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"", "", "149", "HEK293", "CVCL_0045", "", "", "", "NNS", "NXS" ], [ "P0DTC2-1", "343", "Asn", "G71051TA", "N-linked", "protein_xref_glyconnect", "2839", "protein_xref_glyconnect", "2839", "2839", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "8564", "", "Undefined core", "N-Linked", "7,6,4,2,0,0,0,0,0,0,0,0,0,0", "H7N6F4S2", "HexNAc(6)Hex(7)dHex(4)NeuAc(2)", "3537.279", "3539.2699", "Hex:7 HexNAc:6 dHex:4 NeuAc:2", "G71051TA", "", "", "", "19", "BTI-Tn-5B1-4", "CVCL_C190", "", "", "", "NAT", "NXT" ], [ "P0DTC2-1", "801", "Asn", "G05724UK", "N-linked", "protein_xref_glyconnect", "2839", "protein_xref_glyconnect", "2839", "2839", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "998", "", "Undefined core", "N-Linked", "7,2,0,0,0,0,0,0,0,0,0,0,0,0", "H7N2", "HexNAc(2)Hex(7)", "1558.539", "1559.4021", "Hex:7 HexNAc:2", "G05724UK", "", "", "", "19", "BTI-Tn-5B1-4", "CVCL_C190", "", "", "", "NFS", "NXS" ], [ "P0DTC2-1", "282", "Asn", 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"2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "8491", "", "Undefined core", "N-Linked", "6,7,1,0,0,0,0,0,0,0,0,0,0,0", "H6N7F1", "HexNAc(7)Hex(6)dHex(1)", "2557.9411", "2559.3777", "Hex:6 HexNAc:7 dHex:1", "G25379SA", "", "", "", "149", "HEK293", "CVCL_0045", "", "", "", "NAT", "NXT" ] ] }, "readme": "Name\n - SARS-CoV2 Glycosylation sites\n\nVersion\n - 1.8.25\n\nCreated on\n - 2020-09-24T13:36:00.724463\n\nModified on\n - 2020-12-11T14:21:03.916525\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 SARS-CoV2 Glycosylation Sites (GlyConnect) dataset contains SARS-CoV2 [taxid:2697049] UniProtKB canonical accessions with information on reported glycosylation sites in GlyConnect database (https://glyconnect.expasy.org/; PMID: 30574787).A json file was derived through GlyConnect API (https://glyconnect.expasy.org/api/docs/index.html?url=/api/assets/swagger.json#/Glycosylation/listGlycosylationsAsJson) (Query: taxonomy:Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)). 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. The QC checks filter out: 1) any rows where the UniProtKB accession is not included in the GlyGen protein list (https://data.glygen.org/GLYDS000001) and/or 2) 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 (However it does pass if the amino acid +glyco-site is empty (as these records correspond to the \"not reported\" glyco-sites and/or 3) If the glycosylation type does not associate to the glycostlation based on amino acid (i.e if a N-linked is associated with Ser/Thr residue, etc). 4) If the glyco-site is not reported and the glycosylation type is ambigious (c-Linked/o-linked) and/or 5) if the saccharide (GlyTouCan) is not present in the GlyGen glycan masterlist. All the flagged entries are added in the log file (sarscov2_proteoform_glycosylation_sites_glyconnect.1.log)\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: glyconnect_sarscov2.json\n URI: https://data.glygen.org/ln2wwwdata/source/sglyconnect_sarscov2.json\n Name: sarscov2_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/sarscov2_protein_masterlist.csv\n Name: sarscov2_protein_canonicalsequences.fasta\n URI: https://data.glygen.org/ln2wwwdata/reviewed/sarscov2_protein_canonicalsequences.fasta\n Name: glycan_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/glycan_masterlist.csv\n Output Subdomain\n Name: sarscov2_proteoform_glycosylation_sites_glyconnect.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.csv\n Name: sarscov2_proteoform_glycosylation_sites_glyconnect.1.log\n URI: http://data.glygen.org/ln2wwwdata/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.csv\n Name: sarscov2_proteoform_glycosylation_sites_glyconnect.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.stat.csv\n\nFields\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"119\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"119\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"120\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"49\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"118\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"117\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"115\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.8.25/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.csv" }