{ "bcoid": "GLY_000442", "title": "SARS-CoV1 Protein Signal Peptide", "description": "The SARS coronavirus (SARS-CoV-1) Protein Signal Peptide dataset contains sarscov1 [taxid:694009] signal ...", "filename": "sarscov1_protein_signalp_annotation.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-1)", "molecule": "Protein", "tags": "Signal Peptide", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P59635-1...", "..." ], [ "P59594-1...", "S..." ] ], "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" } ], [ "P59635-1", "", "ORF7a protein", "122", "15", "107", "1", "15", "MKIILFLTLIVFTSCELYHYQECVRGTTVLLKEPCPSGTYEGNSPFHPLADNKFALTCTSTHFAFACADGTRHTYQLRARSVSPKLFIRQEEVQQELYSPLFLIVAALVFLILCFTIKRKTE", "MKIILFLTLIVFTSC", "ELYHYQECVRGTTVLLKEPCPSGTYEGNSPFHPLADNKFALTCTSTHFAFACADGTRHTYQLRARSVSPKLFIRQEEVQQELYSPLFLIVAALVFLILCFTIKRKTE", "", "" ], [ "P59594-1", "S", "Spike glycoprotein", "1255", "13", "1242", "1", "13", "MFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYFVGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDPKTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAIHADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSLLRSTSQKSIVAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAAEQDRNTREVFAQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKRSFIEDLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDNTFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKGACSCGSCCKFDEDDSEPVLKGVKLHYT", "MFIFLLFLTLTSG", "SDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYFVGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDPKTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAIHADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSLLRSTSQKSIVAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAAEQDRNTREVFAQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKRSFIEDLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDNTFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKGACSCGSCCKFDEDDSEPVLKGVKLHYT", "ECO_0000255", "MF_04099" ], [ "Q7TFA0-1", "", "ORF8a protein", "39", "15", "24", "1", "15", "MKLLIVLTCISLCSCICTVVQRCASNKPHVLEDPCKVQH", "MKLLIVLTCISLCSC", "ICTVVQRCASNKPHVLEDPCKVQH", "", "" ] ] }, "readme": "Name\n - SARS-CoV1 Protein Signal Peptide\n\nVersion\n - v-2.0.3\n\nCreated on\n - 2020-04-03T11:46:41.584409\n\nModified on\n - 2022-09-26T09:05:56.441566\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.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 SARS coronavirus (SARS-CoV-1) Protein Signal Peptide dataset contains sarscov1 [taxid:694009] 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 log file containing accessions that do not have signal peptide information and processed protein sequence\u2019s files in fasta format. The dataset is derived from 2020-01 UniProtKB release. 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-sars-coronavirus.nt\n URI: /data/shared/glyds/downloads/ebi/2022_05/uniprot-proteome-sars-coronavirus.nt\n Name: uniprot-proteome-sars-coronavirus.nt\n URI: /data/shared/glyds/downloads/ebi/2022_05/uniprot-proteome-sars-coronavirus.nt\n Name: uniprot-proteome-sars-coronavirus.nt\n URI: /data/shared/glyds/downloads/ebi/2022_05/uniprot-proteome-sars-coronavirus.nt\n Name: uniprot-proteome-sars-coronavirus.nt\n URI: /data/shared/glyds/downloads/ebi/2022_05/uniprot-proteome-sars-coronavirus.nt\n Output Subdomain\n Name: sarscov1_protein_signalp_annotation.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/sarscov1_protein_signalp_annotation.csv\n Name: sarscov1_protein_signalp_peptidesequences.fasta\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/sarscov1_protein_signalp_peptidesequences.fasta\n Name: sarscov1_protein_signalp_cleavedsequences.fasta\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/sarscov1_protein_signalp_cleavedsequences.fasta\n Name: sarscov1_protein_signalp_fullsequences.fasta\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/sarscov1_protein_signalp_fullsequences.fasta\n Name: sarscov1_protein_signalp_annotation.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/sarscov1_protein_signalp_annotation.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"3\"\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: \"2\"\n Name: \"uniprotkb_protein_recommended_name\"\n Description: \"The recommended full name of the protein in UniProtKB\"\n Unique Values: \"3\"\n Name: \"uniprotkb_protein_length\"\n Description: \"Length of the protein sequence\"\n Unique Values: \"3\"\n Name: \"uniprotkb_protein_signalp_length\"\n Description: \"The length of the signal peptide sequence in the UniProtKB.\"\n Unique Values: \"2\"\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: \"3\"\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: \"2\"\n Name: \"uniprotkb_protein_sequence\"\n Description: \"The protein sequence in fasta format of a given accession in UniProtKB\"\n Unique Values: \"3\"\n Name: \"uniprotkb_protein_signalp_sequence\"\n Description: \"The signal peptide sequence in a fasta format in UniProtKB\"\n Unique Values: \"3\"\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: \"3\"\n Name: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"2\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) or DOI (Digital Object Identifier) as evidence for the entry/annotation\"\n Unique Values: \"2\"\n Name: sarscov1_protein_signalp_peptidesequences.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/sarscov1_protein_signalp_peptidesequences.stat.csv\n\nFields\n Name: \"sequence\"\n Description: \"Amino acid sequence\"\n Unique Values: \"3\"\n Name: sarscov1_protein_signalp_cleavedsequences.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/sarscov1_protein_signalp_cleavedsequences.stat.csv\n\nFields\n Name: \"sequence\"\n Description: \"Amino acid sequence\"\n Unique Values: \"3\"\n Name: sarscov1_protein_signalp_fullsequences.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/sarscov1_protein_signalp_fullsequences.stat.csv\n\nFields\n Name: \"sequence\"\n Description: \"Amino acid sequence\"\n Unique Values: \"3\"", "downloadurl": "/ln2data/releases/data/v-2.0.3/reviewed/sarscov1_protein_signalp_annotation.csv" }