{ "bcoid": "GLY_000039", "title": "Mouse Glycosylation Sites (UniProtKB)", "description": "The Mouse Glycosylation Sites (UniProtKB) dataset contains mouse [taxid:10090] UniProtKB canonical accessions ...", "filename": "mouse_proteoform_glycosylation_sites_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Mus musculus", "molecule": "Proteoform", "tags": "Glycosylation Sites", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q8CFG9-1...", "124..." ], [ "Q9QXX0-1...", "1045..." ] ], "headers": [ "uniprotkb_ca...", "glycosylatio..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glycosylation_site_uniprotkb" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "saccharide" }, { "type": "string", "label": "glycosylation_type" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" }, { "type": "string", "label": "uniprotkb_glycosylation_annotation_comment" }, { "type": "string", "label": "data_source" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "uniprotkb_ftid" }, { "type": "string", "label": "carb_name" }, { "type": "string", "label": "glycosylation_subtype" } ], [ "Q8CFG9-1", "124", "Asn", "", "n-linked", "protein_xref_uniprotkb_gly", "Q8CFG9", "protein_xref_uniprotkb_gly", "Q8CFG9", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "" ], [ "Q9QXX0-1", "1045", "Asn", "", "n-linked", "protein_xref_uniprotkb_gly", "Q9QXX0", "protein_xref_uniprotkb_gly", "Q9QXX0", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "" ], [ "O08852-1", "1004", "Asn", "", "n-linked", "protein_xref_uniprotkb_gly", "O08852", "protein_xref_uniprotkb_gly", "O08852", "N-linked (GlcNAc...) asparagine", "", "", "", 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"Q5DID3", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "" ], [ "P06802-1", "567", "Asn", "", "n-linked", "protein_xref_uniprotkb_gly", "P06802", "protein_xref_uniprotkb_gly", "P06802", "N-linked (GlcNAc...) asparagine", "PubMed", "ECO_0000269", "", "GlcNAc...", "" ], [ "P06802-1", "567", "Asn", "", "n-linked", "protein_xref_pubmed", "23027977", "protein_xref_uniprotkb_gly", "P06802", "N-linked (GlcNAc...) asparagine", "PubMed", "ECO_0000269", "", "GlcNAc...", "" ], [ "P06802-1", "567", "Asn", "", "n-linked", "protein_xref_pubmed", "23041369", "protein_xref_uniprotkb_gly", "P06802", "N-linked (GlcNAc...) asparagine", "PubMed", "ECO_0000269", "", "GlcNAc...", "" ], [ "O70458-1", "577", "Asn", "", "n-linked", "protein_xref_uniprotkb_gly", "O70458", "protein_xref_uniprotkb_gly", "O70458", "N-linked (GlcNAc...) asparagine", "PubMed", "ECO_0000269", "", "GlcNAc...", "" ], [ "O70458-1", "577", "Asn", "", "n-linked", "protein_xref_pubmed", "19656770", "protein_xref_uniprotkb_gly", "O70458", "N-linked (GlcNAc...) asparagine", "PubMed", "ECO_0000269", "", "GlcNAc...", "" ], [ "Q812C9-1", "589", "Asn", "", "n-linked", "protein_xref_uniprotkb_gly", "Q812C9", "protein_xref_uniprotkb_gly", "Q812C9", "N-linked (GlcNAc...) (complex) asparagine", "UniProtKB", "ECO_0000250", "", "GlcNAc...", "Complex" ], [ "A2ARV4-1", "1497", "Asn", "", "n-linked", "protein_xref_uniprotkb_gly", "A2ARV4", "protein_xref_uniprotkb_gly", "A2ARV4", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "" ], [ "Q07113-1", "2129", "Asn", "", "n-linked", "protein_xref_uniprotkb_gly", "Q07113", "protein_xref_uniprotkb_gly", "Q07113", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "" ], [ "Q9QUN9-1", "204", "Asn", "", "n-linked", "protein_xref_uniprotkb_gly", "Q9QUN9", "protein_xref_uniprotkb_gly", "Q9QUN9", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "" ], [ "P52800-1", "39", "Asn", "", "n-linked", "protein_xref_uniprotkb_gly", "P52800", "protein_xref_uniprotkb_gly", "P52800", "N-linked (GlcNAc...) asparagine", "PubMed", "ECO_0000269", "", "GlcNAc...", "" ], [ "P52800-1", "39", "Asn", "", "n-linked", "protein_xref_pubmed", "11703926", "protein_xref_uniprotkb_gly", "P52800", "N-linked (GlcNAc...) asparagine", "PubMed", "ECO_0000269", "", "GlcNAc...", "" ], [ "Q8R2E9-1", "383", "Asn", "", "n-linked", "protein_xref_uniprotkb_gly", "Q8R2E9", "protein_xref_uniprotkb_gly", "Q8R2E9", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "" ], [ "Q8BRG8-1", "57", "Asn", "", "n-linked", "protein_xref_uniprotkb_gly", "Q8BRG8", "protein_xref_uniprotkb_gly", "Q8BRG8", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "" ], [ "Q7TSK7-1", "435", "Asn", "", "n-linked", "protein_xref_uniprotkb_gly", "Q7TSK7", "protein_xref_uniprotkb_gly", "Q7TSK7", "N-linked (GlcNAc...) asparagine", "", "", "", "GlcNAc...", "" ] ] }, "readme": "Name\n - Mouse Glycosylation Sites (UniProtKB)\n\nVersion\n - 1.5.36\n\nCreated on\n - 2019-01-23T17:21:05.906744\n\nModified on\n - 2020-04-10T12:34:43.152869\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 Mouse Glycosylation Sites (UniProtKB) dataset contains mouse [taxid:10090] 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-mus-musculus.nt\n URI: https://data.glygen.org/ln2wwwdata/source/uniprot-proteome-mus-musculus.nt\n Name: mouse_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_masterlist.csv\n Output Subdomain\n Name: mouse_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_proteoform_glycosylation_sites_uniprotkb.csv\n Name: mouse_proteoform_glycosylation_sites_uniprotkb.stat.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_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: \"3794\"\n Name: \"data_source\"\n Description: \"The source database for the data\"\n Unique Values: \"7\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"1996\"\n Name: \"glycosylation_subtype\"\n Description: \"\"\n Unique Values: \"11\"\n Name: \"xref_id\"\n Description: \"\"\n Unique Values: \"4145\"\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: \"src_xref_key\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"\"\n Unique Values: \"3817\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"1\"\n Name: \"uniprotkb_glycosylation_annotation_comment\"\n Description: \"The glycosylation annotation in UniProtKB that provides more context and description about the glycosylation event on a proein\"\n Unique Values: \"52\"\n Name: \"carb_name\"\n Description: \"\"\n Unique Values: \"13\"\n Name: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"10\"\n Name: \"uniprotkb_ftid\"\n Description: \"A stable feature identifier that allows to construct links directly from position-specific annotation to specialized protein-related databases. (In the dataset the FTID is for glycosylation for residues attached to an oligosaccharide structure annotated in the UniCarbKB database)\"\n Unique Values: \"12\"\n Name: \"xref_key\"\n Description: \"\"\n Unique Values: \"6\"", "downloadurl": "/ln2data/releases/data/v-1.5.36/reviewed/mouse_proteoform_glycosylation_sites_uniprotkb.csv" }