{ "bcoid": "GLY_000473", "title": "SARS-CoV2 Glycosylation Sites (UniProtKB)", "description": "The SARS coronavirus (SARS-CoV-2 or 2019-nCoV) Glycosylation Sites (UniProtKB) dataset contains sarscov2 ...", "filename": "sarscov2_proteoform_glycosylation_sites_uniprotkb.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-2 or 2019-nCoV)", "molecule": "Proteoform", "tags": "Glycosylation Sites", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P0DTC2-1...", "61..." ], [ "P0DTC2-1...", "61..." ] ], "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" } ], [ "P0DTC2-1", "61", "Asn", "", "N-linked", "protein_xref_uniprotkb_gly", "P0DTC2", "protein_xref_uniprotkb_gly", "P0DTC2", "N-linked (GlcNAc...) 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(complex) asparagine; by host", "PubMed", "ECO_0000269", "", "GlcNAc...", "Complex", "NCT", "NXT" ] ] }, "readme": "Name\n - SARS-CoV2 Glycosylation Sites (UniProtKB)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2020-04-19T12:02:17.236691\n\nModified on\n - 2022-01-13T16:47:33.851382\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@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 - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The SARS coronavirus (SARS-CoV-2 or 2019-nCoV) Glycosylation Sites (UniProtKB) dataset contains sarscov2 [taxid:2697049] 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/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: sarscov2_protein_masterlist.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/sarscov2_protein_masterlist.csv\n Name: uniprot-proteome-sars-cov-2.nt\n URI: https://data.glygen.org//ln2downloads/ebi/2021_03/uniprot-proteome-sars-cov-2.nt\n Output Subdomain\n Name: sarscov2_proteoform_glycosylation_sites_uniprotkb.csv\n URI: http://data.glygen.org/datasets/reviewed/sarscov2_proteoform_glycosylation_sites_uniprotkb.csv\n Name: sarscov2_proteoform_glycosylation_sites_uniprotkb.stat.csv\n URI: http://data.glygen.org/datasets/reviewed/sarscov2_proteoform_glycosylation_sites_uniprotkb.stat.csv", "downloadurl": "/ln2data/releases/data/v-1.12.1/reviewed/sarscov2_proteoform_glycosylation_sites_uniprotkb.csv" }