{ "bcoid": "GLY_000330", "title": "Mouse Glycosylation Sites (GlyConnect) ", "description": "The Mouse Glycosylation Sites (GlyConnect) dataset contains mouse [taxid:10090] UniProtKB canonical accessions ...", "filename": "mouse_proteoform_glycosylation_sites_glyconnect.csv", "filetype": "csv", "categories": { "species": "Mus musculus", "molecule": "Proteoform", "tags": "Glycosylation Sites", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P10761-1...", "..." ], [ "P10761-1...", "..." ] ], "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", 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"HexNAc(4)Hex(6)dHex(1)NeuAc(1)", "2239.7983", "2241.0506", "Hex:6 HexNAc:4 dHex:1 NeuAc:1", "G82830MN", "81", "Zona Pellucida", "UBERON_0000086", "", "", "", "", "", "", "", "" ], [ "P10761-1", "", "", "G82830MN", "N-linked", "protein_xref_pubmed", "10713085", "protein_xref_glyconnect", "635", "635", "10090", "Mus musculus", "1435", "G82388RB", "Complex", "N-Linked", "6,4,1,1,0,0,0,0,0,0,0,0,0,0", "H6N4F1S1", "HexNAc(4)Hex(6)dHex(1)NeuAc(1)", "2239.7983", "2241.0506", "Hex:6 HexNAc:4 dHex:1 NeuAc:1", "G82830MN", "81", "Zona Pellucida", "UBERON_0000086", "", "", "", "", "", "", "", "" ] ] }, "readme": "Name\n - Mouse Glycosylation Sites (GlyConnect) \n\nVersion\n - 1.8.25\n\nCreated on\n - 2020-02-10T12:16:18.548585\n\nModified on\n - 2020-08-07T15:07:41.538669\n\nCreated by\n - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n - Frederique Lisacek [frederique.lisacek@sib.swiss], Julien Mariethoz [julien.mariethoz@sib.swiss]\n\nChecksum\n - \n\nUsability Domain\n - The Mouse Glycosylation Sites (GlyConnect) dataset contains mouse [taxid:10090] UniProtKB canonical accessions with information on reported glycosylation sites in GlyConnect database (https://glyconnect.expasy.org/; PMID: 30574787).A json file was derived through GlyConnect API (https://glyconnect.expasy.org/api/docs/index.html?url=/api/assets/swagger.json#/Glycosylation/listGlycosylationsAsJson) (Query: taxonomy:Mus musculus). If you use this dataset please provide proper attribution to GlyConnect and GlyGen.\n\nDescription Domain\n Keywords\n - glycosylation\n - reported glycosylation\n\n Pipeline Steps\n - Step-1: The script loads the glycosylation information from the input JSON file and extracts the data. The QC checks filter out: 1) any rows where the UniProtKB accession is not included in the GlyGen protein list (https://data.glygen.org/GLYDS000001) and/or 2) if the given glycosylation position and amino acid does not match to the amino acid on the .fasta sequence for that protein (However it does pass if the amino acid +glyco-site is empty (as these records correspond to the \"not reported\" glyco-sites and/or 3) If the glycosylation type does not associate to the glycostlation based on amino acid (i.e if a N-linked is associated with Ser/Thr residue, etc). 4) If the glyco-site is not reported and the glycosylation type is ambigious (c-Linked/o-linked) and/or 5) if the saccharide (GlyTouCan) is not present in the GlyGen glycan masterlist. All the flagged entries are added in the log file (mouse_proteoform_glycosylation_sites_glyconnect.1.log)\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: glyconnect_mouse_2020_06_08_10_41_58.json\n URI: https://data.glygen.org/ln2wwwdata/source/glyconnect_mouse_2020_06_08_10_41_58.json\n Name: mouse_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_masterlist.csv\n Name: mouse_protein_canonicalsequences.fasta\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_canonicalsequences.fasta\n Output Subdomain\n Name: mouse_proteoform_glycosylation_sites_glyconnect.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_proteoform_glycosylation_sites_glyconnect.csv\n Name: mouse_proteoform_glycosylation_sites_glyconnect.1.log\n URI: http://data.glygen.org/ln2wwwdata/mouse_proteoform_glycosylation_sites_glyconnect.1.log\n Name: mouse_proteoform_glycosylation_sites_glyconnect.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_proteoform_glycosylation_sites_glyconnect.stat.csv\n\nFields\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"119\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"119\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"120\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"49\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"118\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"117\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"115\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.8.25/reviewed/mouse_proteoform_glycosylation_sites_glyconnect.csv" }