ComplexPortal2FB links and fixes

[hattrill]

This is a ticket to review the load of FB complexes into Complex portal.

DOCS -Original FB download and worksheet

-Complexes - loaded and loading in CP

-Complexes Google folder

-Link to original ticket

[hattrill]

• [x] Check single CV issue for Gene Groups solved
• [x] Check entries that have been highlighted by Sandra are addressed - meeting with Sandra after 30th August to be arranged.
• [x] Attribution for FB
• [x] Add xrefs to CP for gene groups see edit ha9060.edit and sheet for making first batch of CP xlink proforma
• [x] Add new complexes to CP list (see sheet)
• [x] Add new complex gene groups from Complex Portal

[hattrill]

sheet for making first batch of CP xlink proforma

[hattrill]

• Have added as many CPX links as possible for FB2022_06;
• Changed format of CPX dbxrefs [ ] Update doc to reflect standard text for proforma
• CP moving server at moment, so delays to release schedule.
• New sheet template for CPX groups not released, to be added to FB after next CP release.
• 24th Nov 11:30 meeting with Sandra to dicuss next steps.

[hattrill]

Meeting with Sandra summary:

1. FlyBase attribution is there, but is showing as "IntACT" - Sandra will ask devs to fix.
2. Link to FBgg pages will happen after they move servers and for next update
3. Discussed that we were mirroring their way of doing variants and Sandra will update CP groups to relfect this.
4. Can we use their display? The code is available, but want to see if it is widigetizable before we go down that route.
5. Sandra "happy" to keep adding groups - we could train in CP at a later date?

[hattrill]

For FB_2022_06

• [ ] Update wiki text

For FB_2023_01

• [x] Review consistency of linkout names to CP and ammend
• [x] Make ticket to change stand text for Source Material from "The XXX Gene Group has been compiled by FlyBase curators using the following publication(s):" to "The XXX Gene Group has been compiled by curators using the following publication(s):"
• [x] For attribution to CP curated groups change Notes on Group standard text from "was sourced from Complex Portal, curated by IntAct EMBL-EBI." "was sourced from Complex Portal, curated by EMBL-EBI."
• [ ] Update gene groups curation doc to reflect this

[hattrill]

All 94 Complex Portal dbxref links have been updated to this format: Fly XXXX complex XXXX (Complex Portal) via tsv fix

[hattrill]

Fix this accession via tsv:

• [x] *O ComplexPortal:CPX-2695., Fly Glycosylphosphatidylinositol ethanolamine-phosphate transferase III complex (Complex Portal)

[hattrill]

Removed Arf from COPI complex group based on email from Sandra: "Hi Helen

In the Drosophila COPI-I complex, we have included an Arf molecule as part of the assembly. I've just realised I had not included the equivalent Arf molecule as part of yeast. I'm just creating the human complex and reading a paper on the mouse EM structure, and it would seem the Arf joins the complex after initial assembly, in fact its the recruiting factor from the membrane rather than part of the coat structure

https://europepmc.org/article/MED/35101600

"Coat protein complex I (COPI-coated vesicles) mediate the retrieval of proteins from the cis-Golgi to the ER. Analogous to the Sar1 mechanism in recruiting COPII, Arf1-GTP functions to recruit COPI to the Golgi membrane. However, unlike COPII, Arf1-GTP recruits the COPI proteins to the membrane as an en-bloc heteroheptameric complex, known as coatomer. COPI coatomer is composed of two interconnected subcomplexes, i) a trimer that is composed of ε (Sec28), α (Ret1), and β’ (Sec27) subunits and ii) a tetramer that is composed of β (Sec26), γ (Sec21), δ (Ret2) and ζ (Ret3)."

I'd therefore like to remove the Arf from the Drosophila complex to keep consistency across species - does that cause you any problems?

Sandra"

[hattrill]

• [x] update of new xrefs to cp:

https://docs.google.com/spreadsheets/d/1N-X2Va-nlZBWXiGF1X4pi9frLeQsF6HebAIOQg9iQLc/edit#gid=372819431

[hattrill]

• [ ] Cuarte FBrf0241907 for NSl complex, also review question of Rcd5 - is it part of Ino80 complex?