{ "bcoid": "GLY_000330", "title": "Mouse Glycosylation Sites (GlyConnect) ", "description": "The Mouse Glycosylation Sites (GlyConnect) dataset contains mouse [taxid:10090] UniProtKB canonical accessions ...", "filename": "mouse_proteoform_glycosylation_sites_glyconnect.csv", "filetype": "csv", "categories": { "species": [ "Mus musculus" ], "molecule": [ "Proteoform" ], "tags": [ "Glycosylation Sites" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P14220-1...", "..." ], [ "P14220-1...", "..." ] ], "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" 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"HexNAc(2)Hex(3)dHex(2)", "1202.4436", "1203.1185", "Hex:3 HexNAc:2 dHex:2", "G64162JC", "", "", "BTI-Tn-5B1-4", "CVCL_C190", "", "", "", "", "", "", "", "", "", "" ] ] }, "readme": "Name\n - Mouse Glycosylation Sites (GlyConnect) \n\nVersion\n - v-2.1.1\n\nCreated on\n - 2020-02-10T12:16:18.548585\n\nModified on\n - 2022-09-26T09:05:27.645592\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]\n\nAuthors\n - Frederique Lisacek [frederique.lisacek@sib.swiss], Julien Mariethoz [julien.mariethoz@sib.swiss]\n\nChecksum\n - \n\nUsability Domain\n - The Mouse Glycosylation Sites (GlyConnect) dataset contains mouse [taxid:10090] 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:Mus musculus). 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 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 glycosylation 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 ambiguous (c-Linked/o-linked) and/or 5) if the saccharide (GlyTouCan) is not present in the GlyGen glycan master list. All the flagged entries are added in the log file (mouse_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-2.1.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: /data/shared/glyds/downloads/cellosaurus/2023-03-21/cellosaurus.txt\n Name: glycosylations?taxonomy=Mus musculus\n URI: /data/shared/glyds/downloads/glyconnect/2023_05_18/glycosylations?taxonomy=Mus musculus\n Output Subdomain\n Name: mouse_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/mouse_proteoform_glycosylation_sites_glyconnect.csv\n Name: mouse_proteoform_glycosylation_sites_glyconnect.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/mouse_proteoform_glycosylation_sites_glyconnect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"740\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"821\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"4\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"461\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"3\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"3\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"933\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"2\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"896\"\n Name: \"protein_id\"\n Description: \"ID of the protein\"\n Unique Values: \"778\"\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: \"457\"\n Name: \"structure_glytoucan_id\"\n Description: \"GlyTouCan Ac. Assocaiated with the structure\"\n Unique Values: \"258\"\n Name: \"structure_glycan_core\"\n Description: \"Glycan core associated to glytoucan_ac_struture\"\n Unique Values: \"15\"\n Name: \"structure_glycan_type\"\n Description: \"Glycan type associated to glytoucan_ac_struture\"\n Unique Values: \"3\"\n Name: \"composition_format_numeric\"\n Description: \"glycan composition in a numeric format\"\n Unique Values: \"231\"\n Name: \"composition_format_condensed\"\n Description: \"condensed format of the glycan description\"\n Unique Values: \"231\"\n Name: \"composition_format_byonic\"\n Description: \"byonic format of the glycan description\"\n Unique Values: \"231\"\n Name: \"composition_mass_monoisotopic\"\n Description: \"Monoisotopic mass of the glycan\"\n Unique Values: \"226\"\n Name: \"composition_mass\"\n Description: \"Mass of the glycan\"\n Unique Values: \"226\"\n Name: \"composition_format_glyconnect\"\n Description: \"composition format of the glyconnect\"\n Unique Values: \"231\"\n Name: \"composition_glytoucan_id\"\n Description: \"GlyTouCan Ac. Associated with the glycan composition.\"\n Unique Values: \"206\"\n Name: \"source_tissue_name\"\n Description: \"Tissue NAME from GlyConnect\"\n Unique Values: \"22\"\n Name: \"source_tissue_id\"\n Description: \"Tissue ID from GlyConnect\"\n Unique Values: \"22\"\n Name: \"source_cell_line_cellosaurus_name\"\n Description: \"\"\n Unique Values: \"24\"\n Name: \"source_cell_line_cellosaurus_id\"\n Description: \"cellosaurus ID of the cell line\"\n Unique Values: \"24\"\n Name: \"source_cell_component_id\"\n Description: \"Cell component IF from GlyConnect\"\n Unique Values: \"3\"\n Name: \"source_cell_component_go_id\"\n Description: \"Cell component GO ID from GlyConnect\"\n Unique Values: \"3\"\n Name: \"source_cell_component_name\"\n Description: \"Cell Component name from GlyConnect\"\n Unique Values: \"3\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"41\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"821\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"821\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"4\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/mouse_proteoform_glycosylation_sites_glyconnect.csv" }