{ "bcoid": "GLY_000329", "title": "Human Glycosylation Sites (GlyConnect) ", "description": "The Human Glycosylation Sites (GlyConnect) dataset contains human [taxid:9606] UniProtKB canonical accessions ...", "filename": "human_proteoform_glycosylation_sites_glyconnect.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Proteoform", "tags": "Glycosylation Sites", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P19652-1...", "..." ], [ "P19652-1...", "..." ] ], "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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"protein_xref_glyconnect", "688", "protein_xref_glyconnect", "688", "688", "9606", "Homo sapiens", "1295", "G85767HW", "Complex", "N-Linked", "4,5,1,0,0,0,0,0,0,0,0,0,0,0", "H4N5F1", "HexNAc(5)Hex(4)dHex(1)", "1827.6767", "1828.7029", "Hex:4 HexNAc:5 dHex:1", "G03382KH", "227", "Blood Serum", "UBERON_0001977", "", "", "", "", "", "", "NST", "NXT" ], [ "P01859-1", "176", "Asn", "G03382KH", "N-linked", "protein_xref_glyconnect", "688", "protein_xref_glyconnect", "688", "688", "9606", "Homo sapiens", "1295", "G85767HW", "Complex", "N-Linked", "4,5,1,0,0,0,0,0,0,0,0,0,0,0", "H4N5F1", "HexNAc(5)Hex(4)dHex(1)", "1827.6767", "1828.7029", "Hex:4 HexNAc:5 dHex:1", "G03382KH", "227", "Blood Serum", "UBERON_0001977", "", "", "", "", "", "", "NST", "NXT" ], [ "P01859-1", "176", "Asn", "G85767HW", "N-linked", "protein_xref_pubmed", "2363690", "protein_xref_glyconnect", "688", "688", "9606", "Homo sapiens", "1295", "G85767HW", "Complex", "N-Linked", "4,5,1,0,0,0,0,0,0,0,0,0,0,0", "H4N5F1", "HexNAc(5)Hex(4)dHex(1)", "1827.6767", "1828.7029", "Hex:4 HexNAc:5 dHex:1", "G03382KH", "227", "Blood Serum", "UBERON_0001977", "", "", "", "", "", "", "NST", "NXT" ], [ "P01859-1", "176", "Asn", "G03382KH", "N-linked", "protein_xref_pubmed", "2363690", "protein_xref_glyconnect", "688", "688", "9606", "Homo sapiens", "1295", "G85767HW", "Complex", "N-Linked", "4,5,1,0,0,0,0,0,0,0,0,0,0,0", "H4N5F1", "HexNAc(5)Hex(4)dHex(1)", "1827.6767", "1828.7029", "Hex:4 HexNAc:5 dHex:1", "G03382KH", "227", "Blood Serum", "UBERON_0001977", "", "", "", "", "", "", "NST", "NXT" ], [ "P02743-1", "51", "Asn", "G75850OP", "N-linked", "protein_xref_glyconnect", "560", "protein_xref_glyconnect", "560", "560", "9606", "Homo sapiens", "1357", "G75850OP", "Complex", "N-Linked", "5,4,0,1,0,0,0,0,0,0,0,0,0,0", "H5N4S1", "HexNAc(4)Hex(5)NeuAc(1)", "1931.6876", "1932.7652", "Hex:5 HexNAc:4 NeuAc:1", "G06356OH", "227", "Blood Serum", "UBERON_0001977", "", "", "", "", "", "", "NFT", "NXT" ], [ "P02743-1", "51", "Asn", "G06356OH", "N-linked", "protein_xref_glyconnect", "560", "protein_xref_glyconnect", "560", "560", "9606", "Homo sapiens", "1357", "G75850OP", "Complex", "N-Linked", "5,4,0,1,0,0,0,0,0,0,0,0,0,0", "H5N4S1", "HexNAc(4)Hex(5)NeuAc(1)", "1931.6876", "1932.7652", "Hex:5 HexNAc:4 NeuAc:1", "G06356OH", "227", "Blood Serum", "UBERON_0001977", "", "", "", "", "", "", "NFT", "NXT" ], [ "P02743-1", "51", "Asn", "G75850OP", "N-linked", "protein_xref_pubmed", "8202534", "protein_xref_glyconnect", "560", "560", "9606", "Homo sapiens", "1357", "G75850OP", "Complex", "N-Linked", "5,4,0,1,0,0,0,0,0,0,0,0,0,0", "H5N4S1", "HexNAc(4)Hex(5)NeuAc(1)", "1931.6876", "1932.7652", "Hex:5 HexNAc:4 NeuAc:1", "G06356OH", "227", "Blood Serum", "UBERON_0001977", "", "", "", "", "", "", "NFT", "NXT" ], [ "P02743-1", "51", "Asn", "G06356OH", "N-linked", "protein_xref_pubmed", "8202534", "protein_xref_glyconnect", "560", "560", "9606", "Homo sapiens", "1357", "G75850OP", "Complex", "N-Linked", "5,4,0,1,0,0,0,0,0,0,0,0,0,0", "H5N4S1", "HexNAc(4)Hex(5)NeuAc(1)", "1931.6876", "1932.7652", "Hex:5 HexNAc:4 NeuAc:1", "G06356OH", "227", "Blood Serum", "UBERON_0001977", "", "", "", "", "", "", "NFT", "NXT" ] ] }, "readme": "Name\n - Human Glycosylation Sites (GlyConnect) \n\nVersion\n - 1.8.25\n\nCreated on\n - 2020-02-10T10:16:50.152756\n\nModified on\n - 2020-08-19T13:57:36.415562\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 Human Glycosylation Sites (GlyConnect) dataset contains human [taxid:9606] 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:Homo sapiens). 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 provided in the 2019-09 UniProtKB release 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 (human_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_human_2020_06_08_10_37_47.json\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/source/glyconnect_human_2020_06_08_10_37_47.json\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_protein_masterlist.csv\n Name: human_protein_canonicalsequences.fasta\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_protein_canonicalsequences.fasta\n Name: glygen_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/glygen_masterlist.csv\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_glyconnect.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_proteoform_glycosylation_sites_glyconnect.csv\n Name: human_proteoform_glycosylation_sites_glyconnect.1.log\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/logs/human_proteoform_glycosylation_sites_glyconnect.1.log\n Name: human_proteoform_glycosylation_sites_glyconnect.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_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/human_proteoform_glycosylation_sites_glyconnect.csv" }