Shortcomings of SARS-CoV-2 genomic metadata
Abstract Objective The SARS-CoV-2 pandemic has prompted one of the most extensive and expeditious genomic sequencing efforts in history. Each viral genome is accompanied by a set of metadata which supplies important information such as the geographic origin of the sample, age of the host, and the la...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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BMC
2021-05-01
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| Series: | BMC Research Notes |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13104-021-05605-9 |
| _version_ | 1818939795125043200 |
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| author | Landen Gozashti Russell Corbett-Detig |
| author_facet | Landen Gozashti Russell Corbett-Detig |
| author_sort | Landen Gozashti |
| collection | DOAJ |
| description | Abstract Objective The SARS-CoV-2 pandemic has prompted one of the most extensive and expeditious genomic sequencing efforts in history. Each viral genome is accompanied by a set of metadata which supplies important information such as the geographic origin of the sample, age of the host, and the lab at which the sample was sequenced, and is integral to epidemiological efforts and public health direction. Here, we interrogate some shortcomings of metadata within the GISAID database to raise awareness of common errors and inconsistencies that may affect data-driven analyses and provide possible avenues for resolutions. Results Our analysis reveals a startling prevalence of spelling errors and inconsistent naming conventions, which together occur in an estimated ~ 9.8% and ~ 11.6% of “originating lab” and “submitting lab” GISAID metadata entries respectively. We also find numerous ambiguous entries which provide very little information about the actual source of a sample and could easily associate with multiple sources worldwide. Importantly, all of these issues can impair the ability and accuracy of association studies by deceptively causing a group of samples to identify with multiple sources when they truly all identify with one source, or vice versa. |
| first_indexed | 2024-12-20T06:29:25Z |
| format | Article |
| id | doaj.art-52878b18efc3483a98560a01ed328e0d |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-12-20T06:29:25Z |
| publishDate | 2021-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-52878b18efc3483a98560a01ed328e0d2022-12-21T19:50:13ZengBMCBMC Research Notes1756-05002021-05-011411410.1186/s13104-021-05605-9Shortcomings of SARS-CoV-2 genomic metadataLanden Gozashti0Russell Corbett-Detig1Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard UniversityDepartment of Biomolecular Engineering and Genomics Institute, University of California Santa CruzAbstract Objective The SARS-CoV-2 pandemic has prompted one of the most extensive and expeditious genomic sequencing efforts in history. Each viral genome is accompanied by a set of metadata which supplies important information such as the geographic origin of the sample, age of the host, and the lab at which the sample was sequenced, and is integral to epidemiological efforts and public health direction. Here, we interrogate some shortcomings of metadata within the GISAID database to raise awareness of common errors and inconsistencies that may affect data-driven analyses and provide possible avenues for resolutions. Results Our analysis reveals a startling prevalence of spelling errors and inconsistent naming conventions, which together occur in an estimated ~ 9.8% and ~ 11.6% of “originating lab” and “submitting lab” GISAID metadata entries respectively. We also find numerous ambiguous entries which provide very little information about the actual source of a sample and could easily associate with multiple sources worldwide. Importantly, all of these issues can impair the ability and accuracy of association studies by deceptively causing a group of samples to identify with multiple sources when they truly all identify with one source, or vice versa.https://doi.org/10.1186/s13104-021-05605-9SARS-CoV-2MetadataGenomicsDatabasesData qualityCOVID-19 |
| spellingShingle | Landen Gozashti Russell Corbett-Detig Shortcomings of SARS-CoV-2 genomic metadata BMC Research Notes SARS-CoV-2 Metadata Genomics Databases Data quality COVID-19 |
| title | Shortcomings of SARS-CoV-2 genomic metadata |
| title_full | Shortcomings of SARS-CoV-2 genomic metadata |
| title_fullStr | Shortcomings of SARS-CoV-2 genomic metadata |
| title_full_unstemmed | Shortcomings of SARS-CoV-2 genomic metadata |
| title_short | Shortcomings of SARS-CoV-2 genomic metadata |
| title_sort | shortcomings of sars cov 2 genomic metadata |
| topic | SARS-CoV-2 Metadata Genomics Databases Data quality COVID-19 |
| url | https://doi.org/10.1186/s13104-021-05605-9 |
| work_keys_str_mv | AT landengozashti shortcomingsofsarscov2genomicmetadata AT russellcorbettdetig shortcomingsofsarscov2genomicmetadata |