{
    "bcoid": "GLY_001036",
    "title": "Chicken glycosylation sites [Automatic literature Mining] [Manually verified]",
    "description": "List of Gallus gallus [taxid:9031] proteins with information on glycosylation sites detected from PubMed ...",
    "filename": "chicken_proteoform_glycosylation_sites_literature_mining_manually_verified.csv",
    "filetype": "csv",
    "categories": {
        "status": [
            "Reviewed"
        ],
        "molecule": [
            "Proteoform"
        ],
        "species": [
            "Gallus gallus"
        ],
        "tag": [
            "glycosylation sites"
        ],
        "file_type": [
            "csv"
        ],
        "scope": [
            "internal"
        ]
    },
    "minitable": {
        "content": [],
        "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": "n_sequon"
                },
                {
                    "type": "string",
                    "label": "n_sequon_type"
                },
                {
                    "type": "string",
                    "label": "start_pos"
                },
                {
                    "type": "string",
                    "label": "end_pos"
                },
                {
                    "type": "string",
                    "label": "start_aa"
                },
                {
                    "type": "string",
                    "label": "end_aa"
                },
                {
                    "type": "string",
                    "label": "site_seq"
                }
            ]
        ]
    },
    "readme": "Name\n   - Chicken glycosylation sites [Automatic literature Mining] [Manually verified]\n\nVersion\n   - v-2.5.1\n\nModified on\n   - 2024-05-21T14:25:51.391Z\n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@email.gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Kate Warner [k.warner1@gwu.edu]\n\nAuthors\n   - Vijay Shanker [vijay@udel.edu], Karen Ross [ker25@georgetown.edu]\n\nChecksum\n   - \n\nUsability Domain\n   - List of Gallus gallus [taxid:9031] 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-2.5.1/compiled/proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n      Name: dicty_proteoform_glycosylation_sites_glyconnect.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/dicty_proteoform_glycosylation_sites_glyconnect.csv\n      Name: dicty_proteoform_glycosylation_sites_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/dicty_proteoform_glycosylation_sites_uniprotkb.csv\n      Name: fruitfly_proteoform_glycosylation_sites_glyconnect.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/reviewed/fruitfly_proteoform_glycosylation_sites_uniprotkb.csv\n      Name: hcv1a_proteoform_glycosylation_sites_literature.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/hcv1a_proteoform_glycosylation_sites_literature.csv\n      Name: hcv1a_proteoform_glycosylation_sites_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/hcv1a_proteoform_glycosylation_sites_uniprotkb.csv\n      Name: hcv1b_proteoform_glycosylation_sites_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/hcv1b_proteoform_glycosylation_sites_uniprotkb.csv\n      Name: human_proteoform_glycosylation_sites_glyconnect.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/human_proteoform_glycosylation_sites_glyconnect.csv\n      Name: human_proteoform_glycosylation_sites_gptwiki.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/human_proteoform_glycosylation_sites_gptwiki.csv\n      Name: human_proteoform_glycosylation_sites_harvard.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/human_proteoform_glycosylation_sites_harvard.csv\n      Name: human_proteoform_glycosylation_sites_literature.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/reviewed/human_proteoform_glycosylation_sites_uniprotkb.csv\n      Name: mouse_proteoform_glycosylation_sites_glyconnect.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/reviewed/mouse_proteoform_glycosylation_sites_pdb.csv\n      Name: mouse_proteoform_glycosylation_sites_unicarbkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/mouse_proteoform_glycosylation_sites_unicarbkb.csv\n      Name: mouse_proteoform_glycosylation_sites_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/mouse_proteoform_glycosylation_sites_uniprotkb.csv\n      Name: pig_proteoform_glycosylation_sites_glyconnect.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/pig_proteoform_glycosylation_sites_glyconnect.csv\n      Name: pig_proteoform_glycosylation_sites_oglcnac_atlas.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/pig_proteoform_glycosylation_sites_oglcnac_atlas.csv\n      Name: pig_proteoform_glycosylation_sites_oglcnac_mcw.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/pig_proteoform_glycosylation_sites_oglcnac_mcw.csv\n      Name: pig_proteoform_glycosylation_sites_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/pig_proteoform_glycosylation_sites_uniprotkb.csv\n      Name: rat_proteoform_glycosylation_sites_glyconnect.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/reviewed/rat_proteoform_glycosylation_sites_pdb.csv\n      Name: rat_proteoform_glycosylation_sites_unicarbkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/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-2.5.1/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-2.5.1/reviewed/rat_proteoform_glycosylation_sites_uniprotkb.csv\n      Name: sarscov1_proteoform_glycosylation_sites_literature.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/sarscov1_proteoform_glycosylation_sites_literature.csv\n      Name: sarscov1_proteoform_glycosylation_sites_unicarbkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/sarscov1_proteoform_glycosylation_sites_unicarbkb.csv\n      Name: sarscov1_proteoform_glycosylation_sites_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/sarscov1_proteoform_glycosylation_sites_uniprotkb.csv\n      Name: sarscov2_proteoform_glycosylation_sites_glyconnect.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.csv\n      Name: sarscov2_proteoform_glycosylation_sites_unicarbkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/sarscov2_proteoform_glycosylation_sites_unicarbkb.csv\n      Name: sarscov2_proteoform_glycosylation_sites_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/sarscov2_proteoform_glycosylation_sites_uniprotkb.csv\n      Name: yeast_proteoform_glycosylation_sites_glyconnect.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/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-2.5.1/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-2.5.1/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-2.5.1/reviewed/yeast_proteoform_glycosylation_sites_uniprotkb.csv\n      Name: n_sequon_info.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/misc/n_sequon_info.csv\n      Name: sample_mapping.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/misc/sample_mapping.csv\n      Name: cellosaurus.txt\n      URI: https:/data.glygen.org/ln2downloads/cellosaurus/2024_04_02/cellosaurus.txt\n   Output Subdomain\n      Name: chicken_proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/chicken_proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n      Name: chicken_proteoform_glycosylation_sites_literature_mining_manually_verified.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/chicken_proteoform_glycosylation_sites_literature_mining_manually_verified.stat.csv\n\nFields",
    "downloadurl": "/ln2data/releases/data/v-2.5.1/reviewed/chicken_proteoform_glycosylation_sites_literature_mining_manually_verified.csv"
}