{ "bcoid": "GLY_000822", "title": "Dictyostelium Glycosylation Sites (GlyConnect)", "description": "The Dictyostelium Glycosylation Sites (GlyConnect) dataset contains dictyostelium [taxid:44689] UniProtKB ...", "filename_list": "dicty_proteoform_glycosylation_sites_glyconnect.csv", "filename": "dicty_proteoform_glycosylation_sites_glyconnect.csv", "filetype": "csv", "categories": { "molecule": [ "Proteoform" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ], "file_category": [ "glycosylation_sites_" ] }, "minitable": { "content": [ [ "P14328-1...", "..." ], [ "P52285-1...", "..." ] ], "headers": [ "uniprotkb_ca...", "glycosylatio..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glycosylation_site_uniprotkb" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "saccharide" }, { "type": "string", "label": "glycosylation_type" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" }, { "type": "string", "label": "protein_id" }, { "type": "string", "label": "taxonomy_taxonomy_id" }, { "type": "string", "label": "taxonomy_species" }, { "type": "string", "label": "structure_id" }, { "type": "string", "label": "structure_glytoucan_id" }, { "type": "string", "label": "structure_glycan_core" }, { "type": "string", "label": "structure_glycan_type" }, { "type": "string", "label": "composition_format_numeric" }, { "type": "string", "label": "composition_format_condensed" }, { "type": "string", "label": "composition_format_byonic" }, { "type": "string", "label": "composition_mass_monoisotopic" }, { "type": "string", "label": "composition_mass" }, { "type": "string", "label": "composition_format_glyconnect" }, { "type": "string", "label": "composition_glytoucan_id" }, { "type": "string", "label": "source_tissue_name" }, { "type": "string", "label": "source_tissue_id" }, { "type": "string", "label": "source_cell_line_cellosaurus_name" }, { "type": "string", "label": "source_cell_line_cellosaurus_id" }, { "type": "string", "label": "source_cell_component_id" }, { "type": "string", "label": "source_cell_component_go_id" }, { "type": "string", "label": "source_cell_component_name" }, { "type": "string", "label": "n_sequon" }, { "type": "string", "label": "n_sequon_type" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "start_aa" }, { "type": "string", "label": "end_aa" }, { "type": "string", "label": "site_seq" }, { "type": "string", "label": "isoform_mapping_notes" } ], [ "P14328-1", "", "", "G96881BQ", "O-linked", "protein_xref_pubmed", "10766852", "protein_xref_glyconnect", "578", "578", "44689", "Dictyostelium discoideum", "1898", "G96881BQ", "O-Fuc", "O-Linked", "0,0,1,0,0,0,0,0,0,0,0,0,0,0", "F1", "dHex(1)", "164.0685", "164.1583", "dHex:1", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "" ], [ "P52285-1", "", "", "G05897GU", "O-linked", "protein_xref_pubmed", "11358877", "protein_xref_glyconnect", "191", "191", "44689", "Dictyostelium discoideum", "81", "G23721DM", "Undefined core", "O-Linked", "3,1,1,0,0,0,0,0,0,0,0,0,0,0", "H3N1F1", "HexNAc(1)Hex(3)dHex(1)", "853.3063", "853.7805", "Hex:3 HexNAc:1 dHex:1", "G05897GU", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "" ] ] }, "readme": "Name\n - Dictyostelium Glycosylation Sites (GlyConnect)\n\nVersion\n - v-2.12.1\n\nCreated on\n - \n\nModified on\n - 2024-05-17T11:24:14.598Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@gwu.edu]\n\nAuthors\n - Frederique Lisacek [frederique.lisacek@sib.swiss]\n\nChecksum\n - \n\nUsability Domain\n - The Dictyostelium Glycosylation Sites (GlyConnect) dataset contains dictyostelium [taxid:44689] UniProtKB canonical accessions with information on reported glycosylation sites in GlyConnect database (https://glyconnect.expasy.org/; PMID: 30574787).A json file was derived through GlyConnect API (https://glyconnect.expasy.org/api/glycosylations?taxonomy=Dictyostelium%20discoideum).\n\nDescription Domain\n Keywords\n - glycosylation\n - reported glycosylation\n\n Pipeline Steps\n - Step-1: The script loads the glycosylation information from the input JSON file and extracts the data. The QC checks filter out: 1) any rows where the UniProtKB accession is not included in the GlyGen dictyostelium protein masterlist and/or 2) if the given glycosylation position and amino acid does not match to the amino acid on the .fasta sequence provided in the UniProtKB release for that protein (however it does pass if the amino acid +glyco-site is empty, as these records correspond to the \\\"not reported\\\" glyco-sites) and/or 3) If the glycosylation type does not associate to the glycostlation based on amino acid (i.e if a N-linked is associated with Ser/Thr residue, etc). 4) If the glyco-site is not reported and the glycosylation type is ambigious (c-Linked/o-linked) and/or 5) if the saccharide (GlyTouCan) is not present in the GlyGen glycan masterlist (https://data.glygen.org/GLY_000281).\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: n_sequon_info.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2026_06_02/cellosaurus.txt\n Name: glyconnect_dicty.json\n URI: https:/data.glygen.org/ln2downloads/glyconnect/2026_05_28/glyconnect_dicty.json\n Output Subdomain\n Name: dicty_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/dicty_proteoform_glycosylation_sites_glyconnect.csv\n Name: dicty_proteoform_glycosylation_sites_glyconnect.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/dicty_proteoform_glycosylation_sites_glyconnect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\"\n Description: \"\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/dicty_proteoform_glycosylation_sites_glyconnect.csv" }