{
    "bcoid": "GLY_000773",
    "title": "Yeast Protein Signal Peptide",
    "description": "The Yeast Protein Signal Peptide dataset contains Saccharomyces cerevisiae S288C [taxid:559292] signal ...",
    "filename_list": "yeast_protein_signalp_annotation.csv, yeast_protein_signalp_peptidesequences.fasta, yeast_protein_signalp_cleavedsequences.fasta, yeast_protein_signalp_fullsequences.fasta",
    "filename": "yeast_protein_signalp_annotation.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Saccharomyces cerevisiae S288C"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "Signal Peptide"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ]
    },
    "minitable": {
        "content": [
            [
                "P53964-1...",
                "..."
            ],
            [
                "I2HB70-1...",
                "..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "gene_symbol..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "gene_symbol"
                },
                {
                    "type": "string",
                    "label": "uniprotkb_protein_recommended_name"
                },
                {
                    "type": "string",
                    "label": "uniprotkb_protein_length"
                },
                {
                    "type": "string",
                    "label": "uniprotkb_protein_signalp_length"
                },
                {
                    "type": "string",
                    "label": "uniprotkb_protein_signalp_cleaved_length"
                },
                {
                    "type": "string",
                    "label": "signalp_start_pos"
                },
                {
                    "type": "string",
                    "label": "signalp_end_pos"
                },
                {
                    "type": "string",
                    "label": "uniprotkb_protein_sequence"
                },
                {
                    "type": "string",
                    "label": "uniprotkb_protein_signalp_sequence"
                },
                {
                    "type": "string",
                    "label": "uniprotkb_protein_signalp_cleaved_sequence"
                },
                {
                    "type": "string",
                    "label": "eco_id"
                },
                {
                    "type": "string",
                    "label": "evidence"
                }
            ],
            [
                "P53964-1",
                "",
                "Uncharacterized membrane protein YNL033W",
                "284",
                "24",
                "260",
                "1",
                "24",
                "MLYSRESRTTVLFLALVTSLTVLCHSVDVTTVFTTSTITEITTVTAAPQPQNKAETALNTATNIIQTMQFLFNCAPFKWKGPLKITSCALNFIVLLLTAWGYLLKYLQENKLNSDADMEKMVGLGFGEMVGRIFGKGVGKAFTKMDITQKLVYPFEGSNRQKCLLMTVGENSIVPFHDLFTEICFDQYTLDSLSHHNHGSISILDAGSVSALGFADISSKMPSVSELYTLFGDYTIEVLGGITKLASTLNREDWQGERNGFAVLSRDRPNQTLLSVHMYSSSLL",
                "MLYSRESRTTVLFLALVTSLTVLC",
                "HSVDVTTVFTTSTITEITTVTAAPQPQNKAETALNTATNIIQTMQFLFNCAPFKWKGPLKITSCALNFIVLLLTAWGYLLKYLQENKLNSDADMEKMVGLGFGEMVGRIFGKGVGKAFTKMDITQKLVYPFEGSNRQKCLLMTVGENSIVPFHDLFTEICFDQYTLDSLSHHNHGSISILDAGSVSALGFADISSKMPSVSELYTLFGDYTIEVLGGITKLASTLNREDWQGERNGFAVLSRDRPNQTLLSVHMYSSSLL",
                "",
                ""
            ],
            [
                "I2HB70-1",
                "",
                "Uncharacterized protein YMR316C-A",
                "103",
                "21",
                "82",
                "1",
                "21",
                "MTGFKVSSFFYILALSRFFNAGRERACDKLKITVTHLYWFIIRKLLLHEVHVHVSRVCNVSFILSPCLFRNFFTLSLHVLYVMYEQALTPEFFRQWWDIIQSK",
                "MTGFKVSSFFYILALSRFFNA",
                "GRERACDKLKITVTHLYWFIIRKLLLHEVHVHVSRVCNVSFILSPCLFRNFFTLSLHVLYVMYEQALTPEFFRQWWDIIQSK",
                "",
                ""
            ]
        ]
    },
    "readme": "Name\n   - Yeast Protein Signal Peptide\n\nVersion\n   - v-2.8.1\n\nCreated on\n  - 2022-08-31T11:05:56.022652\n\nModified on\n   - 2024-06-03T22:37:18.184Z\n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@email.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 Yeast Protein Signal Peptide dataset contains Saccharomyces cerevisiae S288C [taxid:559292] signal peptide information for the UniProtKB canonical accessions. The dataset contains protein information, signal peptide sequence, signal peptide length, signal peptide start and end position, cleaved protein sequence, eco ids and PMIDs. The dataset contains related files in the output subdomain that includes processed protein sequence files in fasta format viz. Signal peptide sequence, protein sequence after signal peptide is cleaved, and full protein sequences of the proteins that contain signal peptide. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen. \n\nDescription Domain\n   Keywords\n   - signal peptide\n   - ptm processing\n   - UniProtKB\n\n   Pipeline Steps\n   - Step-1: The script extracts the signal peptide information from the triplestore and maps 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: uniprot-proteome-saccharomyces-cerevisiae.nt\n      URI: https:/data.glygen.org/ln2downloads/ebi/2025_01_17/uniprot-proteome-saccharomyces-cerevisiae.nt\n      Name: uniprot-proteome-saccharomyces-cerevisiae.nt\n      URI: https:/data.glygen.org/ln2downloads/ebi/2025_01_17/uniprot-proteome-saccharomyces-cerevisiae.nt\n      Name: uniprot-proteome-saccharomyces-cerevisiae.nt\n      URI: https:/data.glygen.org/ln2downloads/ebi/2025_01_17/uniprot-proteome-saccharomyces-cerevisiae.nt\n      Name: uniprot-proteome-saccharomyces-cerevisiae.nt\n      URI: https:/data.glygen.org/ln2downloads/ebi/2025_01_17/uniprot-proteome-saccharomyces-cerevisiae.nt\n   Output Subdomain\n      Name: yeast_protein_signalp_annotation.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/yeast_protein_signalp_annotation.csv\n      Name: yeast_protein_signalp_peptidesequences.fasta\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/yeast_protein_signalp_peptidesequences.fasta\n      Name: yeast_protein_signalp_cleavedsequences.fasta\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/yeast_protein_signalp_cleavedsequences.fasta\n      Name: yeast_protein_signalp_fullsequences.fasta\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/yeast_protein_signalp_fullsequences.fasta\n      Name: yeast_protein_signalp_annotation.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/yeast_protein_signalp_annotation.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\n     Description: \"\"\n      Unique Values: \"302\"\n      Name: \"gene_symbol\"\n     Description: \"\"Official gene name/symbol assigned to the gene. Human gene names/symbols are approved by the HUGO Gene Nomenclature Committee (HGNC)\"\n      Unique Values: \"255\"\n      Name: \"uniprotkb_protein_recommended_name\"\n     Description: \"The recommended full name of the protein in UniProtKB\"\n      Unique Values: \"302\"\n      Name: \"uniprotkb_protein_length\"\n     Description: \"Length of the protein sequence\"\n      Unique Values: \"232\"\n      Name: \"uniprotkb_protein_signalp_length\"\n     Description: \"The length of the signal peptide sequence in the UniProtKB.\"\n      Unique Values: \"28\"\n      Name: \"uniprotkb_protein_signalp_cleaved_length\"\n     Description: \"The length of the protein sequence after signal peptide is cleaved in UniProtKB\"\n      Unique Values: \"244\"\n      Name: \"signalp_start_pos\"\n     Description: \"The starting amino acid position of the signal peptide sequence in UniProtKB\"\n      Unique Values: \"1\"\n      Name: \"signalp_end_pos\"\n     Description: \"The ending amino acid position of the signal peptide sequence in UniProtKB\"\n      Unique Values: \"28\"\n      Name: \"uniprotkb_protein_sequence\"\n     Description: \"The protein sequence in fasta format of a given accession in UniProtKB\"\n      Unique Values: \"294\"\n      Name: \"uniprotkb_protein_signalp_sequence\"\n     Description: \"The signal peptide sequence in a fasta format in UniProtKB\"\n      Unique Values: \"284\"\n      Name: \"uniprotkb_protein_signalp_cleaved_sequence\"\n     Description: \"The protein fasta sequence after signal peptide is cleaved in a fasta format in UniProtKB\"\n      Unique Values: \"294\"\n      Name: \"eco_id\"\n     Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n      Unique Values: \"3\"\n      Name: \"evidence\"\n     Description: \"NCBI PubMed Id (PMID) or DOI (Digital Object Identifier) as evidence for the entry/annotation\"\n      Unique Values: \"33\"\n      Name: yeast_protein_signalp_peptidesequences.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/yeast_protein_signalp_peptidesequences.stat.csv\n\nFields\n      Name: \"sequence\"\n     Description: \"Amino acid sequence\"\n      Unique Values: \"315\"\n      Name: yeast_protein_signalp_cleavedsequences.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/yeast_protein_signalp_cleavedsequences.stat.csv\n\nFields\n      Name: \"sequence\"\n     Description: \"Amino acid sequence\"\n      Unique Values: \"315\"\n      Name: yeast_protein_signalp_fullsequences.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/yeast_protein_signalp_fullsequences.stat.csv\n\nFields\n      Name: \"sequence\"\n     Description: \"Amino acid sequence\"\n      Unique Values: \"315\"",
    "downloadurl": "/ln2data/releases/data/v-2.8.1/reviewed/yeast_protein_signalp_annotation.csv"
}