{ "bcoid": "GLY_000481", "title": "Human Glycosylation Sites [Automatic Literature Mining] [Automatically verified]", "description": "List of human [taxid:9606] proteins with information on glycosylation sites detected from PubMed database(abstracts-only) ...", "filename": "human_proteoform_glycosylation_sites_literature_mining.csv", "filetype": "csv", "categories": { "status": "Reviewed", "molecule": "Proteoform", "species": "Homo sapiens", "tags": "glycosylation sites", "file_type": "csv", "scope": "internal" }, "minitable": { "content": [ [ "O00300-1...", "183..." ], [ "O00300-1...", "183..." ] ], "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" }, 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"readme": "Name\n - Human Glycosylation Sites [Automatic Literature Mining] [Automatically verified]\n\nVersion\n - 1.10.6\n\nCreated on\n - 2020-04-20T16:47:37.482643\n\nModified on\n - 2021-08-02T15:58:23.629073\n\nCreated by\n - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@email.gwu.edu]\n\nAuthors\n - Rahi Navelkar [rsn13@gwu.edu], Vijay Shanker [vijay@udel.edu], Karen Ross [ker25@georgetown.edu], Xavier Holmes [xavierh@email.gwu.edu]\n\nChecksum\n - \n\nUsability Domain\n - List of human [taxid:9606] proteins with information on glycosylation sites detected from PubMed database(abstracts-only) through Automatic mining tool developed by Dr. Vijay Shanker (University of Delaware). The listed protein (UniProtKB) accessions are part of the GlyGen UniProtKB canonical list (https://data.glygen.org/GLYDS000001)\n\nDescription Domain\n Keywords\n - proteins\n - canonical\n - glycosylation sites\n - GlyTouCan\n - Automatic Literature Mining\n\n Pipeline Steps\n - Step-1: The input file was downloaded from the provider(s) and QC steps were done to validate the protein and site annotation. Additional QC was done to check wether the annotion (protein +site) is already present in GlyGen or not. Only those rows which passed all the QC filters where added to the output file. \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: proteoform_glycosylation_sites_literature_mining.csv\n URI: https://data.glygen.org/ln2wwwdata/source/proteoform_glycosylation_sites_literature_mining.csv\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_literature_mining.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/human_proteoform_glycosylation_sites_literature_mining.csv\n Name: human_proteoform_glycosylation_sites_literature_mining.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/human_proteoform_glycosylation_sites_literature_mining.stat.csv\n\nFields\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"123404\"", "downloadurl": "/ln2data/releases/data/v-1.10.6/reviewed/human_proteoform_glycosylation_sites_literature_mining.csv" }