2.12 Main tasks

[ReneRanzinger]

Domains and Regions

• What is the domain and region data we have from UniProt #3363
• Extract domain data from NT files #3526
• Mockup for Domain data in 2.12 #3531
• Add Domain data to MongoDB #3529
• Add domain data to protein details API #3530
• Add domain data to protein details page #3532
• Add domain data to ProtVista viewer #3533

Antibody

• Check if the uniprot IGG entries are in GlyGen #2004
• Protein of interest: all species #3543

Lectin

• Lectin data for 2.12 #3377
• Display of lectin information #3407
• Download and integrate the UniLectin data #3406
• Add Lectin information to the protein details API #3408
• Add Lectin information to the protein details page #3409

Site by site comparison of 3D files

• Mockup for site by site comparision for 3D files for glycan and protein pages #3656
• Implement 3D site by site comparison page #3657
• Add 3D site by site comparison to details pages #3658

Data for CFDE submission

• XMT files for CFDE #3659
• Generate XMT files for data submission to CFDE #3660
• CFDE asset generation #2725

Metal binding sites

• Mockup for metal binding sites #3557
• Add metal binding sites to the datasets #3661
• Add metal binding sites to the protein details API #3662
• Add metal binding sites to protein details page #3663

AI summary of proteins, glycans and disease

• Explore local LLM for AI summary #3666

GlycoGenius/Veneer library export (Download on list page)

• GlycoGenius/Veneer library export (Download on list page) #3080

VM infrastructure and update

• Separate VM for beta #3097
• TST VM upgrade to new Rocky OS #3668
• Setup UGA backup server #3667

Non-human PDB proteoform datasets

• Update script and create new datasets for rcsb pdb glycosylation sites #3569

XREF page

• Provide latest version of the XREF table #3672
• Review XREF table and generate JSON #3673
• Implement XREF page #3674

iCN3D integegration

• iCN3D project description #2339
• iCN3D preparation #2340
• ICN3D links to frontend #3089
• Add ICN3D links #3088
• Add ICN3D links to frontend #3090

GLYCAM GP 3D structure generation

• Site mapper: Canonical -> PDB #3402
• Glycam glycoprotein dataset – mismatch amino acids #3403

MCP server finalization

• MCP: improve method/tool documentation #3688
• MCP: Select text book knowledge to the with the MCP #3689

GlycoEnzDB XREF

• XREFS to GlycoEnzDB #3391

Glycan modifying enzymes

• New dataset "Glycan modifying enzymes" #3338

GW server update

• TST VM upgrade to new Rocky OS #3668
• Setup new VM for beta #3676
• Setup GlyGen on the new beta VM #3677
• Update production to Rocky OS8 #3678
• IPv4 for beta #3679

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Patching infrastructure - 2.13

• Implement data patching infrastructure #2074

Frontend tool for literature minded data - 2.13

• Frontend tool for Mining data display (Mockup) #2726
• Status of the frontend tool #3665

Protvar integration - 2.13

• Prepare ProtVar data integration #2808
• ProtVar linking #3277
• ProtVar links from tables on details page #3278
• Implement the Protvar integration in the SNV table #3671