{ "bcoid": "GLY_000733", "title": "Rat Glycosylation Sites UniCarbKB Glycomics Study", "description": "The Rat UniCarbKB Glycomics Study contains Rattus norvegicus [taxid: 10116] glycan tissue expression ...", "filename_list": "rat_proteoform_glycosylation_sites_unicarbkb_glycomics_study.csv", "filename": "rat_proteoform_glycosylation_sites_unicarbkb_glycomics_study.csv", "filetype": "csv", "categories": { "species": [ "Rattus norvegicus" ], "molecule": [ "Proteoform" ], "tag": [ "UniCarbKB glycosylation sites glycomics study" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "...", "..." ], [ "...", "..." ] ], "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": "unicarbkb_id" }, { "type": "string", "label": "composition" }, { "type": "string", "label": "curation_notes" }, { "type": "string", "label": "additonal_notes" }, { "type": "string", "label": "protein" }, { "type": "string", "label": "position" }, { "type": "string", "label": "Id" }, { "type": "string", "label": "toucan" }, { "type": "string", "label": "type_amino_acid" }, { "type": "string", "label": "notes" }, { "type": "string", "label": "pmid" }, { "type": "string", "label": "additional_notes" }, { "type": "string", "label": "doi" }, { "type": "string", "label": "glytoucan_structure" }, { "type": "string", "label": "swiss_model" }, { "type": "string", "label": "source_tissue_id" }, { "type": "string", "label": "source_tissue_name" }, { "type": "string", "label": "species" }, { "type": "string", "label": "Uoxf" }, { "type": "string", "label": "HexNAc" }, { "type": "string", "label": "Hex" }, { "type": "string", "label": "dHex" }, { "type": "string", "label": "NeuAc" }, { "type": "string", "label": "abundance" }, { "type": "string", "label": "pdb" }, { "type": "string", "label": "related" }, { "type": "string", "label": "preprint" }, { "type": "string", "label": "peptide" }, { "type": "string", "label": "composition1" }, { "type": "string", "label": "composition2" }, { "type": "string", "label": "composition3" }, { "type": "string", "label": "pos_start" }, { "type": "string", "label": "pos_end" }, { "type": "string", "label": "doid" }, { "type": "string", "label": "disease_name" }, { "type": "string", "label": "RT" }, { "type": "string", "label": "GU" }, { "type": "string", "label": "Sia" }, { "type": "string", "label": "Fuc" }, { "type": "string", "label": "COMPLEX" }, { "type": "string", "label": "HM" }, { "type": "string", "label": "PM" }, { "type": "string", "label": "sample_preparation" }, { "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" } ], [ "", "", "", "G22768VO", "N-linked", "protein_xref_pubmed", "33993882", "protein_xref_unicarbkb_ds", "GLY_000733", "G22768VO", "", "", "Average peak area (%) in LPS-injected striatum", "", "", "G22768VO", "G22768VO", "", "HILIC-UPLC 2AB", "33993882", "Average peak area (%) in LPS-injected striatum", "10.1186/s12974-021-02163-6", "", "", "UBERON:0002435", "striatum", "Rattus norvegicus", "M3", "", "", "", "", "0.3680.078", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "BAO:0002016; lipopolysaccharide", "", "", "", "", "", "", "" ], [ "", "", "", "G35619UY", "N-linked", "protein_xref_pubmed", "33993882", "protein_xref_unicarbkb_ds", "GLY_000733", "G35619UY", "", "", "Average peak area (%) in LPS-injected striatum", "", "", "G35619UY", "G35619UY", "", "HILIC-UPLC 2AB", "33993882", "Average peak area (%) in LPS-injected striatum", "10.1186/s12974-021-02163-6", "", "", "UBERON:0002435", "striatum", "Rattus norvegicus", "M3B", "", "", "", "", "1.8840.183", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "BAO:0002016; lipopolysaccharide", "", "", "", "", "", "", "" ] ] }, "readme": "Name\n - Rat Glycosylation Sites UniCarbKB Glycomics Study\n\nVersion\n - v-2.10.1\n\nCreated on\n - 2023-03-10T03:58:50.149Z\n\nModified on\n - 2025-03-03T16:13:01.653Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@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 - Matthew Campbell [m.campbell2@griffith.edu.au]\n\nChecksum\n - \n\nUsability Domain\n - The Rat UniCarbKB Glycomics Study contains Rattus norvegicus [taxid: 10116] glycan tissue expression data. If you use this dataset please provide proper attribution to UniCarbKB and GlyGen. UniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. \n\nDescription Domain\n Keywords\n - Publications\n - Citations\n - PubMed\n - glycomics\n - UniCarbKB\n - glycan\n\n Pipeline Steps\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-2.10.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2025_09_18/cellosaurus.txt\n Name: known_unicarbkb_glycomics_study.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/known_unicarbkb_glycomics_study.csv\n Output Subdomain\n Name: rat_proteoform_glycosylation_sites_unicarbkb_glycomics_study.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/rat_proteoform_glycosylation_sites_unicarbkb_glycomics_study.csv\n Name: rat_proteoform_glycosylation_sites_unicarbkb_glycomics_study.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/rat_proteoform_glycosylation_sites_unicarbkb_glycomics_study.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: \"1\"\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: \"57\"\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: \"1\"\n Name: \"unicarbkb_id\"\n Description: \"UnicarbKB database identifier\"\n Unique Values: \"57\"\n Name: \"composition\"\n Description: \"Composition of glycan\"\n Unique Values: \"1\"\n Name: \"curation_notes\"\n Description: \"GlycoSuiteDB curation notes\"\n Unique Values: \"1\"\n Name: \"additonal_notes\"\n Description: \"Additonal curation notes from UniCarbKB database\"\n Unique Values: \"6\"\n Name: \"protein\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"position\"\n Description: \"Chromosome position of a gene\"\n Unique Values: \"1\"\n Name: \"Id\"\n Description: \"\"\n Unique Values: \"57\"\n Name: \"toucan\"\n Description: \"\"\n Unique Values: \"57\"\n Name: \"type_amino_acid\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"notes\"\n Description: \"Notes\"\n Unique Values: \"2\"\n Name: \"pmid\"\n Description: \"NCBI PubMed database Identifier\"\n Unique Values: \"2\"\n Name: \"additional_notes\"\n Description: \"\"\n Unique Values: \"6\"\n Name: \"doi\"\n Description: \"Digital Object Identifier of a publication. \"\n Unique Values: \"2\"\n Name: \"glytoucan_structure\"\n Description: \"GlyTouCan accession associated with the structure of the glycan. \"\n Unique Values: \"1\"\n Name: \"swiss_model\"\n Description: \"SWISS-MODEL ID.\"\n Unique Values: \"1\"\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: \"species\"\n Description: \"Species of the protein.\"\n Unique Values: \"1\"\n Name: \"Uoxf\"\n Description: \"\"\n Unique Values: \"59\"\n Name: \"HexNAc\"\n Description: \"Abbreviation for N-Acetylhexosamine monosaccharide residue\"\n Unique Values: \"1\"\n Name: \"Hex\"\n Description: \"Abbreviation for Hexose monosaccharide residue\"\n Unique Values: \"1\"\n Name: \"dHex\"\n Description: \"Abbreviation for Deoxyhexose monosaccharide residue\"\n Unique Values: \"1\"\n Name: \"NeuAc\"\n Description: \"Abbreviation for N-Acetylneuraminic Acid monosaccharide residue\"\n Unique Values: \"1\"\n Name: \"abundance\"\n Description: \" Abundance ratio of the glycan.\"\n Unique Values: \"164\"\n Name: \"pdb\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"related\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"preprint\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"peptide\"\n Description: \"Protein peptide\"\n Unique Values: \"1\"\n Name: \"composition1\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"composition2\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"composition3\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"pos_start\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"pos_end\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"doid\"\n Description: \"Disease ID from Disease ontology database\"\n Unique Values: \"1\"\n Name: \"disease_name\"\n Description: \"The name of the disease\"\n Unique Values: \"1\"\n Name: \"RT\"\n Description: \"\"\n Unique Values: \"40\"\n Name: \"GU\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"Sia\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"Fuc\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"COMPLEX\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"HM\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"PM\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"sample_preparation\"\n Description: \"Method of the sample preparation\"\n Unique Values: \"2\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"1\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"1\"\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-2.10.1/reviewed/rat_proteoform_glycosylation_sites_unicarbkb_glycomics_study.csv" }