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 also provide a custom identifier (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 ?

NCBI Identifier

Yes

Yes

NC_000866.4

Yes, ncbi link

HER Number

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 menu available in the page of the datasource.

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). If there is a correspondence the VHRdb will add the prefix NCBI to this identifier and create a link to this resource. 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.

E. coli MG1655 (NC_000913.3)

ncbi

Ω8 (HER:315)

her

BEN 1045 (APEC O25)

custom

N4 (NC_008720; HER:119952179)

both