Portal release notes: Difference between revisions

Revision as of 10:07, 10 September 2025

The GlyGen portal was first released on September 14th, 2018. A new update has been released every three to fifth months.

Version 2.9

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 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.

Version 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

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

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.
Integrated Carbbank data.
Added PRIDE Cross-reference to Protein details page.
Bug fixing.

Version 2.5

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.
New data for Chicken (Gallus gallus) added.
New proteoform and glycomic data from EMBL, University of Zagreb, and PDC added.

Version 2.4

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

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.
Added support for scheduling GlyGen demo from home page.
New datasets for Slime Mold (Dictyostelium discoideum) added (GLY_000823, ...)
Categories for Protein and Glycan Xrefs created
Bug fixing.

Version 2.2

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 data to GlyGen portal.
Added Mastodon widget in the News section of GlyGen portal.
Updated grant information and added CFDE and GSA links on GlyGen portal.
Bug fixing.

Version 2.1

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.
New interface and search functionality on data.glygen.org
Bug fixing.

Version 2.0

This version was released on April 12th, 2023.

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.

Version 1.12

This version was released on April 28th, 2022.

Implemented BLAST.
Implemented structure search.
Implemented substructure search.
Added GlycoGlyph tool support in structure and substructure search.
Added evidence badges to the publication detail page.
Added digital sequence, cross reference and history to the motif detail page.
Added new papers to the how to cite page.
Bug fixing.

Version 1.11

This version was released on December 24th, 2021.

Redesign of the site view page.
Number of proteins on the motif list page.
Searching by glycosylation subtypes.
Additional columns in the site list page.
Filter options for the site list page.
Improved hit score for glycan list, protein list, and site list pages.
Feature of the month video on the home page.
Improved help text (tooltips) for details pages.
Score column added to expression tissue table.
Subsumption table changes on the glycan detail page.
Added link to glycan structure dictionary from motif detail page.
New Glycan Biosynthetic Pathways knowledge base in the Resources page.
Bug fixes.

Version 1.10

This version was released on October 16th, 2021.

Support of composition strings in simple and global search.
Batch search feedback.
Glycan List export into Byonic format.
Sorting option for publications.
Dropdown for Glycan ID namespace in search.
Search result explanation function (Hit score tooltip).
Glycosylation abundance data.
URL passed searches.
Glycan category on global search result for proteins.
Add tolerance to the site search.
Byonic sequence moved to General section.
New Glycowork library tool in the Resources page.
Updated former team members.
Bug fixes.

Version 1.9

This version was released on July 12th, 2021.

Direct search from protein, glycan details page.
Protein sequence highlighter from alignment page.
Text search in protein sequence from protein details and alignment page.
Filter on protein and glycan list page.
Paper Specific Detail page.
Phosphorylation Data in Protein detail, Sequence section, and Protvista.
Glycation data in Protein detail, Sequence section, and Protvista.
Subsumption information on Glycan details page.
Added notes to Glycosylation, Mutagenesis, Phosphorylation, and Glycation.
Added new database "GPTWiki" resource and fixed links on the Resources page.
New presentations on the Media page.
Bug fixing.

Version 1.8

This version was released April 1st, 2021.

GlyGen Mapper (ID mapping).
Event alert.
New resource and license.
Added new tools to the header.
About us and team members' updates.
New posters in media/portfolio.
Animated GlyGen logo.
Supersearch.
Cell line and tissue data.
Tracking of IDs (merged, renamed, deleted).
Scoring of search results.
Pro integration.
Site-specific search page.
Sand Box tool.
Composition search templates.
SNFG symbols next to the monosaccharide name in composition search tooltip.
The back button on the glycan, protein, and motif details page.
Sand Box tool button from the glycan details page.
Bug fixing.

Version 1.7

This version was released October 30th, 2020.

PTM annotations table in protein details.
List of synthesized Glycans to Enzymes (Proteins) table.
List of motifs page.
Gene and protein names.
Subsumption option for species search on Glycan advanced search page.
Subsumption option for glycan ID search on Glycan advanced search page.
Binding Protein search on Glycan advanced search page.
Glycan Binding Protein section on Glycan details page.
Covalently Attached Glycan search on Protein advanced search page.
Bound Glycan search on Protein advanced search page.
Disease Name search on Protein advanced search page.
Disease ID search on Protein advanced search page.
Pubmed ID typeahead support.
Disease section on the protein details page.
Glycan Ligands section on the protein details page.
Mutagenesis table in protein details.
Glycosylation table with four different categories in protein details.
Single Nucleotide Variation table with two different categories in protein details.
Protvista button on multiple tabs of protein details.
Protvista page with Mutagenesis, Single Nucleotide Variation information.
Site view page with Mutagenesis, Single Nucleotide Variation information. Also, a new API connected.

Update to the New Motif list. Replacing GlyTouCan Motif accessions with GlyGen motif list with GlyTouCan Motifs as X-ref's.
Addition of Motif synonyms.
Including glycosylation annotation (Protein+PMID+Glycan) on unreported sites from GlyConnect.
Refined/corrected BioSynthetic enzyme data.
Addition of new Glycan subtypes (o-fucose, o-mannose).
Updated glycan images from GlyTouCan.
New data: Protein+GAGs data from MatrixDB.
Addition of GlyGen x-ref on GlyConnect protein entry pages.
Addition of GlyGen x-ref on PubChem compound and PubChem protein pages.
Addition of new glycans into ChEBI.
Addition of Mutagenesis data from UniProt
Addition of PMIDs for SNV data
GlyGen dataset BCO prefix changed from DSBCO to GLY

Version 1.6

This version was released August 14th, 2020.

React Migration.
Text and style updates.
Four new search cards on the homepage.
New presentation on the Media page.
Our papers on the How to Cite page.
Updated frameworks.
Informational pages are grouped.
GlyGen members updates.
Updated metadata.
New license resources.

Version 1.5

This version was released January 14th, 2020.

Isoform Alignment.
Homolog Alignment.
New Usecase added in the quick search.
Composition Search.
Go ID search.
PMID search.
Batch search on advanced protein and glycan search page.
Multi-select option for amino acids on advanced glycoprotein search.
Multi-select option for organisms on advanced glycan search.
Integrate subsumption browser.

Version 1.4

This version was released September 23rd, 2019.

New "Media" page displays GlyGen presentations, talks, brochures, posters, logos, and templates.
New "Frameworks" page acknowledgment of libraries and frameworks that used to develop GlyGen.
New "How to cite" page displays GlyGen publications and citations.
Sequon data on sequence view.
Site-Specific page.
Protvista sequence viewer.
Search by GO term.
Add search for pMe structures.
Cascaded type ahead.
Compressed file download support.

Version 1.3

This version was released June 10th, 2019.

Added breadcrumbs on list & detail pages.
Display of error generated by ajax failure method even if javascript code breaks.
Global search page is more intuitive now.
Improved new sequence display with more data and badge.
Orthologous info on protein detail pages.
Feedback widget on each dynamic page with contact API.
Gene location publication and RefSeq summary to protein detail.
Breadcrumbs lead to a proper search page (eg. Global search page when you come to a List page from there).
Replaced "No results found" pop-up alert messages with inline alert messages in search pages and quick search.
Added help tooltip next to each label in search pages.
Added progress bar to the feedback page.
Added map image for mobile view in the about us page.
New team members on the About us page.
Multiple bug fixes and text changes.

Version 1.2

This version was released March 29th, 2019.

Changed the 'Found Glycoproteins' section to a table on the glycan detail page.
The map on the about us page is highlighted four countries with a hover tooltip that involved in GlyGen's project.
A new team member added to the about us page.
Added helpful links to find my accession numbers or IDs with hover tooltips under every input field in every search page.
Added a motif detail page which can be accessed by clicking on one of the motif's links in the glycan detail page.
Implementation of global search functionality.
Added links on the disclaimer, privacy_policy pages to GitHub explaining how we tracking user activity.
Updated Evidence display by adding color badge with the data number.
A new "GlyGen Funding" section on the about us page.
The blue border around the selected question in the quick search page indicates that the user came from the home page.

Version 1.1

This version was released December 7th, 2018.

Added summary table for quick search results.
Added protein sequence highlight tool on protein detail pages.
Created simple search, advanced search, and tutorials for glycan, protein, and glycoprotein searches.
Added download button with an option in various formats on List and Detail pages.
Dynamic display of statistics and version info on the homepage.
Created clickable text examples for search pages.
Improved error handling.
Added link to the Beta server to the header.
Several text updates, bug fixes, and improvements.

Version 1.0

This version was released September 14th, 2018.

The initial release of the GlyGen portal.
GlyGen Portal available with three Protein and Glycan and Glycoprotein advanced search pages.
Result of searches is available in Protein and Glycan and Glycoprotein list pages.
Each list page provides details of Protein and Glycan available with one click on accession.

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 == Version 2.9 ==
-{{main|Portal release notes/2.8}}
+{{main|Portal release notes/2.9}}
 * 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.