{ "bcoid": "GLY_000224", "title": "Rat Glycosylation Sites (UniProtKB)", "description": "The Rat Glycosylation Sites (UniProtKB) dataset contains mouse [taxid:10116] UniProtKB canonical accessions ...", "filename": "rat_proteoform_glycosylation_sites_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Rattus norvegicus" ], "molecule": [ "Protein" ], "tag": [ "Glycosylation Sites" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Q64716-1...", "492..." ], [ "P17438-1...", "229..." ] ], "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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"protein_xref_uniprotkb_gly", "Q63563", "protein_xref_uniprotkb_gly", "Q63563", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NNT", "NXT", "330", "330", "Asn", "Asn", "N" ], [ "P06238-1", "989", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P06238", "protein_xref_uniprotkb_gly", "P06238", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NET", "NXT", "989", "989", "Asn", "Asn", "N" ], [ "P97629-1", "989", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P97629", "protein_xref_uniprotkb_gly", "P97629", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NQS", "NXS", "989", "989", "Asn", "Asn", "N" ], [ "P0C5H6-1", "188", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P0C5H6", "protein_xref_uniprotkb_gly", "P0C5H6", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NGT", "NXT", "188", "188", "Asn", "Asn", "N" ], [ "P08721-1", "132", "Thr", "", "O-linked", "protein_xref_uniprotkb_gly", "P08721", "protein_xref_uniprotkb_gly", "P08721", "O-linked (GalNAc...) threonine", "", "", "", "GalNAc...", "O-GalNAcylation", "", "", "132", "132", "Thr", "Thr", "T" ], [ "O35932-1", "2", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "O35932", "protein_xref_uniprotkb_gly", "O35932", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NES", "NXS", "2", "2", "Asn", "Asn", "N" ], [ "Q63604-1", "411", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q63604", "protein_xref_uniprotkb_gly", "Q63604", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NKS", "NXS", "411", "411", "Asn", "Asn", "N" ], [ "P22057-1", "51", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P22057", "protein_xref_uniprotkb_gly", "P22057", "N-linked (GlcNAc...) asparagine", "PubMed", "ECO_0000269", "", "GlcNAc...", "", "NSS", "NXS", "51", "51", "Asn", "Asn", "N" ], [ "P22057-1", "51", "Asn", "", "N-linked", "protein_xref_pubmed", "2642896", "protein_xref_uniprotkb_gly", "P22057", "N-linked (GlcNAc...) asparagine", "PubMed", "ECO_0000269", "", "GlcNAc...", "", "NSS", "NXS", "51", "51", "Asn", "Asn", "N" ], [ "Q07969-1", "417", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q07969", "protein_xref_uniprotkb_gly", "Q07969", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NET", "NXT", "417", "417", "Asn", "Asn", "N" ], [ "Q9QX75-1", "514", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q9QX75", "protein_xref_uniprotkb_gly", "Q9QX75", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NIT", "NXT", "514", "514", "Asn", "Asn", "N" ], [ "Q6T3U3-1", "479", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q6T3U3", "protein_xref_uniprotkb_gly", "Q6T3U3", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NTS", "NXS", "479", "479", "Asn", "Asn", "N" ], [ "P36953-1", "109", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P36953", "protein_xref_uniprotkb_gly", "P36953", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NFS", "NXS", "109", "109", "Asn", "Asn", "N" ], [ "P98105-1", "192", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P98105", "protein_xref_uniprotkb_gly", "P98105", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NCT", "NXT", "192", "192", "Asn", "Asn", "N" ], [ "Q68G12-1", "58", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q68G12", "protein_xref_uniprotkb_gly", "Q68G12", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NYT", "NXT", "58", "58", "Asn", "Asn", "N" ], [ "P55280-1", "536", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P55280", "protein_xref_uniprotkb_gly", "P55280", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NFT", "NXT", "536", "536", "Asn", "Asn", "N" ], [ "Q63155-1", "628", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q63155", "protein_xref_uniprotkb_gly", "Q63155", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NVS", "NXS", "628", "628", "Asn", "Asn", "N" ], [ "P04634-1", "33", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P04634", "protein_xref_uniprotkb_gly", "P04634", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NIS", "NXS", "33", "33", "Asn", "Asn", "N" ], [ "Q03351-1", "203", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q03351", "protein_xref_uniprotkb_gly", "Q03351", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NIS", "NXS", "203", "203", "Asn", "Asn", "N" ], [ "P52500-1", "24", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P52500", "protein_xref_uniprotkb_gly", "P52500", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NQT", "NXT", "24", "24", "Asn", "Asn", "N" ], [ "Q62840-1", "117", "Ser", "", "O-linked", "protein_xref_uniprotkb_gly", "Q62840", "protein_xref_uniprotkb_gly", "Q62840", "O-linked (GalNAc...) serine", "", "", "", "GalNAc...", "O-GalNAcylation", "", "", "117", "117", "Ser", "Ser", "S" ], [ "P15389-1", "1367", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P15389", "protein_xref_uniprotkb_gly", "P15389", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NQT", "NXT", "1367", "1367", "Asn", "Asn", "N" ], [ "P98158-1", "4329", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P98158", "protein_xref_uniprotkb_gly", "P98158", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NQS", "NXS", "4329", "4329", "Asn", "Asn", "N" ], [ "Q6P767-1", "42", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q6P767", "protein_xref_uniprotkb_gly", "Q6P767", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NRS", "NXS", "42", "42", "Asn", "Asn", "N" ], [ "Q62919-1", "372", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q62919", "protein_xref_uniprotkb_gly", "Q62919", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NCS", "NXS", "372", "372", "Asn", "Asn", "N" ] ] }, "readme": "Name\n - Rat Glycosylation Sites (UniProtKB)\n\nVersion\n - v-2.2.1\n\nCreated on\n - 2019-09-06T14:06:38.952590\n\nModified on\n - 2022-09-26T09:04:47.889690\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 - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Rat Glycosylation Sites (UniProtKB) dataset contains mouse [taxid:10116] UniProtKB canonical accessions with information on reported and predicted glycosylation sites in UniProtKB database. The dataset is derived from 2019-09 UniProtKB release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen. \n\nDescription Domain\n\n Pipeline Steps\n - Step-1: The script loads the glycosylation information from the triplestore containing triples from the nt file and extracts as a csv dataset. \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: glycosylation_subtype.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/misc/glycosylation_subtype.csv\n Name: n_sequon_info.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2023_07_13/cellosaurus.txt\n Name: uniprot-proteome-rattus-norvegicus.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2023_07_11/uniprot-proteome-rattus-norvegicus.nt\n Output Subdomain\n Name: rat_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/rat_proteoform_glycosylation_sites_uniprotkb.csv\n Name: rat_proteoform_glycosylation_sites_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/rat_proteoform_glycosylation_sites_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"2105\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"1487\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"6\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"1\"\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: \"6\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"2248\"\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: \"2124\"\n Name: \"uniprotkb_glycosylation_annotation_comment\"\n Description: \"The glycosylation annotation in UniProtKB that provides more context and description about the glycosylation event on a proein\"\n Unique Values: \"52\"\n Name: \"data_source\"\n Description: \"The source database for the data\"\n Unique Values: \"7\"\n Name: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"8\"\n Name: \"uniprotkb_ftid\"\n Description: \"A stable feature identifier that allows to construct links directly from position-specific annotation to specialized protein-related databases. (In the dataset the FTID is for glycosylation for residues attached to an oligosaccharide structure annotated in the UniCarbKB database)\"\n Unique Values: \"7\"\n Name: \"carb_name\"\n Description: \"carbohydrate name\"\n Unique Values: \"14\"\n Name: \"glycosylation_subtype\"\n Description: \"\"\n Unique Values: \"12\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"46\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"5\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"1487\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"1487\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"6\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"6\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"6\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/rat_proteoform_glycosylation_sites_uniprotkb.csv" }