{
    "bcoid": "GLY_001080",
    "title": "Arabidopsis Transcript Locus (Ensembl Transcript coordinates)",
    "description": "The Arabidopsis Transcript Locus (Ensembl Transcript coordinates) dataset contains UniProtKB Arabidopsis ...",
    "filename_list": "arabidopsis_protein_transcriptlocus.csv",
    "filename": "arabidopsis_protein_transcriptlocus.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Arabidopsis thaliana"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "Transcript Coordinates"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ],
        "file_category": [
            "locus"
        ]
    },
    "minitable": {
        "content": [
            [
                "B6EUC0-1...",
                "B6EUC0-1..."
            ],
            [
                "B6EUC0-1...",
                "A0A1P8AV56-1..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "uniprotkb_is..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "uniprotkb_isoform_ac"
                },
                {
                    "type": "string",
                    "label": "transcript_id"
                },
                {
                    "type": "string",
                    "label": "peptide_id"
                },
                {
                    "type": "string",
                    "label": "chromosome_id"
                },
                {
                    "type": "string",
                    "label": "start_pos"
                },
                {
                    "type": "string",
                    "label": "end_pos"
                },
                {
                    "type": "string",
                    "label": "strand"
                }
            ],
            [
                "B6EUC0-1",
                "B6EUC0-1",
                "AT1G30814.1",
                "AT1G30814.1",
                "1",
                "10942648",
                "10944727",
                "-"
            ],
            [
                "B6EUC0-1",
                "A0A1P8AV56-1",
                "AT1G30814.4",
                "AT1G30814.4",
                "1",
                "10942648",
                "10944727",
                "-"
            ]
        ]
    },
    "readme": "Name\n   - Arabidopsis Transcript Locus (Ensembl Transcript coordinates)\n\nVersion\n   - v-2.12.1\n\nModified on\n   - 2025-11-04T12:27:54.952Z\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 Arabidopsis Transcript Locus (Ensembl Transcript coordinates) dataset contains UniProtKB Arabidopsis thaliana [taxid:3702] canonical accessions mapped to their isoforms with further mapping to the corresponding ENSEMBL Transcript ID, Peptide ID, chromosome ID along with the transcripts' start and end position. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB, Ensembl and GlyGen. \n\nDescription Domain\n   Keywords\n   - transcript locus\n   - ensembl transcript id\n   - ensembl peptide id\n   - chromosome\n   - Ensembl\n\n   Pipeline Steps\n   - Step-1: The script loads the UniProtKB accessions that are mapped to ENSEMBL Transcript and Peptide identifiers from the triplestore containing triples from nt file, and then maps any UniProtKB isoforms to the UniProtKB canonical accession. The transcript ID is then used to extract the transcript's chromosome, start position, end position and forward/reverse strand data from the Ensembl gene annotation GFF3 file which has been converted to a TSV file. The extracted data is then used to create the csv dataset. \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: arabidopsis_protein_masterlist.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/arabidopsis_protein_masterlist.csv\n      Name: arabidopsis_ensembl_coords.tsv\n      URI: https:/data.glygen.org/ln2downloads/ensembl/2026_06_01/arabidopsis_ensembl_coords.tsv\n      Name: Arabidopsis_thaliana.TAIR10.63.uniprot.tsv\n      URI: https:/data.glygen.org/ln2downloads/ensembl/2026_06_01/Arabidopsis_thaliana.TAIR10.63.uniprot.tsv\n   Output Subdomain\n      Name: arabidopsis_protein_transcriptlocus.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/arabidopsis_protein_transcriptlocus.csv\n      Name: arabidopsis_protein_transcriptlocus.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/arabidopsis_protein_transcriptlocus.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\"\n     Description: \"\"\n      Unique Values: \"24728\"",
    "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/arabidopsis_protein_transcriptlocus.csv"
}