{ "bcoid": "GLY_000331", "title": "Rat Glycosylation Sites (GlyConnect) ", "description": "The Rat Glycosylation Sites (GlyConnect) dataset contains rat [taxid:10116] UniProtKB canonical accessions ...", "filename": "rat_proteoform_glycosylation_sites_glyconnect.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Proteoform", "tags": "Glycosylation Sites", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P08289-1...", "..." ], [ "P08289-1...", "..." ] ], "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", 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"6,5,0,0,0,0,0,0,0,0,0,0,0,0", "H6N5", "HexNAc(5)Hex(6)", "2005.7244", "2006.8447", "Hex:6 HexNAc:5", "G20425TQ", "liver", "UBERON:0002107", "", "", "", "", "", "", "", "", "", "", "", "" ], [ "", "", "", "G62531KN", "O-linked", "protein_xref_glyconnect", "63", "protein_xref_glyconnect", "63", "63", "10116", "Rattus norvegicus", "782", "G62531KN", "Undefined core", "O-Linked", "1,2,0,0,0,0,1,0,0,0,0,0,0,0", "H1N2s1", "HexNAc(2)Hex(1)Sulfo(1)", "666.179", "666.6119", "Hex:1 HexNAc:2 Su:1", "", "mammary gland", "UBERON:0001911", "", "", "", "", "", "", "", "", "", "", "", "" ], [ "", "", "", "G62531KN", "O-linked", "protein_xref_pubmed", "6715325", "protein_xref_glyconnect", "63", "63", "10116", "Rattus norvegicus", "782", "G62531KN", "Undefined core", "O-Linked", "1,2,0,0,0,0,1,0,0,0,0,0,0,0", "H1N2s1", "HexNAc(2)Hex(1)Sulfo(1)", "666.179", "666.6119", "Hex:1 HexNAc:2 Su:1", "", "mammary gland", "UBERON:0001911", "", "", "", "", "", "", "", "", "", "", "", "" ] ] }, "readme": "Name\n - Rat Glycosylation Sites (GlyConnect) \n\nVersion\n - v-2.0.3\n\nCreated on\n - 2020-02-10T12:21:08.095461\n\nModified on\n - 2022-09-26T09:05:27.655566\n\nCreated by\n - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@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 Rat Glycosylation Sites (GlyConnect) dataset contains rat [taxid:10116] 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:Rattus Norvegicus). 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 (rat_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: cellline_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/misc/cellline_mapping.csv\n Name: n_sequon_info.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/misc/sample_mapping.csv\n Name: tissue_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/misc/tissue_mapping.csv\n Name: cellosaurus.txt\n URI: /data/shared/glyds/downloads/cellosaurus/2020-09-15/cellosaurus.txt\n Name: glyconnect_rat.json\n URI: /data/shared/glyds/downloads/glyconnect/2022_03_14/glyconnect_rat.json\n Output Subdomain\n Name: rat_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_proteoform_glycosylation_sites_glyconnect.csv\n Name: rat_proteoform_glycosylation_sites_glyconnect.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_proteoform_glycosylation_sites_glyconnect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"19\"\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: \"4\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"377\"\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: \"2\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"89\"\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: \"45\"\n Name: \"protein_id\"\n Description: \"ID of the protein\"\n Unique Values: \"45\"\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: \"274\"\n Name: \"structure_glytoucan_id\"\n Description: \"GlyTouCan Ac. Assocaiated with the structure\"\n Unique Values: \"272\"\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: \"152\"\n Name: \"composition_format_condensed\"\n Description: \"condensed format of the glycan description\"\n Unique Values: \"152\"\n Name: \"composition_format_byonic\"\n Description: \"byonic format of the glycan description\"\n Unique Values: \"152\"\n Name: \"composition_mass_monoisotopic\"\n Description: \"Monoisotopic mass of the glycan\"\n Unique Values: \"151\"\n Name: \"composition_mass\"\n Description: \"Mass of the glycan\"\n Unique Values: \"151\"\n Name: \"composition_format_glyconnect\"\n Description: \"composition format of the glyconnect\"\n Unique Values: \"152\"\n Name: \"composition_glytoucan_id\"\n Description: \"GlyTouCan Ac. Associated with the glycan composition.\"\n Unique Values: \"107\"\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: \"9\"\n Name: \"source_cell_line_cellosaurus_id\"\n Description: \"cellosaurus ID of the cell line\"\n Unique Values: \"9\"\n Name: \"source_cell_component_id\"\n Description: \"Cell component IF from GlyConnect\"\n Unique Values: \"7\"\n Name: \"source_cell_component_go_id\"\n Description: \"Cell component GO ID from GlyConnect\"\n Unique Values: \"7\"\n Name: \"source_cell_component_name\"\n Description: \"Cell Component name from GlyConnect\"\n Unique Values: \"7\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"2\"\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: \"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-2.0.3/reviewed/rat_proteoform_glycosylation_sites_glyconnect.csv" }