{ "bcoid": "GLY_000336", "title": "Mouse Xref GlycoProtDB", "description": "The Mouse (TaxID:10090) Xref GlycoProtDB contains x-refs to IDs present in the GlycoProtDB database ...", "filename": "mouse_protein_xref_glycoprotdb.csv", "filetype": "csv", "categories": { "species": "Mus musculus", "molecule": "Protein", "tags": "GlycoProtDB cross-references", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q8BH24-1...", "GPDB0006196..." ], [ "Q8BH27-1...", "GPDB0006197..." ] ], "headers": [ "uniprotkb_ca...", "database_id..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "database_id" }, { "type": "string", "label": "database_label" } ], [ "Q8BH24-1", "GPDB0006196", "Transmembrane 9 superfamily member 4" ], [ "Q8BH27-1", "GPDB0006197", "Multiple epidermal growth factor-like domains protein 9" ], [ "Q07968-1", "GPDB0003929", "Coagulation factor XIII B chain" ], [ "Q61400-1", "GPDB0005478", "Carcinoembryonic antigen-related cell adhesion molecule 10" ], [ "Q61406-1", "GPDB0005480", "Complement factor H-related 1" ], [ "P70412-1", "GPDB0003775", "CUB and zona pellucida-like domain-containing protein 1" ], [ "P70419-1", "GPDB0003776", "Polypeptide N-acetylgalactosaminyltransferase 3" ], [ "Q9EP78-1", "GPDB0007489", "Carbohydrate sulfotransferase 7" ], [ "Q9EP73-1", "GPDB0007488", "Programmed cell death 1 ligand 1" ], [ "P50429-1", "GPDB0003660", "Arylsulfatase B" ], [ "Q8BTJ4-1", "GPDB0006382", "Bis(5'-adenosyl)-triphosphatase enpp4" ], [ "Q7M729-1", "GPDB0005955", "Sodium channel subunit beta-4" ], [ "P21661-1", "GPDB0003478", "Neuroendocrine convertase 2" ], [ "O88668-1", "GPDB0003221", "Protein CREG1" ], [ "Q3TNL8-1", "GPDB0004304", "Inositol 1,4,5-trisphosphate receptor-interacting protein" ], [ "Q9WVL3-1", "GPDB0007812", "Solute carrier family 12 member 7" ], [ "Q9QUN7-1", "GPDB0007648", "Toll-like receptor 2" ], [ "Q9QUN9-1", "GPDB0007649", "Dickkopf-related protein 3" ], [ "Q9WUZ9-1", "GPDB0007798", "Ectonucleoside triphosphate diphosphohydrolase 5" ], [ "Q9ESN3-1", "GPDB0007533", "Transmembrane protein 8A" ], [ "O88307-1", "GPDB0003201", "Sortilin-related receptor" ], [ "Q8VCU1-1", "GPDB0006965", "Carboxylesterase 3B" ], [ "P35438-1", "GPDB0003585", "Glutamate receptor ionotropic, NMDA 1" ], [ "Q67BT3-1", "GPDB0005671", "Solute carrier family 13 member 5" ], [ "P27467-1", "GPDB0003528", "Protein Wnt-3a" ], [ "Q8VEK0-1", "GPDB0006987", "Cell cycle control protein 50A" ], [ "Q923B6-1", "GPDB0007168", "Metalloreductase STEAP4" ], [ "Q61614-1", "GPDB0005507", "Endothelin-1 receptor" ], [ "P43006-1", "GPDB0003624", "Excitatory amino acid transporter 2" ], [ "P16294-1", "GPDB0003428", "Coagulation factor IX" ], [ "J3QNS5-1", "GPDB0002999", "Protein Mfsd4b4" ], [ "P14429-1", "GPDB0003387", "H-2 class I histocompatibility antigen, Q7 alpha chain" ], [ "Q8BMD6-1", "GPDB0006292", "Transmembrane protein 260" ], [ "Q3UT41-1", "GPDB0004926", "Lipase" ], [ "Q9R0M4-1", "GPDB0007711", "Podocalyxin" ], [ "Q9R0M0-1", "GPDB0007709", "Cadherin EGF LAG seven-pass G-type receptor 2" ], [ "Q9QXC1-1", "GPDB0007659", "Fetuin-B" ], [ "Q8R2S8-1", "GPDB0006862", "CD177 antigen" ], [ "P22437-1", "GPDB0003487", "Prostaglandin G/H synthase 1" ], [ "P34927-1", "GPDB0003577", "Asialoglycoprotein receptor 1" ], [ "Q9EPK8-1", "GPDB0007493", "Transient receptor potential cation channel subfamily V member 4" ], [ "Q9EPK6-1", "GPDB0007492", "Nucleotide exchange factor SIL1" ], [ "Q9JLF7-1", "GPDB0007609", "Toll-like receptor 5" ], [ "Q80T41-1", "GPDB0006029", "Gamma-aminobutyric acid type B receptor subunit 2" ], [ "P01867-1", "GPDB0003255", "Ig gamma-2B chain C region" ], [ "O55026-1", "GPDB0003160", "Ectonucleoside triphosphate diphosphohydrolase 2" ], [ "Q06890-1", "GPDB0003921", "Clusterin" ], [ "O54998-1", "GPDB0003157", "Peptidyl-prolyl cis-trans isomerase FKBP7" ], [ "O54990-1", "GPDB0003150", "Prominin-1" ], [ "O54991-1", "GPDB0003156", "Contactin-associated protein 1" ], [ "P63056-1", "GPDB0003740", "Noelin-3" ], [ "Q80TS3-1", "GPDB0006039", "Adhesion G protein-coupled receptor L3" ], [ "Q80TS8-1", "GPDB0006044", "Protein sel-1 homolog 3" ], [ "Q6S9I3-1", "GPDB0005870", "HMW kininogen-II" ], [ "Q7TQH7-1", "GPDB0006005", "Low-density lipoprotein receptor-related protein 10" ], [ "P11627-1", "GPDB0003354", "Neural cell adhesion molecule L1" ], [ "Q8VBZ3-1", "GPDB0006931", "Cleft lip and palate transmembrane protein 1 homolog" ], [ "Q91Y57-1", "GPDB0007102", "Sialic acid-binding Ig-like lectin 12" ], [ "Q8BPX9-1", "GPDB0006335", "Solute carrier family 15 member 3" ], [ "Q6PZE0-1", "GPDB0005855", "Mucin-19" ], [ "Q64302-1", "GPDB0005628", "Transmembrane 4 L6 family member 1" ], [ "Q3TDQ1-1", "GPDB0004218", "Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B" ], [ "Q9JL06-1", "GPDB0007595", "Lysophosphatidic acid receptor 2" ], [ "V9GXA7-1", "GPDB0007912", "Protein Gm15294" ], [ "Q9JIM1-1", "GPDB0007559", "Equilibrative nucleoside transporter 1" ], [ "P05555-1", "GPDB0003285", "Integrin alpha-M" ], [ "F8VPK8-1", "GPDB0002794", "Protein Pcdh9" ], [ "Q3URE9-1", "GPDB0004905", "Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 2" ], [ "Q3UHN9-1", "GPDB0004800", "Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1" ], [ "Q9DA79-1", "GPDB0007434", "Dipeptidase 3" ], [ "Q9DA75-1", "GPDB0007432", "Sodium-dependent lysophosphatidylcholine symporter 1" ], [ "Q9DA77-1", "GPDB0007433", "Testis-expressed sequence 29 protein" ], [ "Q01279-1", "GPDB0003854", "Epidermal growth factor receptor" ], [ "P15920-1", "GPDB0003418", "V-type proton ATPase 116 kDa subunit a isoform 2" ], [ "Q9QZL9-1", "GPDB0007687", "Dickkopf-like protein 1" ], [ "P70277-1", "GPDB0003770", "Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2" ], [ "P70274-1", "GPDB0003769", "Selenoprotein P" ], [ "Q9WVT6-1", "GPDB0007814", "Carbonic anhydrase 14" ], [ "Q9WUR0-1", "GPDB0007794", "Protein Tinag" ], [ "O35714-1", "GPDB0003131", "Tumor necrosis factor receptor superfamily member 18" ], [ "Q03311-1", "GPDB0003874", "Cholinesterase" ], [ "K9J7B2-1", "GPDB0003021", "UDP-glucuronosyltransferase" ], [ "P09242-1", "GPDB0003320", "Alkaline phosphatase, tissue-nonspecific isozyme" ], [ "P35330-1", "GPDB0003581", "Intercellular adhesion molecule 2" ] ] }, "readme": "Name\n - Mouse Xref GlycoProtDB\n\nVersion\n - 1.5.23\n\nCreated on\n - 2020-02-10T14:47:12.024589\n\nModified on\n - 2020-04-09T18:03:03.346761\n\nCreated by\n - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n - Kiyoko F. Aoki-Kinoshita [kkiyoko@soka.ac.jp]\n\nChecksum\n - \n\nUsability Domain\n - The Mouse (TaxID:10090) Xref GlycoProtDB contains x-refs to IDs present in the GlycoProtDB database (https://acgg.asia/gpdb2/index). If you use this dataset please provide proper attribution to GlycoProtDB and GlyGen. \n\nDescription Domain\n Keywords\n - GlycoProtDB\n - cross-reference\n\n Pipeline Steps\n - Step-1: The input file was received directly from the author (Kiyoko F. Aoki-Kinoshita). all the accessions from the input file were checked in the UniProtKB through ID mapping tool. It was found that all the UniProtKB accessions belonged to the Mouse [TaxID:10090] species. The QC checks mapped the UniProtKB accessions to UniProtKB canonical accessions. Any GlycoProtDB ID which was mapped to a protein outside GlyGen protein master list was excluded from the output file.\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-protein-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: protein_xref_glycoprotdb.csv\n URI: https://data.glygen.org/ln2wwwdata/source/protein_xref_glycoprotdb.csv\n Name: mouse_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_masterlist.csv\n Output Subdomain\n Name: mouse_protein_xref_glycoprotdb.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_xref_glycoprotdb.csv\n Name: mouse_protein_xref_glycoprotdb.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_xref_glycoprotdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"1898\"\n Name: \"database_label\"\n Description: \"Label or name assigned to the corresponding identifier in the source database\"\n Unique Values: \"1890\"\n Name: \"database_id\"\n Description: \"Identifier in the database\"\n Unique Values: \"1898\"", "downloadurl": "/ln2data/releases/data/v-1.5.23/reviewed/mouse_protein_xref_glycoprotdb.csv" }