{ "bcoid": "GLY_000893", "title": "Pig Glycosylation Sites (GlyConnect) ", "description": "The Pig Glycosylation Sites (GlyConnect) dataset contains Sus scrofa [taxid:9823] UniProtKB canonical ...", "filename_list": "pig_proteoform_glycosylation_sites_glyconnect.csv", "filename": "pig_proteoform_glycosylation_sites_glyconnect.csv", "filetype": "csv", "categories": { "species": [ "Sus scrofa" ], "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" } ], [ "", "", "", "G72548AI", "O-linked", "protein_xref_pubmed", "8799292", "protein_xref_glyconnect", "391", "391", "9823", "Sus scrofa", "1575", "G72548AI", "Undefined core", "O-Linked", "2,2,2,0,0,0,1,0,0,0,0,0,0,0", "H2N2F2s1", "HexNAc(2)Hex(2)dHex(2)Sulfo(1)", "1120.3476", "1121.0403", "Hex:2 HexNAc:2 dHex:2 Su:1", "", "small intestine", "UBERON:0002108", "", "", "", "", "", "", "", "", "", "", "", "" ], [ "", "", "", "G69837XX", "O-linked", "protein_xref_pubmed", "8799292", "protein_xref_glyconnect", "391", "391", "9823", "Sus scrofa", "1579", "G69837XX", "Undefined core", "O-Linked", "0,2,0,0,0,0,1,0,0,0,0,0,0,0", "N2s1", "HexNAc(2)Sulfo(1)", "504.1262", "504.4695", "HexNAc:2 Su:1", "", "small intestine", "UBERON:0002108", "", "", "", "", "", "", "", "", "", "", "", "" ] ] }, "readme": "Name\n - Pig Glycosylation Sites (GlyConnect) \n\nVersion\n - v-2.7.1\n\nCreated on\n - \n\nModified on\n - 2024-05-17T11:24:17.316Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.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 Pig Glycosylation Sites (GlyConnect) dataset contains Sus scrofa [taxid:9823] UniProtKB canonical accessions with information on reported glycans in GlyConnect database (https://glyconnect.expasy.org/; PMID: 30574787). A json file was retrieved through GlyConnect API (https://glyconnect.expasy.org/api/glycosylations?taxonomy=Sus%20scrofa)\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/GLY_000001) 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 latest 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 (pig_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-2.7.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2024_09_05/cellosaurus.txt\n Name: glyconnect_pig.json\n URI: https:/data.glygen.org/ln2downloads/glyconnect/2024_09_05/glyconnect_pig.json\n Output Subdomain\n Name: pig_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/pig_proteoform_glycosylation_sites_glyconnect.csv\n Name: pig_proteoform_glycosylation_sites_glyconnect.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/pig_proteoform_glycosylation_sites_glyconnect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"8\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"6\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"2\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"323\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"2\"\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: \"27\"\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: \"14\"\n Name: \"protein_id\"\n Description: \"ID of the protein\"\n Unique Values: \"14\"\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: \"216\"\n Name: \"structure_glytoucan_id\"\n Description: \"GlyTouCan Ac. Assocaiated with the structure\"\n Unique Values: \"215\"\n Name: \"structure_glycan_core\"\n Description: \"Glycan core associated to glytoucan_ac_struture\"\n Unique Values: \"11\"\n Name: \"structure_glycan_type\"\n Description: \"Glycan type associated to glytoucan_ac_struture\"\n Unique Values: \"2\"\n Name: \"composition_format_numeric\"\n Description: \"glycan composition in a numeric format\"\n Unique Values: \"141\"\n Name: \"composition_format_condensed\"\n Description: \"condensed format of the glycan description\"\n Unique Values: \"141\"\n Name: \"composition_format_byonic\"\n Description: \"byonic format of the glycan description\"\n Unique Values: \"141\"\n Name: \"composition_mass_monoisotopic\"\n Description: \"Monoisotopic mass of the glycan\"\n Unique Values: \"140\"\n Name: \"composition_mass\"\n Description: \"Mass of the glycan\"\n Unique Values: \"140\"\n Name: \"composition_format_glyconnect\"\n Description: \"composition format of the glyconnect\"\n Unique Values: \"141\"\n Name: \"composition_glytoucan_id\"\n Description: \"GlyTouCan Ac. Associated with the glycan composition.\"\n Unique Values: \"117\"\n Name: \"source_tissue_name\"\n Description: \"Tissue NAME from GlyConnect\"\n Unique Values: \"11\"\n Name: \"source_tissue_id\"\n Description: \"Tissue ID from GlyConnect\"\n Unique Values: \"11\"\n Name: \"source_cell_line_cellosaurus_name\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"source_cell_line_cellosaurus_id\"\n Description: \"cellosaurus ID of the cell line\"\n Unique Values: \"2\"\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: \"6\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"6\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"6\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.7.1/reviewed/pig_proteoform_glycosylation_sites_glyconnect.csv" }