{
    "bcoid": "GLY_000471",
    "title": "SARS-CoV1 Protein PTM Annotation (UniProtKB)",
    "description": "The SARS coronavirus (SARS-CoV-1) Protein PTM Annotation (UniProtKB) dataset contains sarscov1 [taxid:694009] ...",
    "filename": "sarscov1_protein_ptm_annotation_uniprotkb.csv",
    "filetype": "csv",
    "categories": {
        "species": "SARS coronavirus (SARS-CoV-1)",
        "molecule": "Protein",
        "tags": "PTM annotation",
        "file_type": "csv",
        "status": "Reviewed",
        "scope": "internal"
    },
    "minitable": {
        "content": [
            [
                "P0C6U8-1...",
                "protein_xref..."
            ],
            [
                "P0C6U8-1...",
                "protein_xref..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "xref_key..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "xref_key"
                },
                {
                    "type": "string",
                    "label": "xref_id"
                },
                {
                    "type": "string",
                    "label": "eco_id"
                },
                {
                    "type": "string",
                    "label": "ptm_annotation"
                }
            ],
            [
                "P0C6U8-1",
                "protein_xref_uniprotkb",
                "P0C6U8",
                "",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed (By similarity)."
            ],
            [
                "P0C6U8-1",
                "protein_xref_pubmed",
                "",
                "",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed (By similarity)."
            ],
            [
                "P59594-1",
                "protein_xref_uniprotkb",
                "P59594",
                "ECO_0000255",
                "Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host cell furin or another cellular protease to yield the mature S1 and S2 proteins. Additionally, a second cleavage leads to the release of a fusion peptide after viral attachment to host cell receptor."
            ],
            [
                "P59594-1",
                "protein_xref_pubmed",
                "MF_04099",
                "ECO_0000255",
                "Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host cell furin or another cellular protease to yield the mature S1 and S2 proteins. Additionally, a second cleavage leads to the release of a fusion peptide after viral attachment to host cell receptor."
            ],
            [
                "P59594-1",
                "protein_xref_uniprotkb",
                "P59594",
                "ECO_0000255",
                "The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested within host endosomes."
            ],
            [
                "P59594-1",
                "protein_xref_pubmed",
                "MF_04099",
                "ECO_0000255",
                "The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested within host endosomes."
            ],
            [
                "P59594-1",
                "protein_xref_uniprotkb",
                "P59594",
                "ECO_0000269",
                "The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested by cathepsin CTSL within endosomes."
            ],
            [
                "P59594-1",
                "protein_xref_pubmed",
                "17134730",
                "ECO_0000269",
                "The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested by cathepsin CTSL within endosomes."
            ],
            [
                "P59595-1",
                "protein_xref_uniprotkb",
                "P59595",
                "ECO_0000255",
                "Phosphorylated on serine and threonine residues (By similarity). Phosphorylated by host GSK3A and GSK3B. Phosphorylation allows recruitment of host RNA helicase DDX1 which facilitates template readthrough and enables longer subgenomic mRNA synthesis."
            ],
            [
                "P59595-1",
                "protein_xref_pubmed",
                "MF_04096",
                "ECO_0000255",
                "Phosphorylated on serine and threonine residues (By similarity). Phosphorylated by host GSK3A and GSK3B. Phosphorylation allows recruitment of host RNA helicase DDX1 which facilitates template readthrough and enables longer subgenomic mRNA synthesis."
            ],
            [
                "P59595-1",
                "protein_xref_uniprotkb",
                "P59595",
                "ECO_0000269",
                "Phosphorylated on serine and threonine residues (By similarity). Phosphorylated by host GSK3A and GSK3B. Phosphorylation allows recruitment of host RNA helicase DDX1 which facilitates template readthrough and enables longer subgenomic mRNA synthesis."
            ],
            [
                "P59595-1",
                "protein_xref_pubmed",
                "19106108",
                "ECO_0000269",
                "Phosphorylated on serine and threonine residues (By similarity). Phosphorylated by host GSK3A and GSK3B. Phosphorylation allows recruitment of host RNA helicase DDX1 which facilitates template readthrough and enables longer subgenomic mRNA synthesis."
            ],
            [
                "P59595-1",
                "protein_xref_pubmed",
                "24766657",
                "ECO_0000269",
                "Phosphorylated on serine and threonine residues (By similarity). Phosphorylated by host GSK3A and GSK3B. Phosphorylation allows recruitment of host RNA helicase DDX1 which facilitates template readthrough and enables longer subgenomic mRNA synthesis."
            ],
            [
                "P59595-1",
                "protein_xref_uniprotkb",
                "P59595",
                "ECO_0000255",
                "ADP-ribosylated. The ADP-ribosylation is retained in the virion during infection."
            ],
            [
                "P59595-1",
                "protein_xref_pubmed",
                "MF_04096",
                "ECO_0000255",
                "ADP-ribosylated. The ADP-ribosylation is retained in the virion during infection."
            ],
            [
                "P59632-1",
                "protein_xref_uniprotkb",
                "P59632",
                "ECO_0000269",
                "Exists in both O-glycosylated and non-glycosylated forms. The glycosylated form is associated with the virion."
            ],
            [
                "P59632-1",
                "protein_xref_pubmed",
                "16474139",
                "ECO_0000269",
                "Exists in both O-glycosylated and non-glycosylated forms. The glycosylated form is associated with the virion."
            ],
            [
                "P0C6X7-1",
                "protein_xref_uniprotkb",
                "P0C6X7",
                "",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed (By similarity)."
            ],
            [
                "P0C6X7-1",
                "protein_xref_pubmed",
                "",
                "",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed (By similarity)."
            ]
        ]
    },
    "readme": "Name\n   - SARS-CoV1 Protein PTM Annotation (UniProtKB)\n\nVersion\n   - 1.7.13\n\nCreated on\n  - 2020-04-19T11:41:41.632491\n\nModified on\n   - 2020-04-19T11:48:13.221709\n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n   - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n   - \n\nUsability Domain\n   - The SARS coronavirus (SARS-CoV-1) Protein PTM Annotation (UniProtKB) dataset contains sarscov1 [taxid:694009] PTM annotations for UniProtKB canonical accessions. The annotation is the curated statements of mainly about glycosylation and phosphorylation. The dataset is derived form 2020-01 UniprotKB release. If you use this dataset please give proper attribution to UniProtKB and GlyGen\n\nDescription Domain\n   Keywords\n   - ptm annotation\n   - glycosylation\n   - phosphorylation\n\n   Pipeline Steps\n   - Step-1: The script extracts the PTM annotation strings from the triplestore for the UniProtKB canonical sequnces asnd extracts as a dataset in a csv format\n\nExecution Domain\n   Scripts   - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-protein-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: uniprot-proteome-sars-cov-2.nt\n      URI: https://data.glygen.org/ln2data/releases/data/v-1.7.13/reviewed/uniprot-proteome-sars-cov-2.nt\n      Name: sarscov1_protein_masterlist.csv\n      URI: https://data.glygen.org/ln2data/releases/data/v-1.7.13/reviewed/sarscov1_protein_masterlist.csv\n   Output Subdomain\n      Name: sarscov1_protein_ptm_annotation_uniprotkb.csv\n      URI: http://data.glygen.org/ln2data/releases/data/v-1.7.13/reviewed/sarscov1_protein_ptm_annotation_uniprotkb.csv\n      Name: sarscov1_protein_ptm_annotation_uniprotkb.stat.csv\n      URI: http://data.glygen.org/ln2data/releases/data/v-1.7.13/reviewed/sarscov1_protein_ptm_annotation_uniprotkb.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\n     Description: \"\"\n      Unique Values: \"5\"\n      Name: \"eco_id\"\n     Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n      Unique Values: \"3\"\n      Name: \"ptm_annotation\"\n     Description: \"The Post Translational Modifiaction (PTM) annotation in UniProtKB that provides more context and description about the PTMs occuring on a proein\"\n      Unique Values: \"7\"\n      Name: \"xref_id\"\n     Description: \"ID of the X-ref\"\n      Unique Values: \"12\"\n      Name: \"xref_key\"\n     Description: \"Source key associated to the  xref_id\"\n      Unique Values: \"2\"",
    "downloadurl": "/ln2data/releases/data/v-1.7.13/reviewed/sarscov1_protein_ptm_annotation_uniprotkb.csv"
}