{ "bcoid": "GLY_000558", "title": "GlyGen-iPTMNet Crossreferences Mapping", "description": "The GlyGen-iPTMnet Crossreferences dataset contains UniProtKB glycoprotein accessions for human [taxid:9606], ...", "filename": "protein_glygen_iptmnet_xref_mapping.tsv", "filetype": "tsv", "categories": { "molecule": "Protein", "tags": "GlyGen-iPTMnet Crossreferences", "file_type": "tsv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "A0A075B7F1,\"" ], [ "A0A0A6YY83,\"" ] ], "headers": [ "uniprotkb_ac..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_ac,\"glycosylation_site_uniprotkb\",\"amino_acid\",\"glycosylation_type\",\"pmid\",\"glygen_url\"" } ], [ "A0A075B7F1,\"95\",\"Asn\",\"n-linked\",\"29741879\",\"https://www.glygen.org/Siteview/A0A075B7F1/95\"" ], [ "A0A0A6YY83,\"747\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A0A0A6YY83/747\"" ], [ "A0A1L1SQU7,\"1993\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A0A1L1SQU7/1993\"" ], [ "A0A1L1SQU7,\"41\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A0A1L1SQU7/41\"" ], [ "A0A1L1SQU7,\"999\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A0A1L1SQU7/999\"" ], [ "A0A338P6S8,\"251\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A0A338P6S8/251\"" ], [ "A0A338P6S8,\"37\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A0A338P6S8/37\"" ], [ "A0AV96,\"523\",\"Thr\",\"o-linked\",\"28510447|30059200|29237092\",\"https://www.glygen.org/Siteview/A0AV96/523\"" ], [ "A0AVT1,\"317\",\"Ser\",\"o-linked\",\"23301498|28510447|29351928\",\"https://www.glygen.org/Siteview/A0AVT1/317\"" ], [ "A0FGR8,\"758\",\"Ser\",\"o-linked\",\"28411811|28510447|29351928\",\"https://www.glygen.org/Siteview/A0FGR8/758\"" ], [ "A1A5B4,\"641\",\"Asn\",\"n-linked\",\"24190977\",\"https://www.glygen.org/Siteview/A1A5B4/641\"" ], [ "A1A5B4,\"652\",\"Asn\",\"n-linked\",\"24190977\",\"https://www.glygen.org/Siteview/A1A5B4/652\"" ], [ "A1L0T0,\"121\",\"Thr\",\"o-linked\",\"29351928\",\"https://www.glygen.org/Siteview/A1L0T0/121\"" ], [ "A1L4H1,\"1047\",\"thr\",\"thr\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/1047\"" ], [ "A1L4H1,\"1445\",\"thr\",\"thr\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/1445\"" ], [ "A1L4H1,\"1458\",\"thr\",\"thr\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/1458\"" ], [ "A1L4H1,\"1462\",\"thr\",\"thr\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/1462\"" ], [ "A1L4H1,\"1466\",\"ser\",\"ser\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/1466\"" ], [ "A1L4H1,\"1558\",\"thr\",\"thr\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/1558\"" ], [ "A1L4H1,\"157\",\"thr\",\"thr\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/157\"" ], [ "A1L4H1,\"453\",\"thr\",\"thr\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/453\"" ], [ "A1L4H1,\"581\",\"ser\",\"ser\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/581\"" ], [ "A1L4H1,\"758\",\"ser\",\"ser\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/758\"" ], [ "A1L4H1,\"760\",\"ser\",\"ser\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/760\"" ], [ "A1L4H1,\"764\",\"thr\",\"thr\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/764\"" ], [ "A1L4H1,\"884\",\"thr\",\"thr\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/884\"" ], [ "A1L4H1,\"939\",\"thr\",\"thr\",\"30459171\",\"https://www.glygen.org/Siteview/A1L4H1/939\"" ], [ "A2A259,\"177\",\"Asn\",\"n-linked\",\"29567962\",\"https://www.glygen.org/Siteview/A2A259/177\"" ], [ "A2A259,\"207\",\"Asn\",\"n-linked\",\"29567962\",\"https://www.glygen.org/Siteview/A2A259/207\"" ], [ "A2A259,\"241\",\"Asn\",\"n-linked\",\"29567962\",\"https://www.glygen.org/Siteview/A2A259/241\"" ], [ "A2A690,\"1932\",\"Asn\",\"n-linked\",\"20571061\",\"https://www.glygen.org/Siteview/A2A690/1932\"" ], [ "A2A699,\"265\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A2A699/265\"" ], [ "A2A699,\"66\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A2A699/66\"" ], [ "A2A8L5,\"721\",\"Asn\",\"n-linked\",\"19349973|30899004\",\"https://www.glygen.org/Siteview/A2A8L5/721\"" ], [ "A2A8L5,\"941\",\"Asn\",\"n-linked\",\"19349973|30899004\",\"https://www.glygen.org/Siteview/A2A8L5/941\"" ], [ "A2A8L5,\"957\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A2A8L5/957\"" ], [ "A2A8L5,\"960\",\"Asn\",\"n-linked\",\"19349973\",\"https://www.glygen.org/Siteview/A2A8L5/960\"" ], [ "A2AIR5,\"426\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A2AIR5/426\"" ], [ "A2AJQ3,\"122\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A2AJQ3/122\"" ], [ "A2APX8,\"1403\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A2APX8/1403\"" ], [ "A2AQ25,\"357\",\"Ser\",\"o-linked\",\"16452088\",\"https://www.glygen.org/Siteview/A2AQ25/357\"" ], [ "A2ARV4,\"387\",\"Asn\",\"n-linked\",\"19349973\",\"https://www.glygen.org/Siteview/A2ARV4/387\"" ], [ "A2ASI5,\"339\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A2ASI5/339\"" ], [ "A2BH40,\"1598\",\"Asn\",\"n-linked\",\"30899004\",\"https://www.glygen.org/Siteview/A2BH40/1598\"" ], [ "A2RU67,\"237\",\"Asn\",\"n-linked\",\"23090970|24190977\",\"https://www.glygen.org/Siteview/A2RU67/237\"" ], [ "A2RU67,\"396\",\"Asn\",\"n-linked\",\"24190977\",\"https://www.glygen.org/Siteview/A2RU67/396\"" ], [ "A2RU67,\"399\",\"Asn\",\"n-linked\",\"24190977\",\"https://www.glygen.org/Siteview/A2RU67/399\"" ], [ "A2RUS2,\"854\",\"Ser\",\"o-linked\",\"29351928\",\"https://www.glygen.org/Siteview/A2RUS2/854\"" ], [ "A2RUS2,\"857\",\"Ser\",\"o-linked\",\"29351928\",\"https://www.glygen.org/Siteview/A2RUS2/857\"" ], [ "A2VD12,\"451\",\"asn\",\"asn\",\"24090084\",\"https://www.glygen.org/Siteview/A2VD12/451\"" ], [ "A2VDJ0,\"225\",\"Asn\",\"n-linked\",\"24190977\",\"https://www.glygen.org/Siteview/A2VDJ0/225\"" ], [ "A2VDJ0,\"239\",\"Asn\",\"n-linked\",\"24190977\",\"https://www.glygen.org/Siteview/A2VDJ0/239\"" ], [ "A2VDJ0,\"343\",\"Asn\",\"n-linked\",\"24190977\",\"https://www.glygen.org/Siteview/A2VDJ0/343\"" ], [ "A2VDJ0,\"439\",\"Asn\",\"n-linked\",\"24190977\",\"https://www.glygen.org/Siteview/A2VDJ0/439\"" ], [ "A2VDJ0,\"593\",\"Asn\",\"n-linked\",\"24190977\",\"https://www.glygen.org/Siteview/A2VDJ0/593\"" ], [ "A2VDJ0,\"708\",\"Asn\",\"n-linked\",\"24190977\",\"https://www.glygen.org/Siteview/A2VDJ0/708\"" ], [ "A2VDJ0,\"709\",\"Asn\",\"n-linked\",\"24190977\",\"https://www.glygen.org/Siteview/A2VDJ0/709\"" ], [ "A2VDJ0,\"809\",\"Asn\",\"n-linked\",\"24190977\",\"https://www.glygen.org/Siteview/A2VDJ0/809\"" ], [ "A3KN83,\"108\",\"Thr\",\"o-linked\",\"27655845|30059200|29351928|32119511|28657654|29237092|20068230\",\"https://www.glygen.org/Siteview/A3KN83/108\"" ], [ "A3KN83,\"112\",\"Thr\",\"o-linked\",\"27655845|30059200|29351928|32119511|28657654|29237092|20068230\",\"https://www.glygen.org/Siteview/A3KN83/112\"" ], [ "A3KN83,\"113\",\"Thr\",\"o-linked\",\"27655845|30059200|29351928|32119511|28657654|29237092|20068230\",\"https://www.glygen.org/Siteview/A3KN83/113\"" ], [ "A3KN83,\"126\",\"Thr\",\"o-linked\",\"27655845|30059200|29351928|32119511|28657654|29237092|20068230\",\"https://www.glygen.org/Siteview/A3KN83/126\"" ], [ "A3KN83,\"127\",\"Thr\",\"o-linked\",\"27655845|30059200|29351928|32119511|28657654|29237092|20068230\",\"https://www.glygen.org/Siteview/A3KN83/127\"" ], [ "A3KN83,\"129\",\"Ser\",\"o-linked\",\"27655845|30059200|29351928|32119511|28657654|29237092|20068230\",\"https://www.glygen.org/Siteview/A3KN83/129\"" ], [ "A3KN83,\"130\",\"Thr\",\"o-linked\",\"27655845|30059200|29351928|32119511|28657654|29237092|20068230\",\"https://www.glygen.org/Siteview/A3KN83/130\"" ], [ "A3KN83,\"133\",\"Ser\",\"o-linked\",\"27655845|30059200|29351928|32119511|28657654|29237092|20068230\",\"https://www.glygen.org/Siteview/A3KN83/133\"" ], [ "A3KN83,\"135\",\"Ser\",\"o-linked\",\"27655845|30059200|29351928|32119511|28657654|29237092|20068230\",\"https://www.glygen.org/Siteview/A3KN83/135\"" ], [ "A3KN83,\"138\",\"Thr\",\"o-linked\",\"27655845|30059200|29351928|32119511|28657654|29237092|20068230\",\"https://www.glygen.org/Siteview/A3KN83/138\"" ], [ "A4D161,\"295\",\"Thr\",\"o-linked\",\"28657654\",\"https://www.glygen.org/Siteview/A4D161/295\"" ], [ "A4UGR9,\"2838\",\"Thr\",\"o-linked\",\"28411811|29351928\",\"https://www.glygen.org/Siteview/A4UGR9/2838\"" ], [ "A5D8T8,\"356\",\"thr\",\"thr\",\"30459171\",\"https://www.glygen.org/Siteview/A5D8T8/356\"" ], [ "A5YKK6,\"1038\",\"Thr\",\"o-linked\",\"23301498|27655845|30059200|29351928|32119511|28510447|28657654|29237092\",\"https://www.glygen.org/Siteview/A5YKK6/1038\"" ], [ "A5YKK6,\"1041\",\"Thr\",\"o-linked\",\"23301498|27655845|30059200|29351928|32119511|28510447|28657654|29237092\",\"https://www.glygen.org/Siteview/A5YKK6/1041\"" ], [ "A5YKK6,\"1042\",\"Thr\",\"o-linked\",\"23301498|27655845|30059200|29351928|32119511|28510447|28657654|29237092\",\"https://www.glygen.org/Siteview/A5YKK6/1042\"" ], [ "A5YKK6,\"1043\",\"Ser\",\"o-linked\",\"23301498|27655845|30059200|29351928|32119511|28510447|28657654|29237092\",\"https://www.glygen.org/Siteview/A5YKK6/1043\"" ], [ "A5YKK6,\"1051\",\"Thr\",\"o-linked\",\"23301498|27655845|30059200|29351928|32119511|28510447|28657654|29237092\",\"https://www.glygen.org/Siteview/A5YKK6/1051\"" ], [ "A5YKK6,\"1055\",\"Thr\",\"o-linked\",\"23301498|27655845|30059200|29351928|32119511|28510447|28657654|29237092\",\"https://www.glygen.org/Siteview/A5YKK6/1055\"" ], [ "A5YKK6,\"1058\",\"Thr\",\"o-linked\",\"23301498|27655845|30059200|29351928|32119511|28510447|28657654|29237092\",\"https://www.glygen.org/Siteview/A5YKK6/1058\"" ], [ "A5YKK6,\"1061\",\"Ser\",\"o-linked\",\"23301498|27655845|30059200|29351928|32119511|28510447|28657654|29237092\",\"https://www.glygen.org/Siteview/A5YKK6/1061\"" ], [ "A5YKK6,\"1418\",\"Thr\",\"o-linked\",\"23301498|27655845|30059200|29351928|32119511|28510447|28657654|29237092\",\"https://www.glygen.org/Siteview/A5YKK6/1418\"" ], [ "A5YKK6,\"1775\",\"Ser\",\"o-linked\",\"23301498|27655845|30059200|29351928|32119511|28510447|28657654|29237092\",\"https://www.glygen.org/Siteview/A5YKK6/1775\"" ], [ "A5YKK6,\"1780\",\"Thr\",\"o-linked\",\"23301498|27655845|30059200|29351928|32119511|28510447|28657654|29237092\",\"https://www.glygen.org/Siteview/A5YKK6/1780\"" ], [ "A5YKK6,\"746\",\"Thr\",\"o-linked\",\"23301498|27655845|30059200|29351928|32119511|28510447|28657654|29237092\",\"https://www.glygen.org/Siteview/A5YKK6/746\"" ], [ "A5YKK6,\"758\",\"Ser\",\"o-linked\",\"23301498|27655845|30059200|29351928|32119511|28510447|28657654|29237092\",\"https://www.glygen.org/Siteview/A5YKK6/758\"" ] ] }, "readme": "Name\n - GlyGen-iPTMNet Crossreferences Mapping\n\nVersion\n - 1.11.2\n\nCreated on\n - 2021-05-13T17:15:40.998243\n\nModified on\n - 2021-10-15T15:48:20.842727\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The GlyGen-iPTMnet Crossreferences dataset contains UniProtKB glycoprotein accessions for human [taxid:9606], mouse [taxid:10090] and rat [taxid:10116], hcv1a [taxid:11108], hcv1b [taxid:11116], sarscov1 [taxid:694009] and sarscov2 [taxid:2697049] glycoproteins for the purpose of UniProtKB to GlyGen crossreferences. In the dataset, the UniProtKB glycoprotein accessions, site, amino acid, glycosylation type and corresponding PMIDs and GlyGen Siteview URLs are present. Any accession entries that do not have site info have been removed from the dataset. If you use this dataset please provide proper attribution to GlyGen.\n\nDescription Domain\n Keywords\n - iPTMnet\n - GlyGen\n - crossreferences\n - human\n - mouse\n - rat\n\n Pipeline Steps\n - Step-1: The script extracts the glycosylation info for human, mouse and rat species and extracts into a csv dataset file.\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-species-agnostic-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: rat_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/rat_proteoform_glycosylation_sites_uniprotkb.csv\n Name: human_proteoform_glycosylation_sites_harvard.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/human_proteoform_glycosylation_sites_harvard.csv\n Name: rat_proteoform_glycosylation_sites_pdb.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/rat_proteoform_glycosylation_sites_pdb.csv\n Name: mouse_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/mouse_proteoform_glycosylation_sites_unicarbkb.csv\n Name: mouse_proteoform_glycosylation_sites_glyconnect.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/mouse_proteoform_glycosylation_sites_glyconnect.csv\n Name: human_proteoform_glycosylation_sites_literature_mining.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/human_proteoform_glycosylation_sites_literature_mining.csv\n Name: human_proteoform_glycosylation_sites_gptwiki.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/human_proteoform_glycosylation_sites_gptwiki.csv\n Name: rat_proteoform_glycosylation_sites_literature_mining.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/rat_proteoform_glycosylation_sites_literature_mining.csv\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/human_protein_masterlist.csv\n Name: human_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/human_proteoform_glycosylation_sites_uniprotkb.csv\n Name: human_proteoform_glycosylation_sites_glyconnect.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/human_proteoform_glycosylation_sites_glyconnect.csv\n Name: human_proteoform_glycosylation_sites_pdb.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/human_proteoform_glycosylation_sites_pdb.csv\n Name: mouse_proteoform_glycosylation_sites_pdb.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/mouse_proteoform_glycosylation_sites_pdb.csv\n Name: human_proteoform_glycosylation_sites_o_glcnac_mcw.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/human_proteoform_glycosylation_sites_o_glcnac_mcw.csv\n Name: mouse_proteoform_glycosylation_sites_literature_mining.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/mouse_proteoform_glycosylation_sites_literature_mining.csv\n Name: human_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/human_proteoform_glycosylation_sites_unicarbkb.csv\n Name: mouse_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/mouse_proteoform_glycosylation_sites_uniprotkb.csv\n Name: rat_proteoform_glycosylation_sites_glyconnect.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/rat_proteoform_glycosylation_sites_glyconnect.csv\n Name: rat_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/rat_proteoform_glycosylation_sites_unicarbkb.csv\n Name: rat_protein_masterlist.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/rat_protein_masterlist.csv\n Name: human_proteoform_glycosylation_sites_tyr_o_linked.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/human_proteoform_glycosylation_sites_tyr_o_linked.csv\n Name: human_proteoform_glycosylation_sites_literature.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/human_proteoform_glycosylation_sites_literature.csv\n Name: mouse_protein_masterlist.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/mouse_protein_masterlist.csv\n Output Subdomain\n Name: protein_glygen_iptmnet_xref_mapping.tsv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/protein_glygen_iptmnet_xref_mapping.tsv\n Name: protein_glygen_iptmnet_xref_mapping.stat.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/protein_glygen_iptmnet_xref_mapping.stat.csv", "downloadurl": "/ln2data/releases/data/v-1.12.1/reviewed/protein_glygen_iptmnet_xref_mapping.tsv" }