Japonicus news items

[ValWood]

Include experiments; structures from pdf news item and advanced search common query if there are any japonicas structures

Include Alpha field news item on the japonicus news feed

[kimrutherford]

I've added an article about AlphaFold (for Thursday morning). I forgot to change the load script to add japonicus PDB IDs to Chado so we can't query for genes with PDB IDs yet. I'll fix that and then add a news item.

[ValWood]

I don't know if there are any structures but I think I remember at least 1

[kimrutherford]

https://www.japonicusdb.org/results/from/id/0c97da98-0210-404b-840e-f98bfb2b5aeb

[kimrutherford]

https://www.japonicusdb.org/results/from/id/0c97da98-0210-404b-840e-f98bfb2b5aeb

There's 5 but because the PDB IDs aren't in japonicus Chado, the structures aren't shown.

[kimrutherford]

There's 5 but because the PDB IDs aren't in japonicus Chado, the structures aren't shown.

They should be visible tomorrow on the pages for: PMID:26343758, PMID:35693892, SJAG_03867, SJAG_04265 and SJAG_03542.

I'll check in the morning.

[kimrutherford]

They should be visible tomorrow on the pages for: PMID:26343758, PMID:35693892, SJAG_03867, SJAG_04265 and SJAG_03542.

I'll check in the morning.

That seemed to work:

• https://www.japonicusdb.org/reference/PMID:26343758
• https://www.japonicusdb.org/gene/SJAG_03867

I'll add a news item.

[kimrutherford]

One publication page that for a publication with a structure is missing due to a configuration problem: https://www.japonicusdb.org/reference/PMID:35693892

I've fixed that for tomorrow's update.

[kimrutherford]

I've added a news item about the PDB structures for japonicus. It will be visible in the morning.

[ValWood]

@snezhkaoliferenko there is also a "commonly used query" i the advanced search that will provide all proteins with pdb structures in case you ever want to find them all. Only 3 right now: https://www.japonicusdb.org/results/from/id/13956cc1-e668-409f-a0ea-ae9c30bf3a60

[snezhkaoliferenko]

thanks!