (Application Programming Interface) | Used for programmatic access of data from an online database, bypassing the web interface. |
| Excel format | Microsoft spreadsheet format. |
| JSON format | A language independent data (text) format for data exchange between different resources. |
| MySQL (structured query language) database | A relational database management system. |
| PHP (hypertext preprocessor) services | PHP is a scripting language geared toward web development. The PHP services involve query requests between the user interface and behind-the-scenes MySQL database. |
At the time of writing, there are 231,437 viruses from 233 virus families and 2,578 genera available at VWdb. These viruses are classified to contain eight different types of genomes (e.g., ribovira, monodnaviria, duplodnaviria), including an unclassified class that infect 13 different hosts, as categorized by NCBI (Table 2). Significantly, however, we have also included the Baltimore classification of viral genomes (e.g., ssRNA, dsDNA) gathered from the Viral Zone resource (8) that is not available at NCBI. One can choose to display all the viruses that infect a particular host (e.g., humans, bacteria, and plants) or those containing a particular type of genome or belong to a family or genus. With the exception of the host category, a particular selection (e.g., genome-type) will automatically populate the “downstream” associated categories (e.g., family or genus) in the windows to the right side of the chosen category. Currently, there are 163,512, 13,718, 4,818 viruses that infect humans, bacteria, and plants, respectively. The data displayed in the table according to the selection include taxonomy-ID, virus name, species name, genus, family, genome type, type of host, and a column displaying whether or not any relevant structures are available (Fig. 1A). Furthermore, one can choose to display only the entries having structural details by clicking on the “with structural information” box. Additionally, a search function is found at the top menu bar to search for a particular virus, family name, and taxonomy-ID based on the structural information (e.g., PDB-ID or EMDB-ID). There is also an advanced search option provided to narrow down the results by supplying additional keywords in multiple categories. Of note, the data listed in the table can be downloaded in Excel or JSON formats.
Fig 1
TABLE 2
| Category | Types |
|---|---|
| Hosts | Algae, archaea, bacteria, eukaryotic algae, fungi, human, human stool, insects, invertebrates, land plants, plants, protozoa, vertebrates |
| Genomes (NCBI) | Adnaviria, duplodnaviria, monodnaviria, riboviria, ribozyviria, satellites, varidnaviria, and unclassified |
| Genomes (Baltimore classification) | dsDNA, dsRNA, rtRNA, ssDNA, ssRNA (+), ssRNA (−), circular SSRNA |
An info-page is generated immediately by clicking on each row in the table that contains various relevant information of the virus (Fig. 1B). In addition to the taxonomy information, the info_page (e.g., https://viperdb.org/vw/info_page.php?taxid=12081) contains UniProt-IDs with hyperlinks corresponding to various genes in the viral genome (3) and the structural information that may be available at different structural databases—PDB (4), VIPERdb (5, 6), and EMDB (7) and AlphaFoldDB (9).
To our knowledge, VWdb is the only place where the integrated information on virus taxonomy, susceptible hosts, genome type, sequence, and structure details is available on all the known viruses in an easy-to-use fashion. The viruses that belong to a particular family or contain a specific genome type can be selected and listed in a table form that in turn can be downloaded in Excel or JSON formats. One can also search for a particular virus based on its name, family name, taxonomy-ID, or structural information (e.g., PDB-ID, EMDB-ID). In addition to the details on virus taxonomy, the info_page of each virus contains hyperlinks to the relevant access codes in UniProtKB, PDB, VIPERdb, and EMDB and AlphaFoldDB. Furthermore, we provided an API to programmatically access the metadata that are stored at VWdb in JSON format. The description of which can be found in the Supplementary Information (Fig. S3). We plan to update VWdb at regular intervals as and when new data become available at NCBI. VWdb can be accessed from the URL: https://viperdb.org/vw.
ACKNOWLEDGMENTS
We thank Nelly Santoyo-Rivera for helpful discussions on implementing some of the Python scripts and web-services on VWdb. We also would like to thank Dr. Jeffrey McDonald, the Director of Information Technology and HPC computing at the Hormel Institute, for his assistance in setting up the VIPERdb web server.
This work supported by the startup funds from the Hormel Institute to V.S.R.
The authors declare that there is no conflict of interest.
SUPPLEMENTAL MATERIAL
Fig. S1, Fig. S2, and Fig. S3 - jvi.00620-23-s0001.pdf
This supplemental file provides the details of VWdb schema, flow chart of data acquisition and the description of VirusWorldDB REST API on how to access the metadata.
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Information & Contributors
Information
Published In
Journal of Virology
Volume 97 • Number 8 • 31 August 2023
eLocator: e00620-23
Editor: Felicia Goodrum, The University of Arizona, Tucson, Arizona, USA
PubMed: 37578228
Copyright
© 2023 American Society for Microbiology. All Rights Reserved.
History
Received: 24 April 2023
Accepted: 13 June 2023
Published online: 14 August 2023
Keywords
Data Availability
The data and associated APIs underlying this article are available freely at VWdb. The
Contributors
Editor
Felicia Goodrum
Editor
The University of Arizona, Tucson, Arizona, USA
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Citation
2023.
Virus world database (VWdb), an API-enabled database of virus taxonomy. J Virol
97:e00620-23.
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