{
    "bcoid": "GLY_000296",
    "title": "Glycan Xref ChEBI",
    "description": " The dataset provides cross-references to ChEBI Id's for the associated glycan (GlyTouCan Accession). ...",
    "filename_list": "glycan_xref_chebi.csv",
    "filename": "glycan_xref_chebi.csv",
    "filetype": "csv",
    "categories": {
        "molecule": [
            "Glycan"
        ],
        "tag": [
            "ChEBI cross-references"
        ],
        "status": [
            "Reviewed"
        ],
        "file_type": [
            "csv"
        ],
        "scope": [
            "internal"
        ],
        "species": [
            "Homo sapiens",
            "Mus musculus",
            "Rattus",
            "Rattus norvegicus",
            "Saccharomyces cerevisiae",
            "Drosophila melanogaster",
            "Severe acute respiratory syndrome coronavirus 2",
            "Sus scrofa",
            "Sus scrofa domesticus",
            "Dictyostelium discoideum",
            "Hepatitis C virus (isolate H77)",
            "Severe acute respiratory syndrome-related coronavirus"
        ]
    },
    "minitable": {
        "content": [
            [
                "G68137PO...",
                "27387..."
            ],
            [
                "G29057GU...",
                "138712..."
            ]
        ],
        "headers": [
            "glytoucan_ac...",
            "xref_id..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "glytoucan_ac"
                },
                {
                    "type": "string",
                    "label": "xref_id"
                },
                {
                    "type": "string",
                    "label": "xref_key"
                }
            ],
            [
                "G68137PO",
                "27387",
                "glycan_xref_chebi"
            ],
            [
                "G29057GU",
                "138712",
                "glycan_xref_chebi"
            ]
        ]
    },
    "readme": "Name\n   - Glycan Xref ChEBI\n\nVersion\n   - v-2.7.1\n\nCreated on\n  - 2019-11-13T16:58:52.830892\n\nModified on\n   - 2024-05-17T11:23:55.366Z\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   - Gareth Owen [gowen@ebi.ac.uk]\n\nChecksum\n   - \n\nUsability Domain\n   -  The dataset provides cross-references to ChEBI Id's for the associated glycan (GlyTouCan Accession). The mapping is produced using the direct download files(database_accession.tsv) from the ChEBI-EBI FTP (ftp://ftp.ebi.ac.uk/pub/databases/chebi/). The glycans are mapped/registered into the ChEBI database as follows: 1) GlyTouCan accession is mapped directly to ChEBI ID through PubChem CID (if the PubChem CID has a ChEBI cross-reference) 2) glycans with PubChem CID (which lack a ChEBI cross-reference) are integrated into ChEBI through applications like KNIME (https://europepmc.org/article/med/28757290) and ClassyFire (https://pubmed.ncbi.nlm.nih.gov/27867422/). 2) glycans without a PubChem CID are registered manually into the CHEBI database.\n\nDescription Domain\n   Keywords\n   - Glycan\n   - GlyTouCan Accession\n   - ChEBI\n   - Cross-references\n   - ID/Accession Mapping\n\n   Pipeline Steps\n   - Step-1: The input file (database_accession) was downloaded directly from the CHEBI-EBI FTP dowloads (ftp://ftp.ebi.ac.uk/pub/databases/chebi/). The following rules were applied to generate the final output file: 1) rows where \"SOURCE\" column = GlyTouCan were filtered out. 2) for such rows  \"COMPOUND_ID\" is chebi_id and \"ACCESSION_NUMBER\" is glytoucan_ac. 2) the extracted glytoucan_ac were checked against the GlyGen glycan masterlist (https://data.glygen.org/GLY_000281 or input file glycan_masterlist.csv) and the GlyTouCan accessions not included in the GlyGen glycan masterlist were excluded to generate the final output file. The glycans are submitted into the ChEBI database as follows: 1) GlyTouCan accession is mapped directly to ChEBI ID through PubChem CID (if the PubChem CID has a ChEBI cross-reference) 2) glycans with PubChem CID (which lack a ChEBI cross-reference) are integrated into ChEBI through applications like KNIME (https://europepmc.org/article/med/28757290) and ClassyFire (https://pubmed.ncbi.nlm.nih.gov/27867422/). 2) glycans without a PubChem CID are registered manually into the CHEBI database.\n\nExecution Domain\n   Scripts   - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-species-agnostic-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: glycan_masterlist.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/glycan_masterlist.csv\n      Name: database_accession.tsv\n      URI: https:/data.glygen.org/ln2downloads/chebi/2024_09_05/database_accession.tsv\n   Output Subdomain\n      Name: glycan_xref_chebi.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/glycan_xref_chebi.csv\n      Name: glycan_xref_chebi.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/glycan_xref_chebi.stat.csv\n\nFields\n      Name: \"glytoucan_ac\"\n     Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n      Unique Values: \"9890\"\n      Name: \"xref_id\"\n     Description: \"ID of the X-ref\"\n      Unique Values: \"9882\"\n      Name: \"xref_key\"\n     Description: \"Source key associated to the  xref_id\"\n      Unique Values: \"1\"",
    "downloadurl": "/ln2data/releases/data/v-2.7.1/reviewed/glycan_xref_chebi.csv"
}