{ "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": "uniprotkb_glycosylation_annotation_comment" }, { "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", "O-linked (GalNAc...) threonine", "", "", "CAR_000049", "" ], [ "P05000-1", "N-linked", "GlcNAc...", "Asn", "101", "N-linked (GlcNAc...) asparagine", "", "", "CAR_000050", "" ], [ "P60568-1", "O-linked", "GalNAc...", "Thr", "23", "O-linked (GalNAc...) threonine", "", "", "CAR_000051", "" ], [ "P04070-1", "N-linked", "GlcNAc...", "Asn", "139", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P02743-1", "N-linked", "GlcNAc...", "Asn", "51", "N-linked (GlcNAc...) asparagine", "", "", "CAR_000169", "" ], [ "P19835-1", "N-linked", "GlcNAc...", "Asn", "207", "N-linked (GlcNAc...) (complex) asparagine", "", "", "CAR_000141", "" ], [ "P08861-1", "N-linked", "GlcNAc...", "Asn", "114", "N-linked (GlcNAc...) asparagine", "", "", "CAR_000212", "" ], [ "Q9UQC9-1", "N-linked", "GlcNAc...", "Asn", "522", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q9UQC9-1", "N-linked", "GlcNAc...", "Asn", "150", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q9UQC9-1", "N-linked", "GlcNAc...", "Asn", "822", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P00742-1", "N-linked", "GlcNAc...", "Asn", "221", "N-linked (GlcNAc...) asparagine", "", "", "CAR_000012", "" ], [ "P00742-1", "N-linked", "GlcNAc...", "Asn", "231", "N-linked (GlcNAc...) asparagine", "", "", "CAR_000013", "" ], [ "P01215-1", "N-linked", "GlcNAc...", "Asn", "76", "N-linked (GlcNAc...) asparagine", "", "", "CAR_000036", "" ], [ "P01215-1", "N-linked", "GlcNAc...", "Asn", "102", "N-linked (GlcNAc...) asparagine", "", "", "CAR_000037", "" ], [ "P10144-1", "N-linked", "GlcNAc...", "Asn", "71", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P40197-1", "N-linked", "GlcNAc...", "Asn", "51", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P40197-1", "N-linked", "GlcNAc...", "Asn", "385", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P40197-1", "N-linked", "GlcNAc...", "Asn", "298", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P40197-1", "N-linked", "GlcNAc...", "Asn", "312", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P01854-1", "N-linked", "GlcNAc...", "Asn", "252", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P01854-1", "N-linked", "GlcNAc...", "Asn", "146", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P29460-1", "C-linked", "Man", "Trp", "319", "C-linked (Man) tryptophan", "", "", "CAR_000187", "" ], [ "P19823-1", "N-linked", "GlcNAc...", "Asn", "118", "N-linked (GlcNAc...) (complex) asparagine", "", "", "CAR_000140", "" ], [ "P19823-1", "O-linked", "GalNAc...", "Thr", "666", "O-linked (GalNAc...) threonine; partial", "", "", "CAR_000214", "" ], [ "P19823-1", "O-linked", "GalNAc...", "Ser", "673", "O-linked (GalNAc...) serine", "", "", "CAR_000215", "" ], [ "P19823-1", "O-linked", "GalNAc...", "Thr", "675", "O-linked (GalNAc...) threonine", "", "", "CAR_000216", "" ], [ "P19823-1", "O-linked", "GalNAc...", "Thr", "691", "O-linked (GalNAc...) threonine", "", "", "CAR_000217", "" ], [ "P05783-1", "O-linked", "GlcNAc", "Ser", "30", "O-linked (GlcNAc) serine; alternate", "", "", "CAR_000175", "" ], [ "P05783-1", "O-linked", "GlcNAc", "Ser", "31", "O-linked (GlcNAc) serine; alternate", "", "", "CAR_000193", "" ], [ "P05783-1", "O-linked", "GlcNAc", "Ser", "49", "O-linked (GlcNAc) serine; alternate", "", "", "CAR_000194", "" ], [ "Q86W47-1", "N-linked", "GlcNAc...", "Asn", "90", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q86W47-1", "N-linked", "GlcNAc...", "Asn", "53", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P11831-1", "O-linked", "GlcNAc", "Ser", "277", "O-linked (GlcNAc) serine", "", "", "CAR_000181", "" ], [ "P11831-1", "O-linked", "GlcNAc", "Ser", "316", "O-linked (GlcNAc) serine", "", "", "CAR_000196", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "400", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "820", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "489", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "349", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "196", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "1294", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "1637", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "1144", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "292", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "151", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "14", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "244", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "98", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "2238", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "2044", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "1504", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "337", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "1453", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "161", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "521", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "O95477-1", "N-linked", "GlcNAc...", "Asn", "478", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q15848-1", "O-linked", "GalNAc...", "Thr", "21", "O-linked (GalNAc...) threonine", "", "", "", "" ], [ "Q15848-1", "O-linked", "GalNAc...", "Thr", "22", "O-linked (GalNAc...) threonine", "", "", "", "" ], [ "P25705-1", "O-linked", "GlcNAc", "Ser", "76", "O-linked (GlcNAc) serine; alternate", "", "", "", "" ], [ "Q9BXI9-2", "N-linked", "GlcNAc...", "Asn", "91", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P35070-1", "N-linked", "GlcNAc...", "Asn", "34", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P40259-1", "N-linked", "GlcNAc...", "Asn", "73", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P40259-1", "N-linked", "GlcNAc...", "Asn", "101", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P40259-1", "N-linked", "GlcNAc...", "Asn", "127", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P40259-1", "N-linked", "GlcNAc...", "Asn", "128", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P07711-1", "N-linked", "GlcNAc...", "Asn", "221", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P55291-1", "N-linked", "GlcNAc...", "Asn", "531", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P55291-1", "N-linked", "GlcNAc...", "Asn", "538", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P55291-1", "N-linked", "GlcNAc...", "Asn", "227", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P55291-1", "N-linked", "GlcNAc...", "Asn", "576", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P07858-1", "N-linked", "GlcNAc...", "Asn", "192", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q9BXJ1-1", "N-linked", "GlcNAc...", "Asn", "93", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q08722-1", "N-linked", "GlcNAc...", "Asn", "23", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q08722-1", "N-linked", "GlcNAc...", "Asn", "206", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q08722-1", "N-linked", "GlcNAc...", "Asn", "73", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q08722-1", "N-linked", "GlcNAc...", "Asn", "111", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q08722-1", "N-linked", "GlcNAc...", "Asn", "50", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P08123-1", "N-linked", "GlcNAc...", "Asn", "1267", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P08123-1", "O-linked", "Gal...", "Lys", "177", "O-linked (Gal...) hydroxylysine; alternate", "", "", "", "" ], [ "P09603-1", "N-linked", "GlcNAc...", "Asn", "172", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "P09603-1", "N-linked", "GlcNAc...", "Asn", "154", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q96D31-1", "N-linked", "GlcNAc...", "Asn", "223", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q99062-1", "N-linked", "GlcNAc...", "Asn", "134", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q99062-1", "N-linked", "GlcNAc...", "Asn", "51", "N-linked (GlcNAc...) asparagine", "", "", "", "" ], [ "Q99062-1", "N-linked", "GlcNAc...", "Asn", "389", "N-linked (GlcNAc...) asparagine", "", "", "", "" ] ] }, "readme": "Name\n - Human Glycosylation Sites (UniProtKB)\n\nVersion\n - 1.5.11\n\nCreated on\n - 2019-01-23T17:21:05.905721\n\nModified on\n - 2019-12-04T17:07:57.744044\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 2019-09 UniProtKB 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-homo-sapiens.nt\n URI: https://data.glygen.org/ln2wwwdata/source/uniprot-proteome-homo-sapiens.nt\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_masterlist.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: \"4521\"\n Name: \"data_source\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"2357\"\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: \"7\"\n Name: \"uniprotkb_ftid\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) as evidence for the entry/annotation\"\n Unique Values: \"1\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"17\"\n Name: \"uniprotkb_glycosylation_annotation_comment\"\n Description: \"\"\n Unique Values: \"77\"\n Name: \"eco_id\"\n Description: \"\"\n Unique Values: \"93\"", "downloadurl": "/ln2data/releases/data/v-1.5.11/reviewed/human_proteoform_glycosylation_sites_uniprotkb.csv" }