{ "bcoid": "GLY_000582", "title": "Human glycosylation sites [Automatic literature Mining] [Manually 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_manually_verified.csv", "filetype": "csv", "categories": { "status": [ "Reviewed" ], "molecule": [ "Proteoform" ], "species": [ "Homo sapiens" ], "tag": [ "glycosylation sites" ], "file_type": [ "csv" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "O00555-8...", "283..." ], [ "O00555-8...", "283..." ] ], "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": 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"10887202", "NVT", "NXT", "153", "153", "Asn", "Asn", "N" ], [ "P56817-1", "172", "Asn", "", "N-linked", "protein_xref_automatic_literature_mining", "10887202", "protein_xref_automatic_literature_mining", "10887202", "NGS", "NXS", "172", "172", "Asn", "Asn", "N" ], [ "P56817-1", "172", "Asn", "", "N-linked", "protein_xref_pubmed", "10887202", "protein_xref_automatic_literature_mining", "10887202", "NGS", "NXS", "172", "172", "Asn", "Asn", "N" ], [ "P56817-1", "223", "Asn", "", "N-linked", "protein_xref_automatic_literature_mining", "10887202", "protein_xref_automatic_literature_mining", "10887202", "NQS", "NXS", "223", "223", "Asn", "Asn", "N" ], [ "P56817-1", "223", "Asn", "", "N-linked", "protein_xref_pubmed", "10887202", "protein_xref_automatic_literature_mining", "10887202", "NQS", "NXS", "223", "223", "Asn", "Asn", "N" ] ] }, "readme": "Name\n - Human glycosylation sites [Automatic literature Mining] [Manually verified]\n\nVersion\n - v-2.3.1\n\nCreated on\n - 2021-08-02T15:33:34.395747\n\nModified on\n - 2022-09-26T09:08:12.559953\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@email.gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - Vijay Shanker [vijay@udel.edu], Karen Ross [ker25@georgetown.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). This file contains rows that are detected from automatic literature mining and which failed the automatic QC where the annotation (protein+site) didn't already exist in GlyGen. such rows are then manually verified by curators. 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 - Manual QC\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 where extracted where the rows failed the annotation QC i.e where the annotation didn't already exist in GlyGen. Such rows where manually verified by the curators and again only those rows that passed where added to the file. \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: proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/compiled/proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n Name: fruitfly_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/fruitfly_proteoform_glycosylation_sites_glyconnect.csv\n Name: fruitfly_proteoform_glycosylation_sites_oglcnac_atlas.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/fruitfly_proteoform_glycosylation_sites_oglcnac_atlas.csv\n Name: fruitfly_proteoform_glycosylation_sites_oglcnac_mcw.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/fruitfly_proteoform_glycosylation_sites_oglcnac_mcw.csv\n Name: fruitfly_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/fruitfly_proteoform_glycosylation_sites_uniprotkb.csv\n Name: hcv1a_proteoform_glycosylation_sites_literature.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/hcv1a_proteoform_glycosylation_sites_literature.csv\n Name: hcv1a_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/hcv1a_proteoform_glycosylation_sites_uniprotkb.csv\n Name: hcv1b_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/hcv1b_proteoform_glycosylation_sites_uniprotkb.csv\n Name: human_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_glyconnect.csv\n Name: human_proteoform_glycosylation_sites_gptwiki.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_gptwiki.csv\n Name: human_proteoform_glycosylation_sites_harvard.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_harvard.csv\n Name: human_proteoform_glycosylation_sites_literature.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_literature.csv\n Name: human_proteoform_glycosylation_sites_literature_mining.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_literature_mining.csv\n Name: human_proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n Name: human_proteoform_glycosylation_sites_oglcnac_atlas.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_oglcnac_atlas.csv\n Name: human_proteoform_glycosylation_sites_oglcnac_mcw.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_oglcnac_mcw.csv\n Name: human_proteoform_glycosylation_sites_o_gluc.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_o_gluc.csv\n Name: human_proteoform_glycosylation_sites_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_pdb.csv\n Name: human_proteoform_glycosylation_sites_tyr_o_linked.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_tyr_o_linked.csv\n Name: human_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_unicarbkb.csv\n Name: human_proteoform_glycosylation_sites_unicarbkb_glycomics_study.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_unicarbkb_glycomics_study.csv\n Name: human_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_uniprotkb.csv\n Name: mouse_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/mouse_proteoform_glycosylation_sites_glyconnect.csv\n Name: mouse_proteoform_glycosylation_sites_literature_mining.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/mouse_proteoform_glycosylation_sites_literature_mining.csv\n Name: mouse_proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/mouse_proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n Name: mouse_proteoform_glycosylation_sites_oglcnac_atlas.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/mouse_proteoform_glycosylation_sites_oglcnac_atlas.csv\n Name: mouse_proteoform_glycosylation_sites_oglcnac_mcw.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/mouse_proteoform_glycosylation_sites_oglcnac_mcw.csv\n Name: mouse_proteoform_glycosylation_sites_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/mouse_proteoform_glycosylation_sites_pdb.csv\n Name: mouse_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/mouse_proteoform_glycosylation_sites_unicarbkb.csv\n Name: mouse_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/mouse_proteoform_glycosylation_sites_uniprotkb.csv\n Name: rat_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/rat_proteoform_glycosylation_sites_glyconnect.csv\n Name: rat_proteoform_glycosylation_sites_literature_mining.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/rat_proteoform_glycosylation_sites_literature_mining.csv\n Name: rat_proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/rat_proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n Name: rat_proteoform_glycosylation_sites_oglcnac_atlas.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/rat_proteoform_glycosylation_sites_oglcnac_atlas.csv\n Name: rat_proteoform_glycosylation_sites_oglcnac_mcw.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/rat_proteoform_glycosylation_sites_oglcnac_mcw.csv\n Name: rat_proteoform_glycosylation_sites_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/rat_proteoform_glycosylation_sites_pdb.csv\n Name: rat_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/rat_proteoform_glycosylation_sites_unicarbkb.csv\n Name: rat_proteoform_glycosylation_sites_unicarbkb_glycomics_study.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/rat_proteoform_glycosylation_sites_unicarbkb_glycomics_study.csv\n Name: rat_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/rat_proteoform_glycosylation_sites_uniprotkb.csv\n Name: sarscov1_proteoform_glycosylation_sites_literature.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/sarscov1_proteoform_glycosylation_sites_literature.csv\n Name: sarscov1_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/sarscov1_proteoform_glycosylation_sites_unicarbkb.csv\n Name: sarscov1_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/sarscov1_proteoform_glycosylation_sites_uniprotkb.csv\n Name: sarscov2_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.csv\n Name: sarscov2_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/sarscov2_proteoform_glycosylation_sites_unicarbkb.csv\n Name: sarscov2_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/sarscov2_proteoform_glycosylation_sites_uniprotkb.csv\n Name: yeast_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_proteoform_glycosylation_sites_glyconnect.csv\n Name: yeast_proteoform_glycosylation_sites_oglcnac_atlas.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_proteoform_glycosylation_sites_oglcnac_atlas.csv\n Name: yeast_proteoform_glycosylation_sites_oglcnac_mcw.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_proteoform_glycosylation_sites_oglcnac_mcw.csv\n Name: yeast_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_proteoform_glycosylation_sites_uniprotkb.csv\n Name: n_sequon_info.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2023_10_11/cellosaurus.txt\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n Name: human_proteoform_glycosylation_sites_literature_mining_manually_verified.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_literature_mining_manually_verified.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"94\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"133\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"4\"\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: \"3\"\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: \"105\"\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: \"105\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"45\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"7\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"133\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"133\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"4\"", "downloadurl": "/ln2data/releases/data/v-2.3.1/reviewed/human_proteoform_glycosylation_sites_literature_mining_manually_verified.csv" }