{ "bcoid": "GLY_000493", "title": "Rat Glycosylation Sites [Automatic Literature Mining] [Automatically verified]", "description": "The Rat Glycosylation Sites [Automatic Literature Mining] [Automatically verified] dataset contains a ...", "filename_list": "rat_proteoform_glycosylation_sites_literature_mining.csv", "filename": "rat_proteoform_glycosylation_sites_literature_mining.csv", "filetype": "csv", "categories": { "status": [ "Reviewed" ], "molecule": [ "Proteoform" ], "species": [ "Rattus norvegicus" ], "tag": [ "glycosylation sites" ], "file_type": [ "csv" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "O35433-1...", "604..." ], [ "P09951-1...", "576..." ] ], "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": "mining_tools" }, { "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" }, { "type": "string", "label": "isoform_mapping_notes" } ], [ "O35433-1", "604", "Asn", "", "N-linked", "protein_xref_pubmed", "15931076", "protein_xref_glygen_ds", "GLY_000493", "RLIMS-G_1.0", "NNS", "NXS", "604", "604", "Asn", "Asn", "N", "" ], [ "P09951-1", "576", "Ser", "", "O-linked", "protein_xref_pubmed", "10386995", "protein_xref_glygen_ds", "GLY_000493", "RLIMS-G_1.0;GlycoSiteMiner_1.0", "", "", "576", "576", "Ser", "Ser", "S", "" ] ] }, "readme": "Name\n - Rat Glycosylation Sites [Automatic Literature Mining] [Automatically verified]\n\nVersion\n - v-2.10.1\n\nCreated on\n - 2020-04-30T10:34:38.124446\n\nModified on\n - 2025-04-15T13:37:28.428Z\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 - Vijay Shanker [vijay@udel.edu], Karen Ross [ker25@georgetown.edu]\n\nChecksum\n - \n\nUsability Domain\n - The Rat Glycosylation Sites [Automatic Literature Mining] [Automatically verified] dataset contains a list of Rattus norvegicus [taxid:10116] proteins with information on glycosylation sites detected from PubMed database (abstracts-only) through the Automatic mining tools 'RLIMS-G' developed by Dr. Vijay Shanker (University of Delaware) and 'GlycoSiteMiner' developed by the GlyGen team (https://github.com/glygener/glycositeminer). The listed protein (UniProtKB) accessions are part of the GlyGen UniProtKB canonical list (https://data.glygen.org/GLY_000244)\n\nDescription Domain\n Keywords\n - proteins\n - canonical\n - glycosylation sites\n - GlyTouCan\n - Automatic Literature Mining\n\n Pipeline Steps\n - Step-1: The input file was downloaded from the provider(s) and QC steps were done to validate the protein and site annotation. Additional QC was done to check wether the annotion (protein +site) is already present in GlyGen or not. Only those rows which passed all the QC filters where added to the output file. \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: glycosylation_sites_GlycoSiteMiner_1.0.csv\n URI: https:/data.glygen.org/ln2downloads/lit_min/2021_04_08/glycosylation_sites_GlycoSiteMiner_1.0.csv\n Name: glycosylation_sites_RLIMS-G_1.0.csv\n URI: https:/data.glygen.org/ln2downloads/lit_min/2021_04_08/glycosylation_sites_RLIMS-G_1.0.csv\n Name: glycosylation_sites_GlycoSiteMiner_2.0.csv\n URI: https:/data.glygen.org/ln2downloads/lit_min/2024_09_30/glycosylation_sites_GlycoSiteMiner_2.0.csv\n Name: glycosylation_sites_GlycoSiteMiner_4.0.csv\n URI: https:/data.glygen.org/ln2downloads/lit_min/2025_11_05/glycosylation_sites_GlycoSiteMiner_4.0.csv\n Output Subdomain\n Name: rat_proteoform_glycosylation_sites_literature_mining.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/rat_proteoform_glycosylation_sites_literature_mining.csv\n Name: rat_proteoform_glycosylation_sites_literature_mining.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/rat_proteoform_glycosylation_sites_literature_mining.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"64\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"112\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"5\"\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: \"3\"\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: \"68\"\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: \"mining_tools\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"36\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"6\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"112\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"112\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"5\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"5\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"5\"\n Name: \"isoform_mapping_notes\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.10.1/reviewed/rat_proteoform_glycosylation_sites_literature_mining.csv" }