Populate Jira Assets with Virus and Targets from Genbank file

[sspoon]

When we get a new virus, we need a way to populate the Jira Assets for the Virus and Targets from Genbank. You can decide how you want to handle storing the domain data (the black bars in the Genome Browser). This should work in tandem with the cron job that pulls from CSBID. In the case of a new virus, CSBID will not yet have the virus and targets in their system.

Please work with Andrew and Ryan on this.

[sspoon]

@yonglbl now that we've had some discussions, I think it would be good to prioritize this. Once the data is populated in Assets, @ajtritt will be able to demonstrate the Alphafold automation he has ready to go, as well as maybe a new analysis, which is something that ASCR really wants to see.

[yonglbl]

@ajtritt
in case of this protein YP_009725297.1, it has two subregions.
`
Region 13..127

                 /region_name="SARS-CoV-like_Nsp1_N"

                 /note="N-terminal domain of non-structural protein 1 from

                 Severe acute respiratory syndrome-related coronavirus and

                 betacoronavirus in the B lineage; cd21796"

                 /db_xref="CDD:439285"

Region 128..180

                 /region_name="SARS-CoV-like_Nsp1_C"

                 /note="C-terminal domain of non-structural protein 1 from

                 Severe acute respiratory syndrome-related coronavirus and

                 betacoronavirus in the B lineage; cd22662"

                 /db_xref="CDD:439355"

`

Do you know when they set a Target, is usually one region, multiple regions, or a whole protein?

[ajtritt]

@yonglbl

Do you know when they set a Target, is usually one region, multiple regions, or a whole protein?

They target the whole protein, but tend to focus on regions. I suggest making assets for the whole protein, and individual assets for each region. You will need to make a new asset type for Region. @rly or myself can help with that.

[yonglbl]

if you or @rly can work on the asset structure that will be great,. sounds like you also need a new Protein asset? and in Target asset, probably no need Target ID or Original Target ID, maybe a new protein field that reference to the Protein object.?