{ "bcoid": "GLY_000383", "title": "HCV1b Glycosylation Sites (UniProtKB)", "description": "The Hepatitis C virus (genotype 1b, isolate Japanese) Glycosylation Sites (UniProtKB) dataset contains ...", "filename": "hcv1b_proteoform_glycosylation_sites_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Hepatitis C virus (genotype 1b, isolate Japanese)", "molecule": "Proteoform", "tags": "Glycosylation Sites", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P26662-1...", "O-linked..." ], [ "P26662-1...", "N-linked..." ] ], "headers": [ "uniprotkb_ca...", "glycosylatio..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glycosylation_type" }, { "type": "string", "label": "saccharide" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "glycosylation_site_uniprotkb" }, { "type": "string", "label": "uniprotkb_glycosylation_annotation_comment" }, { "type": "string", "label": "data_source" }, { "type": "string", "label": "evidence" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "uniprotkb_ftid" } ], [ "P26662-1", "O-linked", "Hex...", "Thr", "518", "O-linked (Hex...) threonine; by host", "PubMed", "23242014", "ECO_0000269", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "430", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "448", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "O-linked", "Hex...", "Thr", "396", "O-linked (Hex...) threonine; by host", "PubMed", "23242014", "ECO_0000269", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "250", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "209", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "532", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "423", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "576", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "305", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "234", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "O-linked", "Hex...", "Thr", "385", "O-linked (Hex...) threonine; by host", "PubMed", "23242014", "ECO_0000305", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "417", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "645", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "196", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "623", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "N-linked", "GlcNAc...", "Asn", "556", "N-linked (GlcNAc...) asparagine; by host", "", "", "", "" ], [ "P26662-1", "O-linked", "Hex...", "Thr", "473", "O-linked (Hex...) threonine; by host", "PubMed", "23242014", "ECO_0000269", "" ], [ "P26662-1", "O-linked", "Hex...", "Ser", "404", "O-linked (Hex...) serine; by host", "PubMed", "23242014", "ECO_0000269", "" ], [ "P26662-1", "O-linked", "Hex...", "Ser", "401", "O-linked (Hex...) serine; by host", "PubMed", "23242014", "ECO_0000269", "" ] ] }, "readme": "Name\n - HCV1b Glycosylation Sites (UniProtKB)\n\nVersion\n - 1.5.23\n\nCreated on\n - 2020-03-15T12:27:03.522584\n\nModified on\n - 2020-04-09T18:12:53.311327\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@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 Hepatitis C virus (genotype 1b, isolate Japanese) Glycosylation Sites (UniProtKB) dataset contains hcv1b [taxid:11116] UniProtKB canonical accessions with information on reported and predicted glycosylation sites in UniProtKB database. The dataset is derived from 2019-09 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 conatining 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: uniprot-proteome-hepatitis-c-virus-1b.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/source/uniprot-proteome-hepatitis-c-virus-1b.nt\n Name: hcv1b_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/hcv1b_protein_masterlist.csv\n Output Subdomain\n Name: hcv1b_proteoform_glycosylation_sites_uniprotkb.csv\n URI: http://data.glygen.org/datasets/reviewed/hcv1b_proteoform_glycosylation_sites_uniprotkb.csv\n Name: hcv1b_proteoform_glycosylation_sites_uniprotkb.stat.csv\n URI: http://data.glygen.org/datasets/reviewed/hcv1b_proteoform_glycosylation_sites_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"1\"\n Name: \"data_source\"\n Description: \"The source database for the data\"\n Unique Values: \"2\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"20\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"2\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"3\"\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: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) or DOI (Digital Object Identifier) as evidence for the entry/annotation\"\n Unique Values: \"2\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"2\"\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: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"3\"", "downloadurl": "/ln2data/releases/data/v-1.5.23/reviewed/hcv1b_proteoform_glycosylation_sites_uniprotkb.csv" }