GlyGen-GlycanData-Export-v1.11.1

Minor update release:

• A few new species/taxa annotations for fruitfly.
• No additional accessions or other annotation changes

GlyGen-GlycanData-Export-v1.11.0

• Glycans: 901 insertions, 34657 entries.
• classification.tsv: New type "GAG", new subtype "Keratan sulfate". O-glycan subtypes "O-GlcNAc", "O-mannose", "O-fucose" lose "O-linked" prefix.
• species.tsv, species_expanded.tsv: SARS1 taxonomy id for SARS species, GlyCosmos taxonomy id attribution
• allmotifs.tsv: Fix definition of motif GGM.000119
• glycam_iupac sequences corrected
• Images: 874 new images added, 33843 in total.

GlyGen-GlycanData-Export-v1.10.0

• Glycans: 223 insertions, 33755 entries.
• New files: hasmono.tsv, monocounts.tsv, redendmono.tsv for IUPAC symbol based monosaccharide presence, counts, and reducing end
• subsumption.tsv: Subsumption (GNOme) tweak to missing characterization score values, addition of Leaf predicate
• classification.tsv: New type "GPI anchor", new O-glycan subtype "O-GlcNAc"
• allmotifs.tsv: Glycan Dictionary cross references now included
• Removal of glycotree_svg.zip, glycotree_gct.zip
• New files glycotree_nlinked_gct.zip and glycotree_olinked_gct.zip (N-linked and O-linked GlycoCT files for GlycoTree consumption)
• Corrected GlycoWorkbench sequences (gwb.tsv, gwb.zip)
• Update to images based on GlycanBuilder2 (Oct 13, 2021), 1.13.0
• monocomp.tsv: Monosaccharide counts now reflect repeating glycan structures (+ symbol after integer count)
• Repeating glycan structures now get motif alignments and glycan classifications

GlyGen-GlycanData-Export-v1.9.0

• Glycans: 181 insertions(+), 168 deletions(-): 33728 entries.
• Motif alignments: remove Polysialic Acid alignments (and retired glycan alignments)
• Motifs: Polysialic acid removed (to be re-added later).
• Classification: New N-glycan subtypes: arm fucosylated, alditol-reduced; Match to superclass N-glycan core; relaxation of definition of high-mannose
• Glycam-IUPAC Sequences: Patch at reducing end for compatibility with GLYCAM.
• Glyconnect XRef, Taxa, Species: GlyConnectStructure or GlyConnectComposition designation
• GlycoTree Enzyme files: removed, obtain from the sandbox repository
• GlyGen retired: 47 new entries
• Images: New image generation infrastructure (visual updates), 99% (png), 97%(svg) of accessions, drop CFG images.
• Addition of GlyCosmos cross references
• Remove fully determined annotation and zipfile of Fully Determined GlycoCT sequences. Use Missing Score 0 from subsumption instead.
• FruitFly species annotations added
• MonosaccharideDB removed from GlycanData (not exported)
• Addition of GlycoWorkBench sequence format, TSV file and zip file as with other sequences.
• IUPAC sequences derived from GlyCosmos, not GlyTouCan
• PDB, GlycomeDB, CFG, Carbbank, GLYCOSCIENCES.de CrossRefs missing from GlyTouCan drawn from GlyGen-GlycanData-Export-v1.8.0 export files.
• GlyTouCan missing Taxa annotations drawn from GlyGen-GlycanData-Export-v1.8.0 export files.

GlyGen-GlycanData-Export-v1.8.0

• Correctly handle GlyTouCan retired (replaced) accessions where possible.
• New motif alignment logic from glycomotif (New format: allmotifaligns.tsv)
• Additional annotations for motifs from glycomotif (New fields: allmotifs.tsv)
• New glycan type/subtype annotations and format, multiple types/subtypes per accession, subtype name now includes type. (New format: classification.tsv)
• enz.tsv file removed, use glycotree_* files from GlycoTree integration instead.
• New file: glycotree.tsv - GlyTouCan accessions annotated by GlycoTree with enzyme genes.
• New file: glycotree_sandbox_accessions.tsv - GlyTouCan accessions supported by the GlycoTree sandbox display widget.
• New file: glycotree_annotated_glycans.tsv - Glycan annotation with enzymes from GlycoTree (same format as GlycoTree CSV file, except TSV).
• New file: glycotree_gct.zip, glycotree_svg.zip - input files for GlycoTree alignment.
• New file: glygen_retired_accessions.tsv (used to be .txt, GlyGen accessions no longer considered valid).
• New file: gnome.tsv - GlyTouCan accessions supported by the GNOme display widget.
• SNFG extended PNG images now spans to a third file-segment: images-snfg-extended-png.tbz.{00,01,02}
• IUPAC sequences with commas to indicate undetermined topology are now omitted, GlyTouCan IUPAC sequences with inconsistent format corrected (Thanks: Sriram Neelamegham)
• Addition of X "floating" substituent column to monoaccharide composition file (New format: monocomp.tsv)
• Addition of Semantic Names for glycans from glycomotif "Whole Glycan" alignments (names.tsv)
• Additional relationships to subsumption.tsv: explicit Topology, Composition, BaseComposition relationships and explicit Level (these could be inferred from glycan_properties.tsv file, but are more explicit here); MissingScore; and FullyDetermined - accessions with MissingScore 0 in Descendents.
• 1788 new accessions, one removal.

GlyGen-GlycanData-Export-v1.7.0

• New glycomotif set with new accession format, multiple names, and aglycon information
• New species export file
• Byonic format Human N-Linked glycan compositions file (Byonic glycan database)
• New GlyConnect glycan resource loads directly to GlycanData
• GlyGen datasets as taxonomy annotation source

GlyGen-GlycanData-Export-v1.6.1

Addition of a four newly registered glytoucan accessions.

GlyGen-GlycanData-Export-v1.6.0

• Continue to improve the fully_defined definition set
• Revamp taxonomy annotation infrastructure to support ad-hoc taxonomy annotations with source ids from a variety of sources (GlyConnect, GlyGen, GPTwiki, etc.)
• Revamp of species annotation script to be more flexible for the addition of new species. Fix bug in HCV, addition of SARS.
• Heuristic elimination of false positive O-glycan subtypes where two-arm motifs don't match.
• Initial attempt at Byonic database extraction based on GlycanData annotations (species, classification, subsumption).
• More semantic names, especially for sulphate and phosphate glycans, and better handing of edge-cases. Registration of all GlycanData implied composition strings.
• Removal, cleanup of all non-canonical UniCarbKB composition identifiers

GlyGen-GlycanData-Export-v1.5.0

• Fix bug in fully_defined definition, broaden definition to tolerate missing reducing end anomer and/or ring
• Export subsumption relationships, including Ancestor and Descendant
• New image dump, including SVG and PNG files, CFG and SNFG formats. (concatenate chunks for tar/bzip2)
• Change in the file format for images.tsv to indicate file size, format, and type.
• Fix bug in annotation of PubChem associations, update to latest associations from PubChem
• Update evidence statement for species annotations for Xyl containing glycans
• Substantial increase in GlyTouCan registered MS-style composition glycan descriptions, with accompanying semantic names in names export file.
• Special-purpose scripts to dump the RDF triples directly from the file-system cache and export specific tables where the SPARQL queries took too long to run.
• RDF triples of GlycanData release provided as export file.
• Tweak UniCarbKB SPARQL queries to get better coverage of annotated UniCarbKB glycans

GlyGen-GlycanData-Export-v1.4.0

• New export files: GlycoEpitope and MatrixDB cross references, "semantic" composition names (Byonic, UniCarbKB)
• Additional glytoucan accessions (about 400).
• Taxonomy annotations updated due to change in source databases
• Improved support for substituent in link glycans
• Updated GNOme subsumption relationships