{
    "bcoid": "GLY_001359",
    "title": "Hamster Protein Reactions (Reactome)",
    "description": "The Hamster Protein Reactions (Reactome) dataset contains reactions information for pathways for Cricetulus ...",
    "filename_list": "hamster_protein_reactions_reactome.csv",
    "filename": "hamster_protein_reactions_reactome.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Cricetulus griseus"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "Reactions Reactome"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ]
    },
    "minitable": {
        "content": [
            [
                "R-CGR-203235...",
                "Galactosylat..."
            ],
            [
                "R-CGR-203300...",
                "Sialylation ..."
            ]
        ],
        "headers": [
            "reaction_id...",
            "reaction_nam..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "reaction_id"
                },
                {
                    "type": "string",
                    "label": "reaction_name"
                },
                {
                    "type": "string",
                    "label": "cellular_location"
                },
                {
                    "type": "string",
                    "label": "pmid"
                },
                {
                    "type": "string",
                    "label": "pathway_id"
                },
                {
                    "type": "string",
                    "label": "equation"
                },
                {
                    "type": "string",
                    "label": "reaction_summary"
                }
            ],
            [
                "R-CGR-2032355",
                "Galactosylation of Pre-Notch",
                "Golgi lumen, Golgi membrane",
                "11707585",
                "",
                "",
                "Using Chinese hamster (Cricetulus griseus) ovarian cell lines deficient in different galactosyltransferases, Chen et al. established that beta-4-galactosyltransferase 1 (B4galt1) was necessary for galactosylation of beta 1,3-linked N-acetylglucosaminyl group added by fringe enzymes to O-linked fucosyl residues on Notch1. B4galt1-mediated galactosylation of Notch1 was necessary for fringe-induced modulation of Notch1 signaling. Since the genome of C. griseus has not been completely sequenced, it is possible that annotated C. griseus Notch isoforms do not represent full-length proteins. Annotated C. griseus Notch2 in particular seems truncated. Only those fucosylation and glycosylation sites that are conserved between Chinese hamster, mouse, human and rat are shown. Since the exact preference, if any, of fringe enzymes for Notch O-fucose sites is not known, the extension of an O-fucosyl residue at an unknown position is shown."
            ],
            [
                "R-CGR-2033005",
                "Sialylation of Pre-Notch",
                "Golgi lumen, Golgi membrane",
                "10935626",
                "",
                "",
                "Using Chinese hamster (Cricetulus griseus) ovary cells that express endogenous Notch1 but do not express endogenous Fringe proteins, Moloney et al. found after introduction of mouse Mfng that mature Notch1 had the Sia-alpha2,3-Gal-beta1,4-GlcNAc-beta1,3-fucitol tetrasaccharide attached to conserved serine and threonine residues in EGF repeats of Notch1 (Moloney et al. 2000). Sialyltransferases that could be involved in formation of this type of tetrasaccharide are St3gal3, St3gal4 and St3gal6 (Harduin-Lepers et al. 2001)."
            ]
        ]
    },
    "readme": "Name\n   - Hamster Protein Reactions (Reactome)\n\nVersion\n   - v-2.8.1\n\nCreated on\n  - \n\nModified on\n   - \n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@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], Kate Warner [k.warner1@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 Hamster Protein Reactions (Reactome) dataset contains reactions information for pathways for Cricetulus griseus [taxid:10029] UniProtKB accessions that includes reaction participants, pathway ID, reaction ID, PMID etc from Reactome database. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen.\n\nDescription Domain\n   Keywords\n   - Reactome\n   - Pathway\n   - Reactions\n   - PMID\n\n   Pipeline Steps\n   - Step-1: The script loads the Reactome reaction data from the triplestore containing triples from nt file to retrieve the information associated with the Reactome IDs and maps it to the UniProtKB canonical accessions and extracts the dataset in the csv format\n\nExecution Domain\n   Scripts   - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/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-cricetulus-griseus.nt\n      URI: https:/data.glygen.org/ln2downloads/ebi/2025_01_17/uniprot-proteome-cricetulus-griseus.nt\n   Output Subdomain\n      Name: hamster_protein_reactions_reactome.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/hamster_protein_reactions_reactome.csv\n      Name: hamster_protein_reactions_reactome.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/hamster_protein_reactions_reactome.stat.csv\n\nFields\n      Name: \"reaction_id\"\n     Description: \"The identifier assigned to a reaction in Reactome database\"\n      Unique Values: \"5\"\n      Name: \"reaction_name\"\n     Description: \"The name assigned to a reaction in Reactome database\"\n      Unique Values: \"5\"\n      Name: \"cellular_location\"\n     Description: \"The loaction in the cell where reaction occurs\"\n      Unique Values: \"4\"\n      Name: \"pmid\"\n     Description: \"NCBI PubMed database Identifier\"\n      Unique Values: \"10\"\n      Name: \"pathway_id\"\n     Description: \"Pathway Identifier\"\n      Unique Values: \"1\"\n      Name: \"equation\"\n     Description: \"\"\n      Unique Values: \"1\"\n      Name: \"reaction_summary\"\n     Description: \"\"\n      Unique Values: \"5\"",
    "downloadurl": "/ln2data/releases/data/v-2.8.1/reviewed/hamster_protein_reactions_reactome.csv"
}