{
    "bcoid": "GLY_001271",
    "title": "Zebrafish Protein Function (NCBI Refseq)",
    "description": "The Zebrafish Protein Function (NCBI RefSeq) dataset contains biological function annotation of Danio ...",
    "filename_list": "zebrafish_protein_function_refseq.csv",
    "filename": "zebrafish_protein_function_refseq.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Danio rerio"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "Protein Function"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ]
    },
    "minitable": {
        "content": [
            [
                "Q0H0R9-1...",
                "NP_001041520..."
            ],
            [
                "Q0PJT8-1...",
                "NP_001041528..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "refseq_ac..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "refseq_ac"
                },
                {
                    "type": "string",
                    "label": "xref_key"
                },
                {
                    "type": "string",
                    "label": "xref_id"
                },
                {
                    "type": "string",
                    "label": "annotation"
                }
            ],
            [
                "Q0H0R9-1",
                "NP_001041520",
                "protein_xref_refseq",
                "NP_001041520",
                "##Evidence-Data-START## Transcript exon combination :: DQ372604.1, EH443801.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA3505370, SAMEA3505371 [ECO:0000348] ##Evidence-Data-END## PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence was derived from DQ372604.1. On Sep 14, 2006 this sequence version replaced XP_695661.1. Publication Note:  This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications."
            ],
            [
                "Q0PJT8-1",
                "NP_001041528",
                "protein_xref_refseq",
                "NP_001041528",
                "##Evidence-Data-START## Transcript exon combination :: DQ822508.1, BC171545.1 [ECO:0000332] RNAseq introns :: mixed sample support SAMEA3505370, SAMEA3505371 [ECO:0006172] ##Evidence-Data-END## PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence was derived from DQ822508.1. On Sep 15, 2006 this sequence version replaced XP_684553.1. Publication Note:  This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications."
            ]
        ]
    },
    "readme": "Name\n   - Zebrafish Protein Function (NCBI Refseq)\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 Zebrafish Protein Function (NCBI RefSeq) dataset contains biological function annotation of Danio rerio [taxid:7955] genes from GeneRIF section in the NCBI RefSeq database. If you use this dataset please provide proper attribution to NCBI RefSeq and GlyGen. \n\nDescription Domain\n   Keywords\n   - protein function\n   - NCBI RefSeq\n   - geneRIF\n   - PMID\n\n   Pipeline Steps\n   - Step-1: The script parses the NCBI RefSeq gpff files to extract the geneRIFs that contain protein function. The script also maps RefSeq accession to the UniProtKB Canonical accessions. \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: zebrafish_protein_xref_refseq.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/zebrafish_protein_xref_refseq.csv\n      Name: refseq_protein_all_7955.gpff\n      URI: https:/data.glygen.org/ln2downloads/ncbi/refseq/2025_01_17/refseq_protein_all_7955.gpff\n   Output Subdomain\n      Name: zebrafish_protein_function_refseq.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/zebrafish_protein_function_refseq.csv\n      Name: zebrafish_protein_function_refseq.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/zebrafish_protein_function_refseq.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\n     Description: \"\"\n      Unique Values: \"20716\"\n      Name: \"refseq_ac\"\n     Description: \"Accession in the NCBI RefSeq database\"\n      Unique Values: \"20716\"\n      Name: \"xref_key\"\n     Description: \"Source key associated to the  xref_id\"\n      Unique Values: \"2\"\n      Name: \"xref_id\"\n     Description: \"ID of the X-ref\"\n      Unique Values: \"23680\"\n      Name: \"annotation\"\n     Description: \"Function annotation from UniProtKB|RefSeq database\"\n      Unique Values: \"18573\"",
    "downloadurl": "/ln2data/releases/data/v-2.8.1/reviewed/zebrafish_protein_function_refseq.csv"
}