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"691", "Ser", "Ser", "S" ], [ "P07663-1", "691", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "30703153", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "SVTNT-S-IAGTG", "691", "691", "Ser", "Ser", "S" ], [ "P07663-1", "860", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P07663", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "GGAVG-T-GGVGS", "860", "860", "Thr", "Thr", "T" ], [ "P07663-1", "860", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "30703153", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "GGAVG-T-GGVGS", "860", "860", "Thr", "Thr", "T" ], [ "P07663-1", "865", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P07663", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "TGGVG-S-GGAGV", "865", "865", "Ser", "Ser", "S" ], [ "P07663-1", "865", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "30703153", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "TGGVG-S-GGAGV", "865", "865", "Ser", "Ser", "S" ], [ "P07663-1", "876", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P07663", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "AGGGG-S-GTGVA", "876", "876", "Ser", "Ser", "S" ], [ "P07663-1", "876", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "30703153", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "AGGGG-S-GTGVA", "876", "876", "Ser", "Ser", "S" ], [ "P07663-1", "878", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P07663", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "GGGSG-T-GVAGT", "878", "878", "Thr", "Thr", "T" ], [ "P07663-1", "878", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "30703153", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "GGGSG-T-GVAGT", "878", "878", "Thr", "Thr", "T" ], [ "P07663-1", "883", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P07663", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "TGVAG-T-PEGRA", "883", "883", "Thr", "Thr", "T" ], [ "P07663-1", "883", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "30703153", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "TGVAG-T-PEGRA", "883", "883", "Thr", "Thr", "T" ], [ "P07663-1", "889", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P07663", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "PEGRA-T-TTSGT", "889", "889", "Thr", "Thr", "T" ], [ "P07663-1", "889", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "30703153", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "PEGRA-T-TTSGT", "889", "889", "Thr", "Thr", "T" ], [ "P07663-1", "942", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P07663", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "LWPPF-S-VGITP", "942", "942", "Ser", "Ser", "S" ], [ "P07663-1", "942", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "30703153", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "LWPPF-S-VGITP", "942", "942", "Ser", "Ser", "S" ], [ "P07663-1", "951", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P07663", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "TPPVH-S-THTAM", "951", "951", "Ser", "Ser", "S" ], [ "P07663-1", "951", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "30703153", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "TPPVH-S-THTAM", "951", "951", "Ser", "Ser", "S" ], [ "P07663-1", "952", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P07663", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "PPVHS-T-HTAMA", "952", "952", "Thr", "Thr", "T" ], [ "P07663-1", "952", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "30703153", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "PPVHS-T-HTAMA", "952", "952", "Thr", "Thr", "T" ], [ "P07663-1", "954", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P07663", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "VHSTH-T-AMAQS", "954", "954", "Thr", "Thr", "T" ], [ "P07663-1", "954", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "30703153", "protein_xref_oglcnac_atlas", "P07663", "head", "MS", "LTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000033", "head", "", "", "VHSTH-T-AMAQS", "954", "954", "Thr", "Thr", "T" ], [ "P12080-1", "1234", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P12080", "protein_xref_oglcnac_atlas", "P12080", "embryos", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000922", "embryo", "", "", "RRLRR-S-NDKDG", "1234", "1234", "Ser", "Ser", "S" ], [ "P12080-1", "1234", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "28604694", "protein_xref_oglcnac_atlas", "P12080", "embryos", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000922", "embryo", "", "", "RRLRR-S-NDKDG", "1234", "1234", "Ser", "Ser", "S" ], [ "P12080-1", "1241", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P12080", "protein_xref_oglcnac_atlas", "P12080", "embryos", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000922", "embryo", "", "", "DKDGA-T-EKPLQ", "1241", "1241", "Thr", "Thr", "T" ], [ "P12080-1", "1241", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "28604694", "protein_xref_oglcnac_atlas", "P12080", "embryos", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000922", "embryo", "", "", "DKDGA-T-EKPLQ", "1241", "1241", "Thr", "Thr", "T" ], [ "P13607-1", "591", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P13607", "protein_xref_oglcnac_atlas", "P13607", "embryos", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000922", "embryo", "", "", "GFKFN-T-DDINF", "591", "591", "Thr", "Thr", "T" ], [ "P13607-1", "591", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "28604694", "protein_xref_oglcnac_atlas", "P13607", "embryos", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000922", "embryo", "", "", "GFKFN-T-DDINF", "591", "591", "Thr", "Thr", "T" ], [ "P18289-1", "12", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_atlas", "P18289", "protein_xref_oglcnac_atlas", "P18289", "embryos", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000922", "embryo", "", "", "AAANL-S-IQNAG", "12", "12", "Ser", "Ser", "S" ], [ "P18289-1", "12", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "28604694", "protein_xref_oglcnac_atlas", "P18289", "embryos", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "UBERON:0000922", "embryo", "", "", "AAANL-S-IQNAG", "12", "12", "Ser", "Ser", "S" ] ] }, "readme": "Name\n - Fruitfly O-GlcNAc Glycosylation Sites (O-GlcNAc Atlas)\n\nVersion\n - v-2.4.1\n\nCreated on\n - 2023-02-24T16:22:06.506Z\n\nModified on\n - 2023-03-06T20:15:27.506Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - Jungfeng Ma [junfeng.ma@georgetown.edu ]\n\nChecksum\n - \n\nUsability Domain\n - The Fruitfly O-GlcNAc Glycosylation Sites (O-GlcNAc Atlas) contains fruitfly (taxid:7227) O-GlcNAc modifications on Serine and Threonine extracted from the publication and mapped to the UniProtKB canonical accession and fasta sequence. The GlyTouCan ID for the O-GlcNAc is G49108TO.\n\nDescription Domain\n Keywords\n - \n - O-GlcNAc\n - Serine\n\n Pipeline Steps\n - Step-1: The script maps the UniProtKB accesions to the UniProtKB Canonical accessions and also checks the position and amino acid of O-GlcNAc modified residue against UniProtKB Canonical sequences. The script also maps the sample type to correct sample term id and sample term name. \n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/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: fruitfly_protein_info_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/fruitfly_protein_info_uniprotkb.csv\n Name: fruitfly_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/fruitfly_protein_masterlist.csv\n Name: fruitfly_protein_recnames.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/fruitfly_protein_recnames.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/misc/sample_mapping.csv\n Name: ambiguous_sites_version_2.0.csv\n URI: https:/data.glygen.org/ln2downloads/atlas_oglcnac/2022_10_20/ambiguous_sites_version_2.0.csv\n Name: unambiguous_sites_version_2.0.csv\n URI: https:/data.glygen.org/ln2downloads/atlas_oglcnac/2022_10_20/unambiguous_sites_version_2.0.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2024_01_31/cellosaurus.txt\n Output Subdomain\n Name: fruitfly_proteoform_glycosylation_sites_oglcnac_atlas.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/fruitfly_proteoform_glycosylation_sites_oglcnac_atlas.csv\n Name: fruitfly_proteoform_glycosylation_sites_oglcnac_atlas.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/fruitfly_proteoform_glycosylation_sites_oglcnac_atlas.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"30\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"122\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"2\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"1\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"1\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"34\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"30\"\n Name: \"sample_type\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"method\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"analytical_throughput\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"notes\"\n Description: \"Notes\"\n Unique Values: \"1\"\n Name: \"carb_name\"\n Description: \"carbohydrate name\"\n Unique Values: \"1\"\n Name: \"glycosylation_subtype\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"source_tissue_id\"\n Description: \"Tissue ID from GlyConnect\"\n Unique Values: \"3\"\n Name: \"source_tissue_name\"\n Description: \"Tissue NAME from GlyConnect\"\n Unique Values: \"3\"\n Name: \"source_cell_line_cellosaurus_id\"\n Description: \"cellosaurus ID of the cell line\"\n Unique Values: \"2\"\n Name: \"source_cell_line_cellosaurus_name\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"peptide\"\n Description: \"Protein peptide\"\n Unique Values: \"128\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"122\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"122\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/fruitfly_proteoform_glycosylation_sites_oglcnac_atlas.csv" }