{
    "bcoid": "GLY_001167",
    "title": "Yeast Proteoform Glycosylation Citations (CarbBank)",
    "description": "The Yeast Proteoform Glycosylation Citations (CarbBank) dataset contains Saccharomyces cerevisiae S288C ...",
    "filename_list": "yeast_proteoform_citations_glycosylation_sites_carbbank.csv",
    "filename": "yeast_proteoform_citations_glycosylation_sites_carbbank.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Saccharomyces cerevisiae S288C"
        ],
        "molecule": [
            "Proteoform"
        ],
        "tag": [
            "Protein Citations O-GlcNAc (Carbbank)"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ]
    },
    "minitable": {
        "content": [
            [
                "P0CW41-1...",
                "Glycan modif..."
            ],
            [
                "P0CW41-1...",
                "Glycan modif..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "title..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "title"
                },
                {
                    "type": "string",
                    "label": "journal_name"
                },
                {
                    "type": "string",
                    "label": "publication_date"
                },
                {
                    "type": "string",
                    "label": "authors"
                },
                {
                    "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": "glytoucan_ac"
                }
            ],
            [
                "P0CW41-1",
                "Glycan modification of a thermostable recombinant (1-3, 1-4)-beta-glucanase secreted from Saccharomyces cerevisiae is determined by strain and culture conditions.",
                "Glycoconjugate journal",
                "1995-06",
                "Meldgaard M, Harthill J, Petersen B, Olsen O",
                "protein_xref_pubmed",
                "7496153",
                "protein_xref_glygen_ds",
                "GLY_001116",
                "G08172UF"
            ],
            [
                "P0CW41-1",
                "Glycan modification of a thermostable recombinant (1-3, 1-4)-beta-glucanase secreted from Saccharomyces cerevisiae is determined by strain and culture conditions.",
                "Glycoconjugate journal",
                "1995-06",
                "Meldgaard M, Harthill J, Petersen B, Olsen O",
                "protein_xref_pubmed",
                "7496153",
                "protein_xref_glygen_ds",
                "GLY_001116",
                "G46565HP"
            ]
        ]
    },
    "readme": "Name\n   - Yeast Proteoform Glycosylation Citations (CarbBank)\n\nVersion\n   - v-2.10.1\n\nCreated on\n  - 2024-12-10T21:04:09\n\nModified on\n   - 2024-12-10T22:21:01.184Z\n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@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   - \n\nChecksum\n   - \n\nUsability Domain\n   - The Yeast Proteoform Glycosylation Citations (CarbBank) dataset contains Saccharomyces cerevisiae S288C [taxid:559292] publication information of glycoproteins from the Yeast CarbBank Glycosylation Sites dataset (https://data.glygen.org/GLY_001116). The script accesses the NCBI ENTREZ infrastructure to retrieve the publication information of the given PMID from the CarbBank dataset. CarbBank was a pioneering database that cataloged carbohydrate structures and related biochemical information. Although no longer actively maintained, CarbBank laid the groundwork for modern glycoinformatics tools and databases, influencing subsequent efforts to document carbohydrate-related data systematically. Please cite GlyGen and CarbBank if you use this dataset. \n\nDescription Domain\n   Keywords\n   - glycosylation\n   - reported glycosylation\n   - Carbbank\n\n   Pipeline Steps\n   - Step-1: The script extracts the PMIDs from the dataset and uses the Entrez API to retrieve the publication details and extracts in a csv dataset\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: all_blacklisted_pmids.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/compiled/all_blacklisted_pmids.csv\n      Name: yeast_proteoform_glycosylation_sites_carbbank.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/yeast_proteoform_glycosylation_sites_carbbank.csv\n   Output Subdomain\n      Name: yeast_proteoform_citations_glycosylation_sites_carbbank.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/yeast_proteoform_citations_glycosylation_sites_carbbank.csv\n      Name: yeast_proteoform_citations_glycosylation_sites_carbbank.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/yeast_proteoform_citations_glycosylation_sites_carbbank.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\n     Description: \"\"\n      Unique Values: \"1\"\n      Name: \"title\"\n     Description: \"Title of the published article in the journal\"\n      Unique Values: \"1\"\n      Name: \"journal_name\"\n     Description: \"The name of the journal in which the article is published\"\n      Unique Values: \"1\"\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: \"1\"\n      Name: \"authors\"\n     Description: \"NA\"\n      Unique Values: \"1\"\n      Name: \"xref_key\"\n     Description: \"Source key associated to the  xref_id\"\n      Unique Values: \"1\"\n      Name: \"xref_id\"\n     Description: \"ID of the X-ref\"\n      Unique Values: \"1\"\n      Name: \"src_xref_key\"\n     Description: \"Source Xref  key\"\n      Unique Values: \"1\"\n      Name: \"src_xref_id\"\n     Description: \"Source X-ref ID\"\n      Unique Values: \"1\"\n      Name: \"glytoucan_ac\"\n     Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n      Unique Values: \"11\"",
    "downloadurl": "/ln2data/releases/data/v-2.10.1/reviewed/yeast_proteoform_citations_glycosylation_sites_carbbank.csv"
}