Data release notes
The GlyGen datasets collection is updataed every 2 weeks.
Version 1.8.22
Main article: Data release notes/1.8.22
This version was released at April 1st, 2021
- F protein (P0C045-1) was removed from Hepatitis C virus (genotype 1a, isolate H) proteome
- Hepatitis C Virus (genotype 1a, isolate H) Tax ID changed from 11108 to 63746.
- NCBI GeneID and Refseq datasets for SARS-CoV2 created
- Accession history files created for tracking protein and glycan accessions
- Mouse and rat disease datasets created to add disease data in the disease section
- Data entries for O-GlcNAc data now point to The O-GlcNAc resource instead of the dataset.
- human_proteoform_glycosylation_sites_o_glcnac_mcw updated with new O-GlcNAc data
- n-sequon and n-sequon type fields added to the glycosylation datasets for data validation
- Removed predicted glycosylation data from the UniProtKB data when reported glycosylation data is present for the same data entry.
- Update to the Glycomotif alignment logic, motif keyword, publications
- Update to the GlyConnect data, Automatic Literature Data, Disease data from Genomics England
- Update to the GlyTouCan to ChEBI mapping method.
- Addition of new glycan type and subtypes
- Integration of GlycoTree alignment infrastructure
- addition of semantic names from GlycoMotif
- Addition of ~1800 new GlyTouCan accessions
- Addition of new sections in glycan detail pages:
- subsumption(related glycans through GNOme)
- expression(glycans expressed in cell-line/Tissue)
- History (release no. where the glycan was introduced in GlyGen)
- Addition of glycan keywords (Motif Group), Synonyms, Reducing End information to the Motif detail page.
- Addition of citations from NCFG data for Asparagine-linked glycans
- Addition of GNOme and SandBox references
- Addition of Disease data from Glycosmos
- Addition of evidence to the "Biosynthetic Enzyme" section on the glycan detail page.
- Addition of Rhea and Reactome cross-references to glycan detail pages
- Addition of GlyGen links in ChEBI and GlyTouCan databases.
Version 1.5.36
Main article: Data release notes/1.5.36
Related API version: 1.5.43
This version was released at July 20th, 2020
- Added O-GlcNAc data extracted from the literature by Stephanie Olivier’s group (GLYDS000518)
- Added germline and somatic variation data that has effect on glycosite (loss of glycosylation site and gain of glycosylation sequon) to the mutation section
- Added the literature extracted glycosite for SARS-CoV1 M protein
- Added glycosylation subtypes to the *_proteoform_glycosylation_sites_uniprotkb.csv
- Added species annotation via subsumption (for human, mouse). Rat and HCV to follow in the next release.
- Added updated GlyConnect data. (additional o-GlcNAc sites)
- Added glycosylation sites through text mining (first iteration).
Version 1.5.18
Main article: Data release notes/1.5.18
Related API version: 1.5.26
This version was released at April 15th, 2020
- Added UniProtKB Gene synonyms (search and details)
- Added RefSeq Gene names and synonyms
- Added RefSeq Protein synonyms
- Added UniProtKB Protein synonyms
- Updated the Fasta headers of the protein sequences that now resembles the fasta header of UniProtKB sequences
- Updated BioMuta data with addition of comments that shows which filters were passed
- Created new datasets:mutation literature mining dataset, dbSNP somatic and germline mutations datasets.
- Added GlyGen to Pharos Xref in the protein detail cross-reference section
- Added HCV 1a and 1b, SARS-CoV1 and 2 proteomes
- Added the MIM disease name where DO names were not available
- Updated glycan species annotations.
- Added Human, Mouse, Rat glycosylation data from GlyConnect.
- Added HCV1a glycosylation data from 1 publication.
- Added human glycosylation data from 2 publications.
- Added glycan x-refs to MatrixDB, GlycoEpitope
- Added MatrixDB Protein-GAGs interaction data. (at GlyGen Data)
- Included GlyTouCan-composition accessions.
- Added protein x-refs to GlycoProtDB
- Retired GlycO and GlycomeDB xrefs .
- Added SNFG glycans (at GlyGen Data)
- Added animated GIF and .mp4 video of 3D model of SARS-CoV-2 spike glycoprotein. (at GlyGen Data)
- Updated the synthesized glycan list from Dr. Boons group.
- Included additional 2 FAQs: How do I find a GlyTouCan Boons accession for my glycan composition? and How can I convert my glycan sequence to different formats (e.g IUPAC, WURCS, GlycoCT, LinearCode, etc.)?
Version 1.0
Main article: Data release notes/1.0
This version was released at Nov 22, 2019
- 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.