{ "bcoid": "GLY_000384", "title": "HCV1a Phosphorylation Sites (UniProtKB)", "description": "The Hepatitis C virus (genotype 1a, isolate H) Phosphorylation Sites (UniProtKB) dataset contains hcv1a ...", "filename": "hcv1a_proteoform_phosphorylation_sites_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Hepatitis C virus (genotype 1a, isolate H)" ], "molecule": [ "Proteoform" ], "tags": [ "Phosphorylation Sites" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P27958-1...", "116..." ], [ "P27958-1...", "2197..." ] ], "headers": [ "uniprotkb_ca...", "phosphorylat..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "phosphorylation_site_uniprotkb" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "kinase_uniprotkb_canonical_ac" }, { "type": "string", "label": "kinase_gene_name" }, { "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": "phosphorylated_residue" }, { "type": "string", "label": "phosphorylation_annotation" }, { "type": "string", "label": "eco_id" } ], [ "P27958-1", "116", "Ser", "", "", "protein_xref_uniprotkb", "P27958", "protein_xref_uniprotkb", "P27958", "Phosphoserine", "Phosphoserine; by host PKA", "" ], [ "P27958-1", "2197", "Ser", "", "", "protein_xref_uniprotkb", "P27958", "protein_xref_uniprotkb", "P27958", "Phosphoserine", "Phosphoserine; by host; in p58", "" ], [ "P27958-1", "2201", "Ser", "", "", "protein_xref_uniprotkb", "P27958", "protein_xref_uniprotkb", "P27958", "Phosphoserine", "Phosphoserine; by host; in p56 and p58, regulates intracellular NS5A distribution", "" ], [ "P27958-1", "53", "Ser", "", "", "protein_xref_uniprotkb", "P27958", "protein_xref_uniprotkb", "P27958", "Phosphoserine", "Phosphoserine; by host", "" ], [ "P27958-1", "2462", "Ser", "", "", "protein_xref_uniprotkb", "P27958", "protein_xref_uniprotkb", "P27958", "Phosphoserine", "Phosphoserine; by host", "" ], [ "P27958-1", "2194", "Ser", "", "", "protein_xref_uniprotkb", "P27958", "protein_xref_uniprotkb", "P27958", "Phosphoserine", "Phosphoserine; by host; in p56", "" ], [ "P27958-1", "2204", "Ser", "", "", "protein_xref_uniprotkb", "P27958", "protein_xref_uniprotkb", "P27958", "Phosphoserine", "Phosphoserine; by host; in p58", "" ], [ "P27958-1", "2321", "Ser", "", "", "protein_xref_uniprotkb", "P27958", "protein_xref_uniprotkb", "P27958", "Phosphoserine", "Phosphoserine; by host", "" ], [ "P27958-1", "2449", "Ser", "", "", "protein_xref_uniprotkb", "P27958", "protein_xref_uniprotkb", "P27958", "Phosphoserine", "Phosphoserine; by host", "" ], [ "P27958-1", "2207", "Ser", "", "", "protein_xref_uniprotkb", "P27958", "protein_xref_uniprotkb", "P27958", "Phosphoserine", "Phosphoserine; by host; in p58", "" ], [ "P27958-1", "99", "Ser", "", "", "protein_xref_uniprotkb", "P27958", "protein_xref_uniprotkb", "P27958", "Phosphoserine", "Phosphoserine; by host", "" ], [ "P27958-1", "2210", "Ser", "", "", "protein_xref_uniprotkb", "P27958", "protein_xref_uniprotkb", "P27958", "Phosphoserine", "Phosphoserine; by host; in p58", "" ] ] }, "readme": "Name\n - HCV1a Phosphorylation Sites (UniProtKB)\n\nVersion\n - v-2.1.1\n\nCreated on\n - 2020-03-15T12:29:48.651730\n\nModified on\n - 2022-09-26T09:05:27.636699\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 Hepatitis C virus (genotype 1a, isolate H) Phosphorylation Sites (UniProtKB) dataset contains hcv1a [taxid:11108] UniProtKB canonical accessions with information on reported and predicted phosphoryation sites with evidence 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 - phosphoryation Sites\n - ptm processing\n - UniProtKB\n\n Pipeline Steps\n - Step-1: The script loads the phosphorylation information from the triplestore conatining 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: uniprot-proteome-hepatitis-c-virus-1a.nt\n URI: /data/shared/glyds/downloads/ebi/2023_02/uniprot-proteome-hepatitis-c-virus-1a.nt\n Output Subdomain\n Name: hcv1a_proteoform_phosphorylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/hcv1a_proteoform_phosphorylation_sites_uniprotkb.csv\n Name: hcv1a_proteoform_phosphorylation_sites_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/hcv1a_proteoform_phosphorylation_sites_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"phosphorylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where phosphorylation is observed\"\n Unique Values: \"12\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"1\"\n Name: \"kinase_uniprotkb_canonical_ac\"\n Description: \"The UniProtKB canonical accession for the kinase enzyme that is phosphorylating the protein\"\n Unique Values: \"1\"\n Name: \"kinase_gene_name\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"1\"\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: \"1\"\n Name: \"phosphorylated_residue\"\n Description: \"The amino acid that is modified by phosphorylation\"\n Unique Values: \"1\"\n Name: \"phosphorylation_annotation\"\n Description: \"The phosphorylation annotation in UniProtKB that provides more context and description of a phosphorylation event on a protein.\"\n Unique Values: \"5\"\n Name: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/hcv1a_proteoform_phosphorylation_sites_uniprotkb.csv" }