{ "bcoid": "GLY_000038", "title": "Human Glycosylation Sites (UniProtKB)", "description": "The Human Glycosylation Sites (UniProtKB) dataset contains human [taxid:9606] UniProtKB canonical accessions ...", "filename": "human_proteoform_glycosylation_sites_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Homo Sapiens", "molecule": "Proteoform", "tags": "Glycosylation Sites", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P01563-1...", "O-linked..." ], [ "P05000-1...", "N-linked..." ] ], "headers": [ "uniprotkb_ca...", "glycosylatio..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glycosylation_type" }, { "type": "string", "label": "saccharide" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "glycosylation_site_uniprotkb" }, { "type": "string", "label": "data_source" }, { "type": "string", "label": "evidence" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "uniprotkb_ftid" } ], [ "P01563-1", "O-linked", "GalNAc...", "Thr", "129", "PubMed", "2049076", "ECO_0000269", "CAR_000049" ], [ "P05000-1", "N-linked", "GlcNAc...", "Asn", "101", "PubMed", "1693148", "ECO_0000269", "CAR_000050" ], [ "P60568-1", "O-linked", "GalNAc...", "Thr", "23", "PubMed", "6333684", "ECO_0000269", "CAR_000051" ], [ "P60568-1", "O-linked", "GalNAc...", "Thr", "23", "PubMed", "2793860", "ECO_0000269", "CAR_000051" ], [ "P04070-1", "N-linked", "GlcNAc...", "Asn", "139", "", "", "", "" ], [ "P02743-1", "N-linked", "GlcNAc...", "Asn", "51", "PubMed", "19159218", "ECO_0000269", "CAR_000169" ], [ "P02743-1", "N-linked", "GlcNAc...", "Asn", "51", "PubMed", "16335952", "ECO_0000269", "CAR_000169" ], [ "P19835-1", "N-linked", "GlcNAc...", "Asn", "207", "", "", "CAR_000141", "" ], [ "P08861-1", "N-linked", "GlcNAc...", "Asn", "114", "PubMed", "2737288", "ECO_0000269", "CAR_000212" ], [ "Q9UQC9-1", "N-linked", "GlcNAc...", "Asn", "522", "", "", "", "" ], [ "Q9UQC9-1", "N-linked", "GlcNAc...", "Asn", "150", "", "", "", "" ], [ "Q9UQC9-1", "N-linked", "GlcNAc...", "Asn", "822", "", "", "", "" ], [ "P00742-1", "N-linked", "GlcNAc...", "Asn", "221", "PubMed", "8243461", "ECO_0000269", "CAR_000012" ], [ "P00742-1", "N-linked", "GlcNAc...", "Asn", "231", "PubMed", "8243461", "ECO_0000269", "CAR_000013" ], [ "P01215-1", "N-linked", "GlcNAc...", "Asn", "76", "PubMed", "24692546", "ECO_0000269", "CAR_000036" ], [ "P01215-1", "N-linked", "GlcNAc...", "Asn", "76", "PubMed", "15662415", "ECO_0000269", "CAR_000036" ], [ "P01215-1", "N-linked", "GlcNAc...", "Asn", "76", "PDB", "4MQW", "ECO_0000244", "CAR_000036" ], [ "P01215-1", "N-linked", "GlcNAc...", "Asn", "102", "PubMed", "24692546", "ECO_0000269", "CAR_000037" ], [ "P01215-1", "N-linked", "GlcNAc...", "Asn", "102", "PubMed", "15662415", "ECO_0000269", "CAR_000037" ], [ "P01215-1", "N-linked", "GlcNAc...", "Asn", "102", "PDB", "4MQW", "ECO_0000244", "CAR_000037" ], [ "P10144-1", "N-linked", "GlcNAc...", "Asn", "71", "", "", "", "" ], [ "P40197-1", "N-linked", "GlcNAc...", "Asn", "51", "", "", "", "" ], [ "P40197-1", "N-linked", "GlcNAc...", "Asn", "385", "", "", "", "" ], [ "P40197-1", "N-linked", "GlcNAc...", "Asn", "298", "", "", "", "" ], [ "P40197-1", "N-linked", "GlcNAc...", "Asn", "312", "", "", "", "" ], [ "P01854-1", "N-linked", "GlcNAc...", "Asn", "252", "", "", "", "" ], [ "P01854-1", "N-linked", "GlcNAc...", "Asn", "146", "", "", "", "" ], [ "P29460-1", "C-linked", "Man", "Trp", "319", "PubMed", "10207176", "ECO_0000269", "CAR_000187" ], [ "P19823-1", "N-linked", "GlcNAc...", "Asn", "118", "PubMed", "9677337", "ECO_0000269", "CAR_000140" ], [ "P19823-1", "N-linked", "GlcNAc...", "Asn", "118", "PubMed", "19159218", "ECO_0000269", "CAR_000140" ], [ "P19823-1", "N-linked", "GlcNAc...", "Asn", "118", "PubMed", "12754519", "ECO_0000269", "CAR_000140" ], [ "P19823-1", "N-linked", "GlcNAc...", "Asn", "118", "PubMed", "16335952", "ECO_0000269", "CAR_000140" ], [ "P19823-1", "N-linked", "GlcNAc...", "Asn", "118", "PubMed", "9425062", "ECO_0000269", "CAR_000140" ], [ "P19823-1", "O-linked", "GalNAc...", "Thr", "666", "PubMed", "9677337", "ECO_0000269", "CAR_000214" ], [ "P19823-1", "O-linked", "GalNAc...", "Thr", "666", "PubMed", "9425062", "ECO_0000269", "CAR_000214" ], [ "P19823-1", "O-linked", "GalNAc...", "Ser", "673", "PubMed", "9677337", "ECO_0000269", "CAR_000215" ], [ "P19823-1", "O-linked", "GalNAc...", "Ser", "673", "PubMed", "9425062", "ECO_0000269", "CAR_000215" ], [ "P19823-1", "O-linked", "GalNAc...", "Thr", "675", "PubMed", "9677337", "ECO_0000269", "CAR_000216" ], [ "P19823-1", "O-linked", "GalNAc...", "Thr", "675", "PubMed", "9425062", "ECO_0000269", "CAR_000216" ], [ "P19823-1", "O-linked", "GalNAc...", "Thr", "691", "PubMed", "9677337", "ECO_0000269", "CAR_000217" ], [ "P19823-1", "O-linked", "GalNAc...", "Thr", "691", "PubMed", "7682553", "ECO_0000269", "CAR_000217" ], [ "P19823-1", "O-linked", "GalNAc...", "Thr", "691", "PubMed", "9425062", "ECO_0000269", "CAR_000217" ], [ "P05783-1", "O-linked", "GlcNAc", "Ser", "30", "PubMed", "20729549", "ECO_0000269", "CAR_000175" ], [ "P05783-1", "O-linked", "GlcNAc", "Ser", "30", "PubMed", "7538124", "ECO_0000269", "CAR_000175" ], [ "P05783-1", "O-linked", "GlcNAc", "Ser", "31", "PubMed", "20729549", "ECO_0000269", "CAR_000193" ], [ "P05783-1", "O-linked", "GlcNAc", "Ser", "31", "PubMed", "7538124", "ECO_0000269", "CAR_000193" ], [ "P05783-1", "O-linked", "GlcNAc", "Ser", "49", "PubMed", "20729549", "ECO_0000269", "CAR_000194" ], [ "P05783-1", "O-linked", "GlcNAc", "Ser", "49", "PubMed", "7538124", "ECO_0000269", "CAR_000194" ], [ "Q86W47-1", "N-linked", "GlcNAc...", "Asn", "90", "", "", "", "" ], [ "Q86W47-1", "N-linked", "GlcNAc...", "Asn", "53", "", "", "", "" ], [ "P11831-1", "O-linked", "GlcNAc", "Ser", "277", "PubMed", "1512232", "ECO_0000269", "CAR_000181" ], [ "P11831-1", "O-linked", "GlcNAc", "Ser", "316", "PubMed", "1512232", "ECO_0000269", "CAR_000196" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "70", "PubMed", "22171320", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "70", "PubMed", "15084671", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "70", "PubMed", "19159218", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "70", "PubMed", "16622833", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "70", "PubMed", "16263699", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "70", "PubMed", "12754519", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "70", "PubMed", "16335952", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "70", "PubMed", "19838169", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "70", "PubMed", "14760718", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "107", "PubMed", "19159218", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "107", "PubMed", "16622833", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "107", "PubMed", "16335952", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "107", "PubMed", "19838169", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "107", "PubMed", "19139490", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "271", "PubMed", "22171320", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "271", "PubMed", "15084671", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "271", "PubMed", "19159218", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "271", "PubMed", "16622833", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "271", "PubMed", "12754519", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "271", "PubMed", "16335952", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "271", "PubMed", "19838169", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "271", "PubMed", "14760718", "ECO_0000269", "" ], [ "P01009-1", "N-linked", "GlcNAc...", "Asn", "271", "PubMed", "19139490", "ECO_0000269", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "400", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "820", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "489", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "349", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "196", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "1294", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "1637", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "1144", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "292", "", "", "", "" ] ] }, "readme": "Name\n - Human Glycosylation Sites (UniProtKB)\n\nVersion\n - 1.4.5\n\nCreated on\n - 2019-01-23T17:21:05.905721\n\nModified on\n - 2019-04-25T19:02:55.748795\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Human Glycosylation Sites (UniProtKB) dataset contains human [taxid:9606] UniProtKB canonical accessions with information on reported and predicted glycosylation sites in UniProtKB database. The dataset is derived from 2019-05 UniProt release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - glycosylation\n - reported glycosylation\n - predicted glycosylation\n - UniProtKB\n - PubMed\n - Evidence and conclusion Ontology\n\n Pipeline Steps\n - Step-1: The script loads the glycosylation information from the triplestore conatining triples from the nt file and extracts as a csv dataset\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: uniprot-proteome-9606-homo-sapiens-2018-11.nt\n URI: https://data.glygen.org/ln2wwwdata/source/uniprot-proteome-9606-homo-sapiens-2018-11.nt\n Name: human_protein_idmapping.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_idmapping.csv\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_uniprotkb.csv\n URI: http://data.glygen.org/datasets/reviewed/human_proteoform_glycosylation_sites_uniprotkb.csv\n Name: human_proteoform_glycosylation_sites_uniprotkb.stat.csv\n URI: http://data.glygen.org/datasets/reviewed/human_proteoform_glycosylation_sites_uniprotkb.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: \"4526\"\n Name: \"data_source\"\n Description: \"\"\n Unique Values: \"6\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"2358\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"4\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"10\"\n Name: \"uniprotkb_ftid\"\n Description: \"\"\n Unique Values: \"79\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) as evidence for the entry/annotation\"\n Unique Values: \"1198\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"18\"\n Name: \"eco_id\"\n Description: \"\"\n Unique Values: \"21\"", "downloadurl": "/ln2data/releases/data/v-1.4.5/reviewed/human_proteoform_glycosylation_sites_uniprotkb.csv" }