{ "bcoid": "GLY_000499", "title": "GlyGen-PubChem Protein Crossreferences Mapping", "description": "The GlyGen-PubChem Protein Crossreferences dataset contains UniProtKB glycoprotein accessions for human ...", "filename": "protein_glygen_pubchem_xref_mapping.csv", "filetype": "csv", "categories": { "molecule": "Protein", "tags": "GlyGen-PubChem Protein Crossreferences", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q9P1W8...", "NP_001034597..." ], [ "P24387...", "NP_001873.2..." ] ], "headers": [ "uniprotkb_ac...", "refseq_ac..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_ac" }, { "type": "string", "label": "refseq_ac" }, { "type": "string", "label": "glycosylation_annotation" } ], [ "Q9P1W8", "NP_001034597.1", "4 sites" ], [ "P24387", "NP_001873.2", "1 site" ], [ "Q8N3G9", "NP_001127922.1", "3 sites" ], [ "P14625", "NP_003290.1", "8 sites" ], [ "Q07444", "NP_002252.2", "3 sites" ], [ "D3ZLH5", "NP_001129350.1", "9 sites" ], [ "Q7M758", "NP_001009546.1", "10 sites" ], [ "P15260", "NP_000407.1", "5 sites, 4 N-linked glycans (4 sites)" ], [ "P22272", "NP_034689.2", "3 sites" ], [ "Q80TS8", "NP_766298.2", "3 sites" ], [ "Q5QD23", "NP_001009650.1", "1 site" ], [ "A5D8T8", "NP_001129686.1", "2 sites, 1 O-linked glycan (1 site)" ], [ "O14657", "NP_001304822.1", "2 sites" ], [ "Q9Z137", "NP_072131.1", "2 sites" ], [ "Q96L08", "NP_001273935.1", "1 site" ], [ "Q96LB9", "NP_443123.1", "1 site" ], [ "Q8N394", "NP_001307250.1", "1 site" ], [ "Q9BZW8", "NP_001160135.1", "8 sites" ], [ "P24046", "NP_001243632.1", "3 sites" ], [ "Q6AYF4", "NP_001004263.1", "10 sites" ], [ "Q99MF4", "NP_620816.1", "2 sites" ], [ "Q70EX6", "NP_932166.1", "2 sites" ], [ "Q16538", "NP_055264.1", "1 site" ], [ "P25100", "NP_000669.1", "2 sites" ], [ "P13284", "NP_006323.2", "5 sites, 1 N-linked glycan (1 site)" ], [ "Q14BI1", "NP_001103710.1", "1 site" ], [ "P47801", "NP_001275556.1", "3 sites" ], [ "Q63484", "NP_113763.1", "2 sites" ], [ "P41274", "NP_033430.1", "3 sites" ], [ "O75019", "NP_001265247.1", "6 sites" ], [ "P70663", "NP_034227.3", "3 sites" ], [ "Q9UPC5", "NP_001091048.1", "5 sites" ], [ "A6NHS7", "NP_001139693.1", "3 sites" ], [ "Q8NFQ6", "NP_777592.1", "10 sites" ], [ "Q9WTR5", "NP_062681.2", "8 sites" ], [ "Q09666", "NP_001333374.1", "3 sites, 1 O-linked glycan (3 sites)" ], [ "O88909", "NP_001158106.1", "1 site" ], [ "Q8K596", "NP_001334490.1", "2 sites" ], [ "Q9QYZ9", "NP_038949.2", "2 sites" ], [ "Q8NG95", "NP_001001958.1", "2 sites" ], [ "P10111", "NP_058797.1", "1 site" ], [ "P51868", "NP_058827.3", "1 site" ], [ "Q8VCH9", "NP_666164.1", "2 sites" ], [ "P69478", "NP_001101549.1", "4 sites" ], [ "Q9EPK6", "NP_109674.2", "2 sites" ], [ "Q9UBS5", "NP_001305982.1", "7 sites" ], [ "P07759", "NP_035588.2", "4 sites, 2 N-linked glycans (2 sites)" ], [ "Q16762", "NP_001257412.1", "1 site" ], [ "P11831", "NP_001278930.1", "5 sites" ], [ "P49771", "NP_001191431.1", "2 sites" ], [ "Q9R2B6", "NP_001263354.1", "1 site" ], [ "Q9H7Y0", "NP_078965.2", "1 site" ], [ "Q9QZE3", "NP_640355.1", "2 sites" ], [ "P97707", "NP_062128.1", "2 sites" ], [ "P51674", "NP_001248377.1", "2 sites" ], [ "Q9JM73", "NP_065239.1", "5 sites" ], [ "Q6UVK1", "NP_001888.2", "18 sites, 1 N-linked glycan (1 site), 3 O-linked glycans (2 sites)" ], [ "Q8NHV5", "NP_001158051.1", "1 site" ], [ "Q92911", "NP_000444.1", "2 sites" ], [ "Q3L7M0", "NP_663707.1", "1 site" ], [ "P01592", "NP_690052.2", "1 site, 2 N-linked glycans (1 site)" ], [ "Q9BQT9", "NP_055533.2", "5 sites" ], [ "Q91WN2", "NP_659165.1", "2 sites" ], [ "Q96A11", "NP_149025.1", "4 sites" ], [ "Q8VFK2", "NP_666784.2", "1 site" ], [ "P0C588", "NP_001257979.1", "1 site" ], [ "P01864", "", "1 site" ], [ "P70277", "NP_033206.2", "2 sites" ], [ "Q9EQF4", "NP_075026.1", "2 sites" ], [ "Q96DN0", "NP_001287713.1", "1 site" ], [ "Q9CZ42", "NP_001177286.1", "1 site" ], [ "P51684", "NP_004358.2", "2 sites" ], [ "P43406", "NP_032428.2", "12 sites" ], [ "O14798", "NP_003832.2", "4 sites, 1 O-linked glycan (1 site)" ], [ "P61009", "NP_068747.1", "1 site" ], [ "Q8NGK2", "NP_001005161.2", "1 site" ], [ "Q9P0T7", "NP_001275499.1", "4 sites" ], [ "Q8NHB7", "NP_001004736.2", "1 site" ], [ "Q9QXN2", "NP_612546.1", "3 sites" ], [ "P39039", "NP_034905.1", "4 sites" ], [ "A0A0C4DH28", "", "1 site" ], [ "Q60682", "NP_001095090.1", "2 sites" ], [ "Q96LR9", "NP_001123887.1", "3 sites, 1 O-linked glycan (3 sites)" ], [ "Q9NT22", "NP_443078.1", "6 sites, 1 O-linked glycan (1 site)" ] ] }, "readme": "Name\n - GlyGen-PubChem Protein Crossreferences Mapping\n\nVersion\n - 1.5.30\n\nCreated on\n - 2020-06-04T09:25:12.224023\n\nModified on\n - 2020-06-04T13:29:28.212206\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The GlyGen-PubChem Protein Crossreferences dataset contains UniProtKB glycoprotein accessions for human [taxid:9606], mouse [taxid:10090], rat [taxid:10116], hcv1a [taxid:11108], hcv1b [taxid:11116], sarscov1 [taxid:694009] and sarscov2 [taxid:2697049] glycoproteins for the purpose of PubChem Protein to GlyGen crossreferences. In the dataset, the UniProtKB glycoprotein accessions are mapped to the RefSeq accesions and glycosylation annotation corresponding to glycoprotein have been added. The glycosylation annotation provides information about total (N,O,S,C) glycosylation sites followed by (if available) reported N-glycans and/or reported O-glycans with the number of sites. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB, NCBI RefSeq and GlyGen\n\nDescription Domain\n Keywords\n - PubChem Protein\n - GlyGen\n - crossreferences\n - human\n - mouse\n - rat\n - hcv1a\n - hcv1b\n - sarscov1\n - sarscov2\n - NCBI RefSeq\n\n Pipeline Steps\n - Step-1: The script loads the GlyGen's UniProtKB protein accessions for human, mouse, rat, hcv1a, hcv1b, sarscov1 and sarscov2 species and maps it to the refseq accessions and adds the corresponding glycosylation annotation to extract it into a csv dataset file\n\nExecution Domain\n Scripts\n\n Software Prerequisites\n\nI/O Domain\n Input Subdomain\n Name: human_proteoform_glycosylation_sites_glyconnect.csv\n URI: human_proteoform_glycosylation_sites_glyconnect.csv\n Name: human_proteoform_glycosylation_sites_gptwiki.csv\n URI: human_proteoform_glycosylation_sites_gptwiki.csv\n Name: human_proteoform_glycosylation_sites_harvard.csv\n URI: human_proteoform_glycosylation_sites_harvard.csv\n Name: human_proteoform_glycosylation_sites_literature.csv\n URI: human_proteoform_glycosylation_sites_literature.csv\n Name: human_proteoform_glycosylation_sites_pdb.csv\n URI: human_proteoform_glycosylation_sites_pdb.csv\n Name: human_proteoform_glycosylation_sites_tyr_o_linked.csv\n URI: human_proteoform_glycosylation_sites_tyr_o_linked.csv\n Name: human_proteoform_glycosylation_sites_unicarbkb.csv\n URI: human_proteoform_glycosylation_sites_unicarbkb.csv\n Name: human_proteoform_glycosylation_sites_uniprotkb.csv\n URI: human_proteoform_glycosylation_sites_uniprotkb.csv\n Name: mouse_proteoform_glycosylation_sites_glyconnect.csv\n URI: mouse_proteoform_glycosylation_sites_glyconnect.csv\n Name: mouse_proteoform_glycosylation_sites_pdb.csv\n URI: mouse_proteoform_glycosylation_sites_pdb.csv\n Name: mouse_proteoform_glycosylation_sites_unicarbkb.csv\n URI: mouse_proteoform_glycosylation_sites_unicarbkb.csv\n Name: mouse_proteoform_glycosylation_sites_uniprotkb.csv\n URI: mouse_proteoform_glycosylation_sites_uniprotkb.csv\n Name: rat_proteoform_glycosylation_sites_glyconnect.csv\n URI: rat_proteoform_glycosylation_sites_glyconnect.csv\n Name: rat_proteoform_glycosylation_sites_pdb.csv\n URI: rat_proteoform_glycosylation_sites_pdb.csv\n Name: rat_proteoform_glycosylation_sites_unicarbkb.csv\n URI: rat_proteoform_glycosylation_sites_unicarbkb.csv\n Name: rat_proteoform_glycosylation_sites_uniprotkb.csv\n URI: rat_proteoform_glycosylation_sites_uniprotkb.csv\n Name: sarscov1_proteoform_glycosylation_sites_uniprotkb.csv\n URI: sarscov1_proteoform_glycosylation_sites_uniprotkb.csv\n Name: sarscov2_proteoform_citations_unicarbkb_literature.csv\n URI: sarscov2_proteoform_citations_unicarbkb_literature.csv\n Name: sarscov2_proteoform_glycosylation_sites_unicarbkb.csv\n URI: sarscov2_proteoform_glycosylation_sites_unicarbkb.csv\n Name: sarscov2_proteoform_glycosylation_sites_uniprotkb.csv\n URI: sarscov2_proteoform_glycosylation_sites_uniprotkb.csv\n Name: hcv1a_proteoform_glycosylation_sites_literature.csv\n URI: hcv1a_proteoform_glycosylation_sites_literature.csv\n Name: hcv1a_proteoform_glycosylation_sites_uniprotkb.csv\n URI: hcv1a_proteoform_glycosylation_sites_uniprotkb.csv\n Name: hcv1b_proteoform_glycosylation_sites_uniprotkb.csv\n URI: hcv1b_proteoform_glycosylation_sites_uniprotkb.csv\n Name: human_protein_xref_refseq.csv\n URI: human_protein_xref_refseq.csv\n Name: mouse_protein_xref_refseq.csv\n URI: mouse_protein_xref_refseq.csv\n Name: rat_protein_xref_refseq.csv\n URI: rat_protein_xref_refseq.csv\n Name: sarscov1_protein_xref_refseq.csv\n URI: sarscov1_protein_xref_refseq.csv\n Output Subdomain\n Name: protein_glygen_pubchem_xref_mapping.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/protein_glygen_pubchem_xref_mapping.csv\n Name: protein_glygen_pubchem_xref_mapping.stat.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/protein_glygen_pubchem_xref_mapping.stat.csv\n\nFields\n Name: \"uniprotkb_ac\"\n Description: \"Accession assigned to the protein in the UniProtKB database\"\n Unique Values: \"11240\"\n Name: \"refseq_ac\"\n Description: \"Accession in the NCBI RefSeq database\"\n Unique Values: \"10489\"\n Name: \"glycosylation_annotation\"\n Description: \"\"\n Unique Values: \"585\"", "downloadurl": "/ln2data/releases/data/v-1.5.30/reviewed/protein_glygen_pubchem_xref_mapping.csv" }