{ "bcoid": "GLY_000955", "title": "Pig O-GlcNAc Glycosylation Sites (O-GlcNAc Atlas)", "description": "The Pig O-GlcNAc Glycosylation Sites (O-GlcNAc Atlas) contains Sus scrofa (taxid:9823) O-GlcNAc modifications ...", "filename_list": "pig_proteoform_glycosylation_sites_oglcnac_atlas.csv", "filename": "pig_proteoform_glycosylation_sites_oglcnac_atlas.csv", "filetype": "csv", "categories": { "species": [ "Sus scrofa" ], "molecule": [ "Proteoform" ], "tag": [ "O-GlcNAc Glycosylation Sites (O-GlcNAc Atlas)" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "...", "28..." ], [ "Q8WMH1-1...", "28..." ] ], "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": "sample_type" }, { "type": "string", "label": "method" }, { "type": "string", "label": "analytical_throughput" }, { "type": "string", "label": "condition" }, { "type": "string", "label": "log2Ratio" }, { "type": "string", "label": "p_value" }, { "type": "string", "label": "notes" }, { "type": "string", "label": "carb_name" }, { "type": "string", "label": "glycosylation_subtype" }, { "type": "string", "label": "source_tissue_id" }, { "type": "string", "label": "source_tissue_name" }, { "type": "string", "label": "source_cell_line_cellosaurus_id" }, { "type": "string", "label": "source_cell_line_cellosaurus_name" }, { "type": "string", "label": "peptide" }, { "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" } ], [ "", "28", "", "G49108TO", "O-linked", "protein_xref_pubmed", "26192747", "protein_xref_oglcnac_atlas", "", "brain", "MS", "HTP", "", "", "", "", "", "", "UBERON:0000955", "brain", "", "", "", "28", "28", "", "", "" ], [ "Q8WMH1-1", "28", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "30740091", "protein_xref_oglcnac_atlas", "Q8WMH1", "nasal tissue", "MS", "LTP", "", "", "", "This site was described as 'S13' in the original paper.", "GlcNAc", "O-GlcNAcylation", "NCIT:C164006", "Nasal Soft Tissue", "", "", "DPFEL-S-GKWIT", "28", "28", "Ser", "Ser", "S" ] ] }, "readme": "Name\n - Pig O-GlcNAc Glycosylation Sites (O-GlcNAc Atlas)\n\nVersion\n - v-2.8.1\n\nCreated on\n - \n\nModified on\n - 2024-05-17T11:24:19.755Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Jingyue Wu [jingyue.wu@email.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 - Jungfeng Ma [junfeng.ma@georgetown.edu ]\n\nChecksum\n - \n\nUsability Domain\n - The Pig O-GlcNAc Glycosylation Sites (O-GlcNAc Atlas) contains Sus scrofa (taxid:9823) O-GlcNAc modifications on Serine and Threonine extracted from the publication and mapped to the UniProtKB canonical accession and fasta sequence. The GlyTouCan ID for the O-GlcNAc is G49108TO.\n\nDescription Domain\n Keywords\n - O-GlcNAc\n - Serine\n - Threonine\n\n Pipeline Steps\n - Step-1: The script maps the UniProtKB accesions to the UniProtKB Canonical accessions and also checks the position and amino acid of O-GlcNAc modified residue against UniProtKB Canonical sequences. The script also maps the sample type to correct sample term id and sample term name.\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: pig_protein_info_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/pig_protein_info_uniprotkb.csv\n Name: pig_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/pig_protein_masterlist.csv\n Name: pig_protein_recnames.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/pig_protein_recnames.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/misc/sample_mapping.csv\n Name: ambiguous_sites.csv\n URI: https:/data.glygen.org/ln2downloads/atlas_oglcnac/2025_01_14/ambiguous_sites.csv\n Name: unambiguous_sites.csv\n URI: https:/data.glygen.org/ln2downloads/atlas_oglcnac/2025_01_14/unambiguous_sites.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2025_01_13/cellosaurus.txt\n Output Subdomain\n Name: pig_proteoform_glycosylation_sites_oglcnac_atlas.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/pig_proteoform_glycosylation_sites_oglcnac_atlas.csv\n Name: pig_proteoform_glycosylation_sites_oglcnac_atlas.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/pig_proteoform_glycosylation_sites_oglcnac_atlas.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\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: \"2\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"2\"\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: \"2\"\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: \"2\"\n Name: \"sample_type\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"method\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"analytical_throughput\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"condition\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"log2Ratio\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"p_value\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"notes\"\n Description: \"Notes\"\n Unique Values: \"3\"\n Name: \"carb_name\"\n Description: \"carbohydrate name\"\n Unique Values: \"2\"\n Name: \"glycosylation_subtype\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"source_tissue_id\"\n Description: \"Tissue ID from GlyConnect\"\n Unique Values: \"2\"\n Name: \"source_tissue_name\"\n Description: \"Tissue NAME from GlyConnect\"\n Unique Values: \"2\"\n Name: \"source_cell_line_cellosaurus_id\"\n Description: \"cellosaurus ID of the cell line\"\n Unique Values: \"1\"\n Name: \"source_cell_line_cellosaurus_name\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"peptide\"\n Description: \"Protein peptide\"\n Unique Values: \"3\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"2\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"2\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.8.1/reviewed/pig_proteoform_glycosylation_sites_oglcnac_atlas.csv" }