Next species targets (2.5+)

[ReneRanzinger]

with adding pig in the current release, we will finish our high target species list. We need to select new targets for 2.5 and onwards. We had a species collection based on one of my games from the F2F:

https://gwu0.sharepoint.com/:x:/r/sites/GlyGenTeam-GRP/_layouts/15/Doc.aspx?sourcedoc=%7BB4FE21C6-4AB7-417C-9AB7-D9A0FF6546C1%7D&file=Species-Evaluation-Mockup.xlsx&action=default&mobileredirect=true

Sheet: Species

We also have Nathans old statistic about available species annotations:

https://docs.google.com/spreadsheets/d/1uTjCUd6CHuNz-WT589TaFzjpiKT-lJDCvsXJIrNpdj4/edit#gid=1592450874

Based on Nathans list cow, hamster, E.coli or Chicken seem to be next choices. But a quick review in GlyConnect showed that hamster and E. coli are essentially non existing.

Let me know you suggestions for the next 3-5 targets.

[ReneRanzinger]

Raja My preferences First one is Arabidopsis. Reasons

• Having a plant in our db will help us engage with that community.
• lots of glycan site info
• hard to get separate funding for plants
• there seems to be at least one large scale paper and several small scale 2nd preference HIV
• get us to discuss how to visualize and integrate something which has a lot of data for a specific site. We have discussed it but till we do it we wouldn't know
• not sure if we can get standalone virus funding and we already have added two of them

[ReneRanzinger]

Mike I can agree on arabidopsis but we need to keep in mind how to circumscribe our effort. Like bacteria, the funky monosaccharides and crazy polymers might be a black hole. Limit to N-glycans??

Chicken has historic value and might attract some immunologists/vaccinologists. And, might interface in interesting ways with campy if we get the NSF.

HIV presents challenges that might also help us think about antibody glycosylation as well. Can we consider antibodies as a 'species'?

Hamster interfaces with CHO cell as a resource. I would be surprised if there is that much hamster data that is not really CHO cells??

So, I guess I would rank in the order listed above: arabidopsis, chicken, HIV, Ab, hamster.

[ReneRanzinger]

Raja Agree with Mike's list. And yes Ab can be a special category. We might need to collaborate with a UniProt curator to do that one to make our life easier.

[ReneRanzinger]

1. arabidopsis
2. Chicken
3. HIV
4. Hamster