Release notes

Version 2.9

Main article: Portal release notes/2.9

Main article: Data release notes/2.9.1

Main article: API release notes/2.9

This version was released on September 1st, 2025.

• Added the Disease Search tool to enable users to search for diseases based on their IDs and name, and discover their association with glycans, proteins and biomarkers.
• Added functionality to download Disease details and list page data.
• Added Batch Retrieval tool to enrich proteins/genes tables with additional information from GlyGen and annotate them.
• Added functionality to download Batch Retrieval data.
• Updated Super search graph. Added link from Disease node to Glycan node.
• Added condition information to biomarker table on Protein, Glycan and Publication details pages.
• Added Cross reference section on Biomarker details pages.
• Added RCSB PDB human glycan and glycosylation site data and cross-references.
• Added IEDB cross-references to protein pages.
• Added glycan tissue data from GlycomeAtlas.  
• Reincorporated updated GlycoProtDB data.  
• Improved the usability of the "Add to Cart" tool.
• Improvements to Global and simple search performance.

Version 2.8

Main article: Portal release notes/2.8

Main article: Data release notes/2.8.1

Main article: API release notes/2.8

This version was released on May 5th, 2025.

• Implemented job status page to list structure search, sub-structure search, isoform mapper and blast jobs.
• Implemented cart for storing glycan, protein, glycan list and protein list ids.
• Updated Glycosylation Evidence Type options on protein advanced search page.
• Implemented GlyGen notify option for the user to report job, cart issues.
• Added support for Hamster and Zebrafish across Glycan, Protein, Quick Search, Publication Details, and Search pages.
• Added TableMaker glycomics data.
• Added GlyCosmos glycoproteomics data.
• Updated IsoGlyp predictions for existing GlyGen species and introduced predictions for Hamster and Zebrafish.
• Added Alliance Genome Resource (AGR) ortholog data and cross-references to protein pages.
• Updated xref badges for protein and glycan accessions to link to BiomarkerKB.
• Added additional glycosylation site data through automatic literature mining with GlycoSiteMiner for yeast, pig, SARS-CoV2, chicken, and fruit fly.

Version 2.7

Main article: Portal release notes/2.7

Main article: Data release notes/2.7.1

This version was released on December 13th, 2024.

• Implemented full screen version of details page tables.
• Implemented filters for glycosylation tables on Protein details page.
• Implemented of dynamic list columns feature for Glycan, Protein and Site list pages.
• Enhanced Download option on Glycan, Protein and Site list pages to support dynamic columns, column reorder.
• Enhanced Download option to support filters for glycosylation tables on Protein details page.
• Text mining algorithm support in Protein glycosylation text mining table.
• Added support for Bovine on glycan, protein, quick search, publication details and search pages.
• Introduced filtering options for glycan, protein, and site data to support customized data exploration.
• Bug fixing.

Version 2.6

Main article: Portal release notes/2.6

Main article: Data release notes/2.6

This version was released on August 30th, 2024.

• Implemented 3D structure display of Alphafold and PDB structures on Protein details page.
• Added 3D file download support for glycan and protein pdb files.
• Implemented support for highlighting consensus sequences on protein sequences viewer.
• Implemented GlyGen Isoform Mapper functionality.
• Modified Sequence Viewer to display protein sequence in a user-friendly manner.
• Added support for Arabidopsis on Glycan, Protein, Quick Search, Publication details and search pages.
• Added reducing end monosaccharides to GlyTouCan structures.
• Updated xref badges for user-submitted data.
• Carbbank data.
• Added PRIDE Cross-reference to Protein details page.
• Bug fixing.

Version 2.5

Main article: Portal release notes/2.5

Main article: Data release notes/2.5.1

This version was released on June 1st, 2024.

• Implemented Biomarker search, list and details pages.
• Added support for Chicken on Glycan, Protein, Quick search, Publication details and search pages.
• Biomarker table download supported from Protein, Glycan, Publication and Motif details pages.
• Implemented direct search from Motif list and Glycan list pages.
• Bug fixing.

Version 2.4

Main article: Portal release notes/2.4

Main article: Data release notes/2.4.1

This version was released on April 1st, 2024.

• Implemented new Organism display on Glycan, Publication details page.
• Added support for Pig on Glycan, Protein, Quick search and details pages.
• Added support for isoforms on blast search and blast result page.
• Bug fixing.

Version 2.3

Main article: Portal release notes/2.3

Main article: Data release notes/2.3.1

This version was released on January 22nd, 2024.

• Implemented Glycan Highlighting Widget for Glycan details page.
• Implemented motif highlighting on Motif details page.
• Implemented outreach page.
• ProtVista page improvements.
• Categorized databases on Cross Reference section of Protein and Glycan details pages.
• Added support for scheduling GlyGen demo from home page.

• Bug fixing.
• New datasets for Slime Mold (Dictyostelium discoideum) added (GLY_000823, ...).
• Glycan, Protein and Proteoform datasets updated for the current organisms in GlyGen.
• Added new records from literature mining of 30k publications (GLY_000481, GLY_000492).
• New supporting JSON files for glymagesvg semantic highlighting (GLY_000821).
• New datasets on disease information for Yeast and Fruitfly from Alliance of Genome Resources added.

Version 2.2

Main article: Portal release notes/2.2

Main article: Data release notes/2.2.1

This version was released on October 2nd, 2023.

• Implemented server side pagination for tables in protein, glycan and publication details pages.
• Added biomarker data to the GlyGen portal.
• Added Yeast (Saccharomyces cerevisiae) data to GlyGen portal and datasets to data.glygen.org.
• Changed organism names to match with NCBI Taxonomy names on GlyGen and GlyGen Data portal. (Sars coronavirus (sars-cov-1) to Severe acute respiratory syndrome-related coronavirus, Sars coronavirus (sars-cov-2 or 2019-ncov) to Severe acute respiratory syndrome coronavirus 2, Hepatitis c virus (genotype 1a, isolate h) to Hepatitis c virus (isolate h) and Hepatitis c virus (genotype 1b, isolate japanese) to Hepatitis c virus (isolate japanese).
• Added ViralGlycome Cross-reference for SARS-CoV2 to protein details page.
• Added CFDE submitted datasets and EuropePMC Linkout datasets.
• Added Mastodon widget in the News section of GlyGen portal.
• Updated grant information and added CFDE and GSA links on GlyGen portal.
• Updated Glycan, Protein and Proteoform datasets.
• Updated Biomarker datasets.
• Datasets for CFDE (submitted) and EuropePMC linkouts created and added to data.glygen.org.
• Added new disease, tissue and cell line expression records to glycan details page.
• Glycan abundance data added to publication details page.
• New GlycoCT{xml} dataset added to data.glygen.org (GLY_000817).
• Addition of Yeast, Dictyostelium and Pig glycan species annotations.
• Bug fixing.

Version 2.1

Main article: Portal release notes/2.1

Main article: Data release notes/2.1.1

This version was released on July 3rd, 2023.

• Download icon for tabular data section (all pages).
• Send filter as part of download request on list pages.
• Download API changes on list and details pages.
• Change Opacity, Size of carbohydrates in 3d glycan structures.
• "Please wait" icon for all downloads.
• Integrate Nathans Sandbox links into frontend.
• Update Raja's Photo in About page.
• 3D structures not visible on beta.
• Updated Glycan, Protein and Proteoform datasets.
• Removal of SNV/mutation entries from COSMIC resource from the human_protein_mutation_cancer.csv dataset [GLY_000024].
• Updated SPARQL endpoint with newer data.
• New interface and search functionality on data.glygen.org.
• Bug fixing.

Version 2.0

Main article: Portal release notes/2.0

Main article: Data release notes/2.0.3

This version was released on April 12th, 2023.

• Protein and Glycan datasets updated with new release data
• O-GlcNAc data added from O-GlcNAc atlas (GLY_000708, GLY_000709, GLY_000710, GLY_000711).
• O-Glucosylation data added from the dataset shared from the lab of Robert S Haltiwanger by Daniel Williamson (author) (GLY_000716).
• Glyconnect cross-references datasets created and added to the GlyGen Mapper tool.
• Glycan Structure Dictionary dataset updated GLY_000557.
• SNV/ cancer mutation data from OncoMX was updated. The new data is as per genome assembly reference GRCh38.
• Names of few citations files changed. Missing citations files were created.
• Addition of new monosaccharides.
• Addition of biomarker data to data.glygen.org (Glycan - GLY_000737 | Protein - GLY_000625)
• Migration to recent React Framework.
• 3D structure viewer for Glycans.
• N-Glycan Gnome Browser integration.
• Update About us page.
• Update menu structure.
• BLAST Improvements.
• BLAST and GSD on Homepage.
• Accession history error messages.
• Bug fixing.