{ "bcoid": "GLY_000733", "title": "Rat Glycosylation Sites UniCarbKB Glycomics Study", "description": "", "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-2.5.1\n\nCreated on\n - 2023-03-10T03:58:50.149Z\n\nModified on\n - 2024-05-17T11:24:11.105Z\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\nDescription Domain\n Keywords\n - Publications\n - Citations\n - PubMed\n - glycomics\n - UniCarbKB\n - glycan\n\n Pipeline Steps\n - Step-1: \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-2.5.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2024_04_02/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-2.5.1/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-2.5.1/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: \"55\"\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: \"55\"\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: \"55\"\n Name: \"toucan\"\n Description: \"\"\n Unique Values: \"55\"\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: \"57\"\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: \"159\"\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: \"38\"\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-2.5.1/reviewed/rat_proteoform_glycosylation_sites_unicarbkb_glycomics_study.csv" }