{ "bcoid": "GLY_001100", "title": "Arabidopsis Glycosylation Sites (GlyConnect) ", "description": "The Arabidopsis Glycosylation Sites (GlyConnect) dataset contains Arabidopsis thaliana [taxid:3702] UniProtKB ...", "filename_list": "arabidopsis_proteoform_glycosylation_sites_glyconnect.csv", "filename": "arabidopsis_proteoform_glycosylation_sites_glyconnect.csv", "filetype": "csv", "categories": { "species": [ "Arabidopsis thaliana" ], "molecule": [ "Proteoform" ], "tag": [ "Glycosylation Sites" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "...", "..." ], [ "...", "..." ] ], "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" } ], [ "", "", "", "G25409XH", "N-linked", "protein_xref_pubmed", "9952469", "protein_xref_glyconnect", "858", "858", "3702", "Arabidopsis thaliana", "1056", "G25409XH", "Pauci-Mannose", "N-Linked", "4,2,0,0,0,1,0,0,0,0,0,0,0,0", "H4N2P1", "HexNAc(2)Hex(4)Pent(1)", "1204.4229", "1205.091", "Hex:4 HexNAc:2 Pent:1", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "" ], [ "", "", "", "G06110VR", "N-linked", "protein_xref_pubmed", "9952469", "protein_xref_glyconnect", "858", "858", "3702", "Arabidopsis thaliana", "1443", "G55220VL", "High-Mannose", "N-Linked", "5,2,0,0,0,0,0,0,0,0,0,0,0,0", "H5N2", "HexNAc(2)Hex(5)", "1234.4334", "1235.1173", "Hex:5 HexNAc:2", "G06110VR", "", "", "", "", "", "", "", "", "", "", "", "", "", "" ] ] }, "readme": "Name\n - Arabidopsis Glycosylation Sites (GlyConnect) \n\nVersion\n - v-2.8.1\n\nCreated on\n - 2020-02-10T10:16:50.152756\n\nModified on\n - 2024-07-23T14:22:11.963Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@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], Julien Mariethoz [julien.mariethoz@sib.swiss]\n\nChecksum\n - \n\nUsability Domain\n - The Arabidopsis Glycosylation Sites (GlyConnect) dataset contains Arabidopsis thaliana [taxid:3702] 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/docs/index.html?url=/api/assets/swagger.json#/Glycosylation/listGlycosylationsAsJson) (Query: taxonomy: Arabidopsis thaliana). If you use this dataset please provide proper attribution to GlyConnect and GlyGen.\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 protein list (https://data.glygen.org/GLYDS000001) 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 2019-09 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. All the flagged entries are added in the log file (arabidopsis_proteoform_glycosylation_sites_glyconnect.1.log)\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-proteoform-dataset.py\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-2.8.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2025_01_13/cellosaurus.txt\n Name: glyconnect_arabidopsis.json\n URI: https:/data.glygen.org/ln2downloads/glyconnect/2025_01_14/glyconnect_arabidopsis.json\n Output Subdomain\n Name: arabidopsis_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/arabidopsis_proteoform_glycosylation_sites_glyconnect.csv\n Name: arabidopsis_proteoform_glycosylation_sites_glyconnect.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/arabidopsis_proteoform_glycosylation_sites_glyconnect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"1\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"1\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"21\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"1\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"1\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"2\"\n Name: \"protein_id\"\n Description: \"ID of the protein\"\n Unique Values: \"2\"\n Name: \"taxonomy_taxonomy_id\"\n Description: \"Taxonomy ID associated with species name \"\n Unique Values: \"1\"\n Name: \"taxonomy_species\"\n Description: \"Taxonomy species name\"\n Unique Values: \"1\"\n Name: \"structure_id\"\n Description: \"Structure ID\"\n Unique Values: \"16\"\n Name: \"structure_glytoucan_id\"\n Description: \"GlyTouCan Ac. Assocaiated with the structure\"\n Unique Values: \"16\"\n Name: \"structure_glycan_core\"\n Description: \"Glycan core associated to glytoucan_ac_struture\"\n Unique Values: \"3\"\n Name: \"structure_glycan_type\"\n Description: \"Glycan type associated to glytoucan_ac_struture\"\n Unique Values: \"1\"\n Name: \"composition_format_numeric\"\n Description: \"glycan composition in a numeric format\"\n Unique Values: \"14\"\n Name: \"composition_format_condensed\"\n Description: \"condensed format of the glycan description\"\n Unique Values: \"14\"\n Name: \"composition_format_byonic\"\n Description: \"byonic format of the glycan description\"\n Unique Values: \"14\"\n Name: \"composition_mass_monoisotopic\"\n Description: \"Monoisotopic mass of the glycan\"\n Unique Values: \"14\"\n Name: \"composition_mass\"\n Description: \"Mass of the glycan\"\n Unique Values: \"14\"\n Name: \"composition_format_glyconnect\"\n Description: \"composition format of the glyconnect\"\n Unique Values: \"14\"\n Name: \"composition_glytoucan_id\"\n Description: \"GlyTouCan Ac. Associated with the glycan composition.\"\n Unique Values: \"6\"\n Name: \"source_tissue_name\"\n Description: \"Tissue NAME from GlyConnect\"\n Unique Values: \"1\"\n Name: \"source_tissue_id\"\n Description: \"Tissue ID from GlyConnect\"\n Unique Values: \"1\"\n Name: \"source_cell_line_cellosaurus_name\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"source_cell_line_cellosaurus_id\"\n Description: \"cellosaurus ID of the cell line\"\n Unique Values: \"1\"\n Name: \"source_cell_component_id\"\n Description: \"Cell component IF from GlyConnect\"\n Unique Values: \"1\"\n Name: \"source_cell_component_go_id\"\n Description: \"Cell component GO ID from GlyConnect\"\n Unique Values: \"1\"\n Name: \"source_cell_component_name\"\n Description: \"Cell Component name from GlyConnect\"\n Unique Values: \"1\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"1\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"1\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.8.1/reviewed/arabidopsis_proteoform_glycosylation_sites_glyconnect.csv" }