{ "bcoid": "GLY_000530", "title": "SARS-CoV2 Glycosylation sites", "description": "The SARS-CoV2 Glycosylation Sites (GlyConnect) dataset contains SARS-CoV2 [taxid:2697049] UniProtKB canonical ...", "filename": "sarscov2_proteoform_glycosylation_sites_glyconnect.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...", "17..." ], [ "P0DTC2-1...", "17..." ] ], "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": 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"CVCL_D603", "", "", "", "NIT", "NXT" ], [ "P0DTC2-1", "61", "Asn", "G29880MM", "N-linked", "protein_xref_glyconnect", "2839", "protein_xref_glyconnect", "2839", "2839", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "556", "", "Undefined core", "N-Linked", "4,3,1,0,0,0,0,0,0,0,0,0,0,0", "H4N3F1", "HexNAc(3)Hex(4)dHex(1)", "1421.5179", "1422.3129", "Hex:4 HexNAc:3 dHex:1", "G29880MM", "", "", "", "19", "BTI-Tn-5B1-4", "CVCL_C190", "", "", "", "NVT", "NXT" ], [ "P0DTC2-1", "61", "Asn", "G29880MM", "N-linked", "protein_xref_pubmed", "32518941", "protein_xref_glyconnect", "2839", "2839", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "556", "", "Undefined core", "N-Linked", "4,3,1,0,0,0,0,0,0,0,0,0,0,0", "H4N3F1", "HexNAc(3)Hex(4)dHex(1)", "1421.5179", "1422.3129", "Hex:4 HexNAc:3 dHex:1", "G29880MM", "", "", "", "19", "BTI-Tn-5B1-4", "CVCL_C190", "", "", "", "NVT", "NXT" ], [ "P0DTC2-1", "17", "Asn", "G29880MM", "N-linked", "protein_xref_glyconnect", "2840", "protein_xref_glyconnect", "2840", "2840", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "556", "", "Undefined core", "N-Linked", "4,3,1,0,0,0,0,0,0,0,0,0,0,0", "H4N3F1", "HexNAc(3)Hex(4)dHex(1)", "1421.5179", "1422.3129", "Hex:4 HexNAc:3 dHex:1", "G29880MM", "", "", "", "154", "FreeStyle 293-F", "CVCL_D603", "", "", "", "NLT", "NXT" ], [ "P0DTC2-1", "17", "Asn", "G29880MM", "N-linked", "protein_xref_pubmed", "32366695", "protein_xref_glyconnect", "2840", "2840", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "556", "", "Undefined core", "N-Linked", "4,3,1,0,0,0,0,0,0,0,0,0,0,0", "H4N3F1", "HexNAc(3)Hex(4)dHex(1)", "1421.5179", "1422.3129", "Hex:4 HexNAc:3 dHex:1", "G29880MM", "", "", "", "154", "FreeStyle 293-F", "CVCL_D603", "", "", "", "NLT", "NXT" ], [ "P0DTC2-1", "61", "Asn", "G29880MM", "N-linked", "protein_xref_glyconnect", "2840", "protein_xref_glyconnect", "2840", "2840", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "556", "", "Undefined core", "N-Linked", "4,3,1,0,0,0,0,0,0,0,0,0,0,0", "H4N3F1", "HexNAc(3)Hex(4)dHex(1)", "1421.5179", "1422.3129", "Hex:4 HexNAc:3 dHex:1", "G29880MM", "", "", "", "154", "FreeStyle 293-F", "CVCL_D603", "", "", "", "NVT", "NXT" ], [ "P0DTC2-1", "61", "Asn", "G29880MM", "N-linked", "protein_xref_pubmed", "32366695", "protein_xref_glyconnect", "2840", "2840", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "556", "", "Undefined core", "N-Linked", "4,3,1,0,0,0,0,0,0,0,0,0,0,0", "H4N3F1", "HexNAc(3)Hex(4)dHex(1)", "1421.5179", "1422.3129", "Hex:4 HexNAc:3 dHex:1", "G29880MM", "", "", "", "154", "FreeStyle 293-F", "CVCL_D603", "", "", "", "NVT", "NXT" ], [ "P0DTC2-1", "74", "Asn", "G29880MM", "N-linked", "protein_xref_glyconnect", "2840", "protein_xref_glyconnect", "2840", "2840", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "556", "", "Undefined core", "N-Linked", "4,3,1,0,0,0,0,0,0,0,0,0,0,0", "H4N3F1", "HexNAc(3)Hex(4)dHex(1)", "1421.5179", "1422.3129", "Hex:4 HexNAc:3 dHex:1", "G29880MM", "", "", "", "154", "FreeStyle 293-F", "CVCL_D603", "", "", "", "NGT", "NXT" ], [ "P0DTC2-1", "74", "Asn", "G29880MM", "N-linked", "protein_xref_pubmed", "32366695", "protein_xref_glyconnect", "2840", "2840", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "556", "", "Undefined core", "N-Linked", "4,3,1,0,0,0,0,0,0,0,0,0,0,0", "H4N3F1", "HexNAc(3)Hex(4)dHex(1)", "1421.5179", "1422.3129", "Hex:4 HexNAc:3 dHex:1", "G29880MM", "", "", "", "154", "FreeStyle 293-F", "CVCL_D603", "", "", "", "NGT", "NXT" ], [ "P0DTC2-1", "61", "Asn", "G23453IV", "N-linked", "protein_xref_glyconnect", "2839", "protein_xref_glyconnect", "2839", "2839", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "578", "", "Undefined core", "N-Linked", "4,3,0,0,0,0,0,0,0,0,0,0,0,0", "H4N3", "HexNAc(3)Hex(4)", "1275.46", "1276.1699", "Hex:4 HexNAc:3", "G23453IV", "", "", "", "19", "BTI-Tn-5B1-4", "CVCL_C190", "", "", "", "NVT", "NXT" ], [ "P0DTC2-1", "61", "Asn", "G23453IV", "N-linked", "protein_xref_pubmed", "32518941", "protein_xref_glyconnect", "2839", "2839", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "578", "", "Undefined core", "N-Linked", "4,3,0,0,0,0,0,0,0,0,0,0,0,0", "H4N3", "HexNAc(3)Hex(4)", "1275.46", "1276.1699", "Hex:4 HexNAc:3", "G23453IV", "", "", "", "19", "BTI-Tn-5B1-4", "CVCL_C190", "", "", "", "NVT", "NXT" ], [ "P0DTC2-1", "74", "Asn", "G23453IV", "N-linked", "protein_xref_glyconnect", "2839", "protein_xref_glyconnect", "2839", "2839", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "578", "", "Undefined core", "N-Linked", "4,3,0,0,0,0,0,0,0,0,0,0,0,0", "H4N3", "HexNAc(3)Hex(4)", "1275.46", "1276.1699", "Hex:4 HexNAc:3", "G23453IV", "", "", "", "19", "BTI-Tn-5B1-4", "CVCL_C190", "", "", "", "NGT", "NXT" ], [ "P0DTC2-1", "74", "Asn", "G23453IV", "N-linked", "protein_xref_pubmed", "32518941", "protein_xref_glyconnect", "2839", "2839", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "578", "", "Undefined core", "N-Linked", "4,3,0,0,0,0,0,0,0,0,0,0,0,0", "H4N3", "HexNAc(3)Hex(4)", "1275.46", "1276.1699", "Hex:4 HexNAc:3", "G23453IV", "", "", "", "19", "BTI-Tn-5B1-4", "CVCL_C190", "", "", "", "NGT", "NXT" ], [ "P0DTC2-1", "17", "Asn", "G23453IV", "N-linked", "protein_xref_glyconnect", "2840", "protein_xref_glyconnect", "2840", "2840", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "578", "", "Undefined core", "N-Linked", "4,3,0,0,0,0,0,0,0,0,0,0,0,0", "H4N3", "HexNAc(3)Hex(4)", "1275.46", "1276.1699", "Hex:4 HexNAc:3", "G23453IV", "", "", "", "154", "FreeStyle 293-F", "CVCL_D603", "", "", "", "NLT", "NXT" ], [ "P0DTC2-1", "17", "Asn", "G23453IV", "N-linked", "protein_xref_pubmed", "32366695", "protein_xref_glyconnect", "2840", "2840", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "578", "", "Undefined core", "N-Linked", "4,3,0,0,0,0,0,0,0,0,0,0,0,0", "H4N3", "HexNAc(3)Hex(4)", "1275.46", "1276.1699", "Hex:4 HexNAc:3", "G23453IV", "", "", "", "154", "FreeStyle 293-F", "CVCL_D603", "", "", "", "NLT", "NXT" ], [ "P0DTC2-1", "61", "Asn", "G23453IV", "N-linked", "protein_xref_glyconnect", "2840", "protein_xref_glyconnect", "2840", "2840", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "578", "", "Undefined core", "N-Linked", "4,3,0,0,0,0,0,0,0,0,0,0,0,0", "H4N3", "HexNAc(3)Hex(4)", "1275.46", "1276.1699", "Hex:4 HexNAc:3", "G23453IV", "", "", "", "154", "FreeStyle 293-F", "CVCL_D603", "", "", "", "NVT", "NXT" ], [ "P0DTC2-1", "61", "Asn", "G23453IV", "N-linked", "protein_xref_pubmed", "32366695", "protein_xref_glyconnect", "2840", "2840", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "578", "", "Undefined core", "N-Linked", "4,3,0,0,0,0,0,0,0,0,0,0,0,0", "H4N3", "HexNAc(3)Hex(4)", "1275.46", "1276.1699", "Hex:4 HexNAc:3", "G23453IV", "", "", "", "154", "FreeStyle 293-F", "CVCL_D603", "", "", "", "NVT", "NXT" ] ] }, "readme": "Name\n - SARS-CoV2 Glycosylation sites\n\nVersion\n - 1.11.2\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], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.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/ln2data/releases/data/v-1.11.2/source/sglyconnect_sarscov2.json\n Name: sarscov2_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/sarscov2_protein_masterlist.csv\n Name: sarscov2_protein_canonicalsequences.fasta\n URI: https://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/sarscov2_protein_canonicalsequences.fasta\n Name: glycan_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/glycan_masterlist.csv\n Output Subdomain\n Name: sarscov2_proteoform_glycosylation_sites_glyconnect.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.csv\n Name: sarscov2_proteoform_glycosylation_sites_glyconnect.1.log\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.csv\n Name: sarscov2_proteoform_glycosylation_sites_glyconnect.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"23\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"19\"\n Name: \"sift_prediction\"\n Description: \"The SIFT qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"3\"\n Name: \"somatic_status\"\n Description: \"The status of the variant whether it is germline (somatic status =0) or somatic (somatic status =1) variant\"\n Unique Values: \"1\"\n Name: \"chr_pos\"\n Description: \"Chromosome Position of a gene\"\n Unique Values: \"19\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"10\"\n Name: \"dbsnp_id\"\n Description: \"\"A reference SNP ID number\"\n Unique Values: \"19\"\n Name: \"evidence_ECO:0000313\"\n Description: \"A type of evidence that is imported information used in an automatic assertion\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"19\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\n Name: \"description\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"begin_aa_pos\"\n Description: \"Start position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"cytogenic_band\"\n Description: \"One of the subregions of a chromosome visible microscopically after special staining\"\n Unique Values: \"14\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"18\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"9\"\n Name: \"sift_score\"\n Description: \"SIFT predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. The data we provide for each amino acid substitution is a score and a qualitative prediction (either 'tolerated' or 'deleterious'). The score is the normalized probability that the amino acid change is tolerated so scores nearer zero are more likely to be deleterious. The qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"10\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"24\"\n Name: \"disease_xrefs\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"polyphen_score\"\n Description: \"The score assigned to a amino acid substitution by a tool called as PolyPhen (=Polymorphism Phenotyping) which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. The PolyPhen score ranges from 0.0 (tolerated) to 1.0 (deleterious). Variants with scores of 0.0 are predicted to be benign. Values closer to 1.0 are more confidently predicted to be deleterious\"\n Unique Values: \"1\"\n Name: \"polyphen_prediction\"\n Description: \"\"The PolyPhen prediction values are - greater than 0.908 - \"\"Probably Damaging\"\"; greater than 0.446 and less than or equal to 0.908 - \"\"Possibly Damaging\"\"; less than or equal to 0.446 - \"\"Benign\"\"\"\n Unique Values: \"1\"\n Name: \"is_known_glycoprotein\"\n Description: \"Yes or no flag to denote if a protein is experimentally proven glycoprotein\"\n Unique Values: \"1\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"1\"\n Name: \"protein_name\"\n Description: \"Protein name in the UniProtKB\"\n Unique Values: \"16\"\n Name: \"disease_evidence_ECO:0000313\"\n Description: \"The evidence that could be a PMID or a ClinVar ID that associates disease with the variant\"\n Unique Values: \"1\"\n Name: \"effect\"\n Description: \"The effect on glycosylation or N-sequon due to variation at site of glycosylated amino acid.\"\n Unique Values: \"3\"\n Name: \"end_aa_pos\"\n Description: \"End position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"mutation_type\"\n Description: \"Denotes whether mutation was reported with reference to amino acid or nucleotide\"\n Unique Values: \"1\"\n Name: \"disease_description\"\n Description: \"The disease description and/or definition \"\n Unique Values: \"1\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"1\"\n Name: \"evidence_ECO:0000269\"\n Description: \"A type of experimental evidence that is used in a manual assertion. Usually the values are PMIDs\"\n Unique Values: \"1\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"disease\"\n Description: \"The disease name for the cell line\"\n Unique Values: \"1\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"10\"\n Name: \"cosmic_id\"\n Description: \"Legacy mutation identifier (COSM) in Catalogue of Somatic Mutations in Cancer (COSMIC) represents existing COSM mutation identifiers. This identifier remains the same between different assemblies (GRCh37 and GRCh38). All the COSM ids at the same genomic location have been collapsed into one representative COSM id. These ids are maintained to help track existing mutations\"\n Unique Values: \"1\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"20\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"minor_allelic_frequency\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"gene_name\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\"\n Unique Values: \"17\"\n Name: \"disease_evidence_ECO:0000269\"\n Description: \"The PMID evidence for the association of the disease with the variant.\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.11.2/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.csv" }