{ "bcoid": "GLY_000480", "title": "Human Glycosylation Sites [GPTwiki]", "description": "Human Glycosylation Sites [GPTwiki], provided by the Clinical and Translational Glycoscience Research ...", "filename_list": "human_proteoform_glycosylation_sites_gptwiki.csv", "filename": "human_proteoform_glycosylation_sites_gptwiki.csv", "filetype": "csv", "categories": { "status": [ "Reviewed" ], "molecule": [ "Proteoform" ], "species": [ "Homo sapiens" ], "tag": [ "glycosylation sites" ], "file_type": [ "csv" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "O00754-1...", "692..." ], [ "O00754-1...", "930..." ] ], "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": "glycopeptide_id" }, { "type": "string", "label": "composition" }, { "type": "string", "label": "glycan_xref_key" }, { "type": "string", "label": "glycan_xref_id" }, { "type": "string", "label": "n_sequon" }, { "type": "string", "label": "n_sequon_type" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "start_aa" }, { "type": "string", "label": "end_aa" }, { "type": "string", "label": "site_seq" } ], [ "O00754-1", "692", "Asn", "G28681TP", "N-linked", "protein_xref_gptwiki", "O00754@N692", "protein_xref_gptwiki", "O00754@N692", "PE001986", "HexNAc(2)Hex(3)", "glycan_xref_gptwiki", "G28681TP", "NFS", "NXS", "692", "692", "Asn", "Asn", "N" ], [ "O00754-1", "930", "Asn", "G41247ZX", "N-linked", "protein_xref_gptwiki", "O00754@N930", "protein_xref_gptwiki", "O00754@N930", "PE002013", "HexNAc(2)Hex(6)", "glycan_xref_gptwiki", "G41247ZX", "NLS", "NXS", "930", "930", "Asn", "Asn", "N" ] ] }, "readme": "Name\n - Human Glycosylation Sites [GPTwiki]\n\nVersion\n - v-2.9.1\n\nCreated on\n - 2020-04-20T16:33:02.961632\n\nModified on\n - 2024-05-17T11:24:02.137Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@email.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 - Nathan Edwards [Georgetown University], Radoslav Goldman [rg26@georgetown.edu]\n\nChecksum\n - \n\nUsability Domain\n - Human Glycosylation Sites [GPTwiki], provided by the Clinical and Translational Glycoscience Research Center (CTGRC), Georgetown University. The database contains list of human [taxid:9606] proteins with information on glycosylation sites and associated glycans from GPTwiki database [https://edwardslab.bmcb.georgetown.edu/gptwiki/Main_Page]. The listed protein (UniProtKB) accessions are part of the GlyGen UniProtKB canonical list (https://data.glygen.org/GLYDS000001)\n\nDescription Domain\n Keywords\n - proteins\n - canonical\n - glycosylation sites\n - glycan\n - GPTwiki\n - GlyTouCan\n\n Pipeline Steps\n - Step-1: The input file was downloaded from the provider(s). Following QC steps were done using a python script: 1. Map the first column (UniProt) to UniProtKB canonical accession 2. Validate the Site and AminoAcid column with the canonical .fasta sequences. 3. Split the rows if the last column (Glycopeptides) has multiple values (separated by | ) 4. Add a new column for \"database\" with value \"GPTwiki\"\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: n_sequon_info.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2025_05_19/cellosaurus.txt\n Name: glycosites.csv\n URI: https:/data.glygen.org/ln2downloads/gptwiki/gpt_2021_06_23_14_51_10/glycosites.csv\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_gptwiki.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/human_proteoform_glycosylation_sites_gptwiki.csv\n Name: human_proteoform_glycosylation_sites_gptwiki.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/human_proteoform_glycosylation_sites_gptwiki.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"140\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"217\"\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: \"101\"\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: \"280\"\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: \"280\"\n Name: \"glycopeptide_id\"\n Description: \"Glycopeptide Id from GPTwiki database. \"\n Unique Values: \"1701\"\n Name: \"composition\"\n Description: \"Composition of glycan\"\n Unique Values: \"101\"\n Name: \"glycan_xref_key\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"glycan_xref_id\"\n Description: \"\"\n Unique Values: \"101\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"38\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"217\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"217\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.9.1/reviewed/human_proteoform_glycosylation_sites_gptwiki.csv" }