{ "bcoid": "GLY_001154", "title": "HCV1a Predicted O-Glycosylation Sites (IsoGlyP)", "description": "The HCV1a Predicted O-Glycosylation Sites dataset contains predicted Hepatitis C virus (isolate H77) ...", "filename_list": "hcv1a_proteoform_glycosylation_sites_predicted_isoglyp.csv", "filename": "hcv1a_proteoform_glycosylation_sites_predicted_isoglyp.csv", "filetype": "csv", "categories": { "species": [ "Hepatitis C virus (isolate H77)" ], "molecule": [ "Proteoform" ], "tag": [ "O-Glycosylation Sites" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P27958-1...", "110..." ], [ "P27958-1...", "243..." ] ], "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": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "start_aa" }, { "type": "string", "label": "end_aa" } ], [ "P27958-1", "110", "Thr", "", "O-linked", "protein_xref_glygen_ds", "GLY_001154", "protein_xref_glygen_ds", "GLY_001154", "110", "110", "Thr", "Thr" ], [ "P27958-1", "243", "Thr", "", "O-linked", "protein_xref_glygen_ds", "GLY_001154", "protein_xref_glygen_ds", "GLY_001154", "243", "243", "Thr", "Thr" ] ] }, "readme": "Name\n - HCV1a Predicted O-Glycosylation Sites (IsoGlyP)\n\nVersion\n - v-2.10.1\n\nCreated on\n - 2024-08-01T15:52:59\n\nModified on\n - 2024-12-05T16:25:35.119Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@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 HCV1a Predicted O-Glycosylation Sites dataset contains predicted Hepatitis C virus (isolate H77) (TaxID: 63746) O-linked Glycosylation sites derived from the IsoGlyP tool and mapped to UniProtKB canonical accessions . This tool was developed by Jonathon E Mohl and colleagues and aims to identify position-specific enhancement values that are derived from GalNAc-T isoform-specific amino acid preferences in order to estimate the likelihood of a site being glycosylated by a specific transferase. Predicted sites included in the dataset were selected based on meeting a stringent EVP threshold score of 10 or higher (https://isoglyp.utep.edu/).\n\nDescription Domain\n Keywords\n - O-Glycosylation\n - Predicted\n\n Pipeline Steps\n - Step-1: The script takes a path twords a canonical sequences fasta and runs it through the IsoGlyP O-Glycosylation prediction software. This process is slow so it is broken into 10 seperate processes.\n - Step-2: The script takes the output of the previous step and combines them into one final dataset.\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/\n - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/\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: output.hcv1a_legacy.csv\n URI: https:/data.glygen.org/ln2downloads/isoglyp/outputdb/output.hcv1a_legacy.csv\n Output Subdomain\n Name: hcv1a_proteoform_glycosylation_sites_predicted_isoglyp.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/hcv1a_proteoform_glycosylation_sites_predicted_isoglyp.csv\n Name: hcv1a_proteoform_glycosylation_sites_predicted_isoglyp.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/hcv1a_proteoform_glycosylation_sites_predicted_isoglyp.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"3\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"1\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"1\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\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: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"3\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"3\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.10.1/reviewed/hcv1a_proteoform_glycosylation_sites_predicted_isoglyp.csv" }