{ "bcoid": "GLY_000495", "title": "SARS-CoV1 Glycosylation Sites (UniProtKB)", "description": "The SARS coronavirus (SARS-CoV-1) Glycosylation Sites (UniProtKB) dataset contains sarscov1 [taxid:694009] ...", "filename": "sarscov1_proteoform_glycosylation_sites_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Severe acute respiratory syndrome-related coronavirus" ], "molecule": [ "Proteoform" ], "tag": [ "Glycosylation Sites" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P59594-1...", "1080..." ], [ "P59594-1...", "1080..." ] ], "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": "uniprotkb_glycosylation_annotation_comment" }, { "type": "string", "label": "data_source" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "uniprotkb_ftid" }, { "type": "string", "label": "carb_name" }, { "type": "string", "label": "glycosylation_subtype" }, { "type": "string", "label": "n_sequon" }, { "type": "string", "label": "n_sequon_type" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "start_aa" }, { "type": "string", "label": "end_aa" }, { "type": "string", "label": "site_seq" } ], [ "P59594-1", "1080", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P59594", "protein_xref_uniprotkb_gly", "P59594", "N-linked (GlcNAc...) asparagine; 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by host", "hamap-rule", "ECO_0000255", "", "GlcNAc...", "", "NAS", "NXS", "589", "589", "Asn", "Asn", "N" ], [ "P59594-1", "589", "Asn", "", "N-linked", "protein_xref_hamap-rule", "MF_04099", "protein_xref_uniprotkb_gly", "P59594", "N-linked (GlcNAc...) asparagine; by host", "hamap-rule", "ECO_0000255", "", "GlcNAc...", "", "NAS", "NXS", "589", "589", "Asn", "Asn", "N" ] ] }, "readme": "Name\n - SARS-CoV1 Glycosylation Sites (UniProtKB)\n\nVersion\n - v-2.3.1\n\nCreated on\n - 2020-05-07T18:18:49.168950\n\nModified on\n - 2022-09-26T09:05:56.555699\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 SARS coronavirus (SARS-CoV-1) Glycosylation Sites (UniProtKB) dataset contains sarscov1 [taxid:694009] UniProtKB canonical accessions with information on reported and predicted glycosylation sites in UniProtKB database. The dataset is derived from 2020-01 UniProtKB release. 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 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-2.3.1/misc/glycosylation_subtype.csv\n Name: n_sequon_info.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2023_10_11/cellosaurus.txt\n Name: uniprot-proteome-sars-coronavirus.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2023_10_30/uniprot-proteome-sars-coronavirus.nt\n Output Subdomain\n Name: sarscov1_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/sarscov1_proteoform_glycosylation_sites_uniprotkb.csv\n Name: sarscov1_proteoform_glycosylation_sites_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/sarscov1_proteoform_glycosylation_sites_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"28\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"3\"\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: \"3\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"6\"\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: \"3\"\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: \"3\"\n Name: \"data_source\"\n Description: \"The source database for the data\"\n Unique Values: \"3\"\n Name: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"4\"\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: \"2\"\n Name: \"glycosylation_subtype\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"16\"\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: \"28\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"28\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"3\"", "downloadurl": "/ln2data/releases/data/v-2.3.1/reviewed/sarscov1_proteoform_glycosylation_sites_uniprotkb.csv" }