{
    "bcoid": "GLY_000472",
    "title": "SARS-CoV2 Protein PTM Annotation (UniProtKB)",
    "description": "The SARS coronavirus (SARS-CoV-2 or 2019-nCoV) Protein PTM Annotation (UniProtKB) dataset contains sarscov2 ...",
    "filename": "sarscov2_protein_ptm_annotation_uniprotkb.csv",
    "filetype": "csv",
    "categories": {
        "species": "SARS coronavirus (SARS-CoV-2 or 2019-nCoV)",
        "molecule": "Protein",
        "tags": "PTM annotation",
        "file_type": "csv",
        "status": "Reviewed",
        "scope": "internal"
    },
    "minitable": {
        "content": [
            [
                "P0DTD1-1...",
                "protein_xref..."
            ],
            [
                "P0DTD1-1...",
                "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"
                }
            ],
            [
                "P0DTD1-1",
                "protein_xref_uniprotkb",
                "P0DTD1",
                "ECO_0000250",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed."
            ],
            [
                "P0DTD1-1",
                "protein_xref_pubmed",
                "P0C6X7",
                "ECO_0000250",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed."
            ],
            [
                "P0DTC3-1",
                "protein_xref_uniprotkb",
                "P0DTC3",
                "ECO_0000250",
                "Exists in both O-glycosylated and non-glycosylated forms. The glycosylated form is associated with the virion."
            ],
            [
                "P0DTC3-1",
                "protein_xref_pubmed",
                "P59632",
                "ECO_0000250",
                "Exists in both O-glycosylated and non-glycosylated forms. The glycosylated form is associated with the virion."
            ],
            [
                "P0DTC2-1",
                "protein_xref_uniprotkb",
                "P0DTC2",
                "ECO_0000255",
                "The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested within host endosomes."
            ],
            [
                "P0DTC2-1",
                "protein_xref_pubmed",
                "MF_04099",
                "ECO_0000255",
                "The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested within host endosomes."
            ],
            [
                "P0DTC2-1",
                "protein_xref_uniprotkb",
                "P0DTC2",
                "ECO_0000269",
                "Highly decorated by heterogeneous N-linked glycans protruding from the trimer surface (PubMed:32075877, PubMed:32155444, PubMed:32929138). Highly glycosylated by host both on S1 and S2 subunits, occluding many regions across the surface of the protein (PubMed:32366695, PubMed:32363391, PubMed:32929138). Approximately 40% of the protein surface is shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor binding domain (PubMed:32929138)."
            ],
            [
                "P0DTC2-1",
                "protein_xref_pubmed",
                "32929138",
                "ECO_0000269",
                "Highly decorated by heterogeneous N-linked glycans protruding from the trimer surface (PubMed:32075877, PubMed:32155444, PubMed:32929138). Highly glycosylated by host both on S1 and S2 subunits, occluding many regions across the surface of the protein (PubMed:32366695, PubMed:32363391, PubMed:32929138). Approximately 40% of the protein surface is shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor binding domain (PubMed:32929138)."
            ],
            [
                "P0DTC2-1",
                "protein_xref_pubmed",
                "32075877",
                "ECO_0000269",
                "Highly decorated by heterogeneous N-linked glycans protruding from the trimer surface (PubMed:32075877, PubMed:32155444, PubMed:32929138). Highly glycosylated by host both on S1 and S2 subunits, occluding many regions across the surface of the protein (PubMed:32366695, PubMed:32363391, PubMed:32929138). Approximately 40% of the protein surface is shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor binding domain (PubMed:32929138)."
            ],
            [
                "P0DTC2-1",
                "protein_xref_pubmed",
                "32366695",
                "ECO_0000269",
                "Highly decorated by heterogeneous N-linked glycans protruding from the trimer surface (PubMed:32075877, PubMed:32155444, PubMed:32929138). Highly glycosylated by host both on S1 and S2 subunits, occluding many regions across the surface of the protein (PubMed:32366695, PubMed:32363391, PubMed:32929138). Approximately 40% of the protein surface is shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor binding domain (PubMed:32929138)."
            ],
            [
                "P0DTC2-1",
                "protein_xref_pubmed",
                "32363391",
                "ECO_0000269",
                "Highly decorated by heterogeneous N-linked glycans protruding from the trimer surface (PubMed:32075877, PubMed:32155444, PubMed:32929138). Highly glycosylated by host both on S1 and S2 subunits, occluding many regions across the surface of the protein (PubMed:32366695, PubMed:32363391, PubMed:32929138). Approximately 40% of the protein surface is shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor binding domain (PubMed:32929138)."
            ],
            [
                "P0DTC2-1",
                "protein_xref_pubmed",
                "32155444",
                "ECO_0000269",
                "Highly decorated by heterogeneous N-linked glycans protruding from the trimer surface (PubMed:32075877, PubMed:32155444, PubMed:32929138). Highly glycosylated by host both on S1 and S2 subunits, occluding many regions across the surface of the protein (PubMed:32366695, PubMed:32363391, PubMed:32929138). Approximately 40% of the protein surface is shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor binding domain (PubMed:32929138)."
            ],
            [
                "P0DTC2-1",
                "protein_xref_uniprotkb",
                "P0DTC2",
                "ECO_0000269",
                "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 (PubMed:32155444). Additionally, a second cleavage leads to the release of a fusion peptide after viral attachment to host cell receptor (By similarity). The presence of a furin polybasic cleavage site sets SARS-CoV-2 S apart from SARS-CoV S that possesses a monobasic S1/S2 cleavage site processed upon entry of target cells (PubMed:32155444, PubMed:32362314)."
            ],
            [
                "P0DTC2-1",
                "protein_xref_pubmed",
                "32155444",
                "ECO_0000269",
                "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 (PubMed:32155444). Additionally, a second cleavage leads to the release of a fusion peptide after viral attachment to host cell receptor (By similarity). The presence of a furin polybasic cleavage site sets SARS-CoV-2 S apart from SARS-CoV S that possesses a monobasic S1/S2 cleavage site processed upon entry of target cells (PubMed:32155444, PubMed:32362314)."
            ],
            [
                "P0DTC2-1",
                "protein_xref_pubmed",
                "32362314",
                "ECO_0000269",
                "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 (PubMed:32155444). Additionally, a second cleavage leads to the release of a fusion peptide after viral attachment to host cell receptor (By similarity). The presence of a furin polybasic cleavage site sets SARS-CoV-2 S apart from SARS-CoV S that possesses a monobasic S1/S2 cleavage site processed upon entry of target cells (PubMed:32155444, PubMed:32362314)."
            ],
            [
                "P0DTC2-1",
                "protein_xref_uniprotkb",
                "P0DTC2",
                "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 (PubMed:32155444). Additionally, a second cleavage leads to the release of a fusion peptide after viral attachment to host cell receptor (By similarity). The presence of a furin polybasic cleavage site sets SARS-CoV-2 S apart from SARS-CoV S that possesses a monobasic S1/S2 cleavage site processed upon entry of target cells (PubMed:32155444, PubMed:32362314)."
            ],
            [
                "P0DTC2-1",
                "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 (PubMed:32155444). Additionally, a second cleavage leads to the release of a fusion peptide after viral attachment to host cell receptor (By similarity). The presence of a furin polybasic cleavage site sets SARS-CoV-2 S apart from SARS-CoV S that possesses a monobasic S1/S2 cleavage site processed upon entry of target cells (PubMed:32155444, PubMed:32362314)."
            ],
            [
                "P0DTC1-1",
                "protein_xref_uniprotkb",
                "P0DTC1",
                "ECO_0000250",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed."
            ],
            [
                "P0DTC1-1",
                "protein_xref_pubmed",
                "P0C6X7",
                "ECO_0000250",
                "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed."
            ],
            [
                "P0DTC9-1",
                "protein_xref_uniprotkb",
                "P0DTC9",
                "ECO_0000255",
                "ADP-ribosylated. The ADP-ribosylation is retained in the virion during infection."
            ],
            [
                "P0DTC9-1",
                "protein_xref_pubmed",
                "MF_04096",
                "ECO_0000255",
                "ADP-ribosylated. The ADP-ribosylation is retained in the virion during infection."
            ],
            [
                "P0DTC9-1",
                "protein_xref_uniprotkb",
                "P0DTC9",
                "ECO_0000255",
                "Phosphorylated on serine and threonine residues."
            ],
            [
                "P0DTC9-1",
                "protein_xref_pubmed",
                "MF_04096",
                "ECO_0000255",
                "Phosphorylated on serine and threonine residues."
            ]
        ]
    },
    "readme": "Name\n   - SARS-CoV2 Protein PTM Annotation (UniProtKB)\n\nVersion\n   - 1.8.25\n\nCreated on\n  - 2020-04-19T11:44:49.318101\n\nModified on\n   - 2020-04-19T11:48:48.458026\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-2 or 2019-nCoV) Protein PTM Annotation (UniProtKB) dataset contains sarscov2 [taxid:2697049] 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-1.8.25/reviewed/uniprot-proteome-sars-cov-2.nt\n      Name: sarscov2_protein_masterlist.csv\n      URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/sarscov2_protein_masterlist.csv\n   Output Subdomain\n      Name: sarscov2_protein_ptm_annotation_uniprotkb.csv\n      URI: http://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/sarscov2_protein_ptm_annotation_uniprotkb.csv\n      Name: sarscov2_protein_ptm_annotation_uniprotkb.stat.csv\n      URI: http://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/sarscov2_protein_ptm_annotation_uniprotkb.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/sarscov2_protein_ptm_annotation_uniprotkb.csv"
}