{ "bcoid": "GLY_000808", "title": "Yeast Glycosylation Sites (UniProtKB)", "description": "The Yeast Glycosylation Sites (UniProtKB) dataset contains yeast [taxid:559292] UniProtKB canonical accessions ...", "filename": "yeast_proteoform_glycosylation_sites_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Proteoform" ], "tag": [ "Glycosylation Sites" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P46992-1...", "99..." ], [ "P27614-1...", "525..." ] ], "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", 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"125", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q03674", "protein_xref_uniprotkb_gly", "Q03674", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NRT", "NXT", "125", "125", "Asn", "Asn", "N" ], [ "Q05934-1", "688", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q05934", "protein_xref_uniprotkb_gly", "Q05934", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NHS", "NXS", "688", "688", "Asn", "Asn", "N" ], [ "P31755-1", "281", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P31755", "protein_xref_uniprotkb_gly", "P31755", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NIT", "NXT", "281", "281", "Asn", "Asn", "N" ], [ "P26725-1", "77", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P26725", "protein_xref_uniprotkb_gly", "P26725", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NYT", "NXT", "77", "77", "Asn", "Asn", "N" ], [ "P32802-1", "61", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P32802", "protein_xref_uniprotkb_gly", "P32802", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NVS", "NXS", "61", "61", "Asn", "Asn", "N" ], [ "P31755-1", "393", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P31755", "protein_xref_uniprotkb_gly", "P31755", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NDT", "NXT", "393", "393", "Asn", "Asn", "N" ], [ "Q08673-1", "200", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q08673", "protein_xref_uniprotkb_gly", "Q08673", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NTT", "NXT", "200", "200", "Asn", "Asn", "N" ], [ "P47190-1", "124", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P47190", "protein_xref_uniprotkb_gly", "P47190", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NGS", "NXS", "124", "124", "Asn", "Asn", "N" ], [ "P38693-1", "97", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P38693", "protein_xref_uniprotkb_gly", "P38693", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NYT", "NXT", "97", "97", "Asn", "Asn", "N" ], [ "P32768-1", "734", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P32768", "protein_xref_uniprotkb_gly", "P32768", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NDT", "NXT", "734", "734", "Asn", "Asn", "N" ], [ "Q12275-1", "98", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q12275", "protein_xref_uniprotkb_gly", "Q12275", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NST", "NXT", "98", "98", "Asn", "Asn", "N" ], [ "P53983-1", "46", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P53983", "protein_xref_uniprotkb_gly", "P53983", "N-linked (GlcNAc...) asparagine", "prosite-prorule", "ECO_0000255", "", "GlcNAc...", "", "NST", "NXT", "46", "46", "Asn", "Asn", "N" ], [ "P53983-1", "46", "Asn", "", "N-linked", "protein_xref_prosite-prorule", "PRU00498", "protein_xref_uniprotkb_gly", "P53983", "N-linked (GlcNAc...) asparagine", "prosite-prorule", "ECO_0000255", "", "GlcNAc...", "", "NST", "NXT", "46", "46", "Asn", "Asn", "N" ], [ "Q08693-1", "669", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q08693", "protein_xref_uniprotkb_gly", "Q08693", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NFT", "NXT", "669", "669", "Asn", "Asn", "N" ], [ "P31382-1", "155", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P31382", "protein_xref_uniprotkb_gly", "P31382", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NAS", "NXS", "155", "155", "Asn", "Asn", "N" ], [ "Q12465-1", "333", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q12465", "protein_xref_uniprotkb_gly", "Q12465", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NLT", "NXT", "333", "333", "Asn", "Asn", "N" ], [ "Q04119-1", "58", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "Q04119", "protein_xref_uniprotkb_gly", "Q04119", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "", "NES", "NXS", "58", "58", "Asn", "Asn", "N" ] ] }, "readme": "Name\n - Yeast Glycosylation Sites (UniProtKB)\n\nVersion\n - v-2.4.1\n\nCreated on\n - 2022-09-06T09:50:57.220135\n\nModified on\n - 2023-09-11T20:46:55\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], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@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 Yeast Glycosylation Sites (UniProtKB) dataset contains yeast [taxid:559292] UniProtKB canonical accessions with information on reported and predicted glycosylation sites in UniProtKB database. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - glycosylation\n - reported glycosylation\n - predicted glycosylation\n - UniProtKB\n - PubMed\n - Evidence and conclusion Ontology\n\n Pipeline Steps\n - Step-1: The script loads the glycosylation information from the triplestore conatining 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-2.4.1/misc/glycosylation_subtype.csv\n Name: n_sequon_info.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2024_01_31/cellosaurus.txt\n Name: uniprot-proteome-saccharomyces-cerevisiae.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2024_02_19/uniprot-proteome-saccharomyces-cerevisiae.nt\n Output Subdomain\n Name: yeast_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_proteoform_glycosylation_sites_uniprotkb.csv\n Name: yeast_proteoform_glycosylation_sites_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_proteoform_glycosylation_sites_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"432\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"750\"\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: \"1\"\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: \"5\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"473\"\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: \"432\"\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: \"8\"\n Name: \"data_source\"\n Description: \"The source database for the data\"\n Unique Values: \"6\"\n Name: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"6\"\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: \"1\"\n Name: \"carb_name\"\n Description: \"carbohydrate name\"\n Unique Values: \"4\"\n Name: \"glycosylation_subtype\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"39\"\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: \"750\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"750\"\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-2.4.1/reviewed/yeast_proteoform_glycosylation_sites_uniprotkb.csv" }