{ "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": [ [ "P48199-1...", "147..." ], [ "P48199-1...", "147..." ] ], "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_id" }, { "type": "string", "label": "source_tissue_name" }, { "type": "string", "label": "source_tissue_uberon_id" }, { "type": "string", "label": "source_cell_line_id" }, { "type": "string", "label": "source_cell_line_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" } ], [ "P48199-1", "147", "Asn", "G84467IZ", "N-Linked", "protein_xref_glyconnect", "114", "protein_xref_glyconnect", "114", "114", "10116", "Rattus norvegicus", "1378", "G84467IZ", "Complex", "N-Linked", "5,4,0,2,0,0,0,0,0,0,0,0,0,0", "H5N4S2", "HexNAc(4)Hex(5)NeuAc(2)", "2222.783", "2224.0231", "Hex:5 HexNAc:4 NeuAc:2", "G48414YA", "", "", "", "", "", "", "", "", "" ], [ "P48199-1", "147", "Asn", "G48414YA", "N-Linked", "protein_xref_glyconnect", "114", "protein_xref_glyconnect", "114", "114", "10116", "Rattus norvegicus", "1378", "G84467IZ", "Complex", "N-Linked", "5,4,0,2,0,0,0,0,0,0,0,0,0,0", "H5N4S2", "HexNAc(4)Hex(5)NeuAc(2)", "2222.783", "2224.0231", "Hex:5 HexNAc:4 NeuAc:2", "G48414YA", "", "", "", "", "", "", "", "", "" ], [ "P48199-1", "147", "Asn", "G84467IZ", "N-Linked", "protein_xref_pubmed", "8486673", "protein_xref_glyconnect", "114", "114", "10116", "Rattus norvegicus", "1378", "G84467IZ", "Complex", "N-Linked", "5,4,0,2,0,0,0,0,0,0,0,0,0,0", "H5N4S2", "HexNAc(4)Hex(5)NeuAc(2)", "2222.783", "2224.0231", "Hex:5 HexNAc:4 NeuAc:2", "G48414YA", "", "", "", "", "", "", "", "", "" ], [ "P48199-1", "147", "Asn", "G48414YA", "N-Linked", "protein_xref_pubmed", "8486673", "protein_xref_glyconnect", "114", "114", "10116", "Rattus norvegicus", "1378", "G84467IZ", "Complex", "N-Linked", "5,4,0,2,0,0,0,0,0,0,0,0,0,0", "H5N4S2", "HexNAc(4)Hex(5)NeuAc(2)", "2222.783", "2224.0231", "Hex:5 HexNAc:4 NeuAc:2", "G48414YA", "", "", "", "", "", "", "", "", "" ], [ "P48199-1", "147", "Asn", "G76675AB", "N-Linked", "protein_xref_glyconnect", "114", "protein_xref_glyconnect", "114", "114", "10116", "Rattus norvegicus", "1080", "G76675AB", "Complex", "N-Linked", "5,4,0,1,0,0,0,0,0,0,0,0,0,0", "H5N4S1", "HexNAc(4)Hex(5)NeuAc(1)", "1931.6876", "1932.7652", "Hex:5 HexNAc:4 NeuAc:1", "G06356OH", "", "", "", "", "", "", "", "", "" ], [ "P48199-1", "147", "Asn", "G06356OH", "N-Linked", "protein_xref_glyconnect", "114", "protein_xref_glyconnect", "114", "114", "10116", "Rattus norvegicus", "1080", "G76675AB", "Complex", "N-Linked", "5,4,0,1,0,0,0,0,0,0,0,0,0,0", "H5N4S1", "HexNAc(4)Hex(5)NeuAc(1)", "1931.6876", "1932.7652", "Hex:5 HexNAc:4 NeuAc:1", "G06356OH", "", "", "", "", "", "", "", "", "" ], [ "P48199-1", "147", "Asn", "G76675AB", "N-Linked", "protein_xref_pubmed", "8486673", "protein_xref_glyconnect", "114", "114", "10116", "Rattus norvegicus", "1080", "G76675AB", "Complex", "N-Linked", "5,4,0,1,0,0,0,0,0,0,0,0,0,0", "H5N4S1", "HexNAc(4)Hex(5)NeuAc(1)", "1931.6876", "1932.7652", "Hex:5 HexNAc:4 NeuAc:1", "G06356OH", "", "", "", "", "", "", "", "", "" ], [ "P48199-1", "147", "Asn", "G06356OH", "N-Linked", "protein_xref_pubmed", "8486673", "protein_xref_glyconnect", "114", "114", "10116", "Rattus norvegicus", "1080", "G76675AB", "Complex", "N-Linked", "5,4,0,1,0,0,0,0,0,0,0,0,0,0", "H5N4S1", "HexNAc(4)Hex(5)NeuAc(1)", "1931.6876", "1932.7652", "Hex:5 HexNAc:4 NeuAc:1", "G06356OH", "", "", "", "", "", "", "", "", "" ] ] }, "readme": "Name\n - Rat Glycosylation Sites (GlyConnect) \n\nVersion\n - 1.5.36\n\nCreated on\n - 2020-02-10T12:21:08.095461\n\nModified on\n - 2020-02-10T12:45:27.721901\n\nCreated by\n - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@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 directly from authors ( Frederique Lisacek; Julien Mariethoz) on 10/09/2019. 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 associated with Rat [TaxID:10116] UniProtKB accessions. The QC checks filter out any rows where the UniProtKB accession is not included in the GlyGen protein list (https://data.glygen.org/GLYDS000244) and/or 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.\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: glygen_2019_10_09_56_06.json\n URI: https://data.glygen.org/ln2wwwdata/source/glygen_2019_10_09_56_06.json\n Name: rat_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/rat_protein_masterlist.csv\n Name: rat_protein_canonicalsequences.fasta\n URI: https://data.glygen.org/reviewed/rat_protein_canonicalsequences.fasta\n Output Subdomain\n Name: rat_proteoform_glycosylation_sites_glyconnect.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/rat_proteoform_glycosylation_sites_glyconnect.csv\n Name: rat_proteoform_glycosylation_sites_glyconnect.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/rat_proteoform_glycosylation_sites_glyconnect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\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: \"composition_glytoucan_id\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"1\"\n Name: \"src_xref_key\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"composition_format_byonic\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"composition_format_glyconnect\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"composition_mass\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"source_cell_component_id\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"taxonomy_taxonomy_id\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"source_tissue_id\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"source_cell_component_name\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"source_tissue_name\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"composition_format_condensed\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"4\"\n Name: \"protein_id\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"structure_glycan_type\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"composition_mass_monoisotopic\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"composition_format_numeric\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"source_cell_line_id\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"source_cell_line_name\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"structure_glycan_core\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"source_tissue_uberon_id\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"structure_id\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"source_cell_component_go_id\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"source_cell_line_cellosaurus_id\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"1\"\n Name: \"structure_glytoucan_id\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"taxonomy_species\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"xref_key\"\n Description: \"\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-1.5.36/reviewed/rat_proteoform_glycosylation_sites_glyconnect.csv" }