Identifying viruses and hosts
Nature of identifiers
Both viruses and hosts can be identified with NCBI identifier in nuccore (https://www.ncbi.nlm.nih.gov/nuccore). In addition, for bacterial viruses the identifier (HER Number) from the Felix d’Hérelle collection (https://www.phage.ulaval.ca/en/home/) can also be added. Users can provide a custom identifier as well (e.g. “MYCODE_631”, “BOB1”, …). All identifiers must be entered between parentheses using a semicolon ; as a separator if needed.
Example of identifiers:
Kind of identifier |
Virus |
Host |
Example |
Outgoing link(s) ? |
|---|---|---|---|---|
Yes |
Yes |
NC_000866.4 |
Yes, nuccore link and tax link |
|
Yes |
No |
27 |
Yes, her link |
|
Custom identifier |
Yes |
Yes |
DE 123 |
No |
How to add identifiers ?
Preferably, identifiers should be included in the source file. Adding NCBI identifiers, when available, is strongly encouraged. Users can also add identifiers after uploading their file by using the Edit menus available in the page of the datasource (section Hosts or Virus, in the lower part of the page).
How to specify an identifier in a compatible file ?
Identifiers must be specified in the same cell as to the ID of any virus or host and delimited by parentheses. Entrez api is used to detect automatically if the identifier corresponds to a referenced sequence (i.e, the identifier match in nuccore), and if so also fetch the NCBI TaxID associated. If there is a correspondence the VHRdb will add the prefix NCBI to this identifier and create links to this resource in nuccore and the Taxonomy Browser. If there is no correspondence, the VHRdb will considered the identifier as “custom”, unless it is preceded by a specific prefix. For example, the prefix HER: (e.g. “HER:27”) corresponds to an identifier linked to the Félix d’Hérelle collection of bacterial viruses.
|
|
|
|
|
|
|
|
