{ "bcoid": "GLY_000465", "title": "SARS-CoV1 Protein Site Annotation", "description": "The SARS coronavirus (SARS-CoV-1) Protein Site Annotation (UniProtKB) dataset contains sarscov1 [taxid:694009] ...", "filename": "sarscov1_protein_site_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "SARS coronavirus (SARS-CoV-1)" ], "molecule": [ "Protein" ], "tags": [ "site annotation" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P59596-1...", "M..." ], [ "P59596-1...", "M..." ] ], "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": "ann_type" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "annotation" }, { "type": "string", "label": "ecoid" }, { "type": "string", "label": "ref_aa" }, { "type": "string", "label": "alt_aa" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" } ], [ "P59596-1", "M", "Glycosylation_Annotation", "4", "4", "N-linked (GlcNAc...) asparagine; 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when associated with A-1251.", "ECO_0000269", "H", "A", "protein_xref_uniprotkb", "P59594" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "1253", "1253", "Decrease in Golgi localization, and complete loss of COPI binding; when associated with A-1251.", "ECO_0000269", "H", "A", "protein_xref_pubmed", "17166901" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "463", "463", "Partial loss of human ACE2 binding in vitro.", "ECO_0000269", "D", "A", "protein_xref_uniprotkb", "P59594" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "463", "463", "Partial loss of human ACE2 binding in vitro.", "ECO_0000269", "D", "A", "protein_xref_pubmed", "14670965" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "480", "480", "No effect on human ACE2 binding in vitro.", "ECO_0000269", "D", "A", "protein_xref_uniprotkb", "P59594" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "480", "480", "No effect on human ACE2 binding in vitro.", "ECO_0000269", "D", "A", "protein_xref_pubmed", "14670965" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "474", "474", "Complete loss of human ACE2 binding in vitro.", "ECO_0000269", "C", "A", "protein_xref_uniprotkb", "P59594" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "474", "474", "Complete loss of human ACE2 binding in vitro.", "ECO_0000269", "C", "A", "protein_xref_pubmed", "14670965" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "672", "672", "No effect on cell-cell fusion.", "ECO_0000269", "K", "S", "protein_xref_uniprotkb", "P59594" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "672", "672", "No effect on cell-cell fusion.", "ECO_0000269", "K", "S", "protein_xref_pubmed", "16519916" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "348", "348", "Complete loss of human ACE2 binding in vitro.", "ECO_0000269", "C", "A", "protein_xref_uniprotkb", "P59594" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "348", "348", "Complete loss of human ACE2 binding in vitro.", "ECO_0000269", "C", "A", "protein_xref_pubmed", "14670965" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "1251", "1251", "Decrease in Golgi localization, and complete loss of COPI binding; when associated with A-1253.", "ECO_0000269", "K", "A", "protein_xref_uniprotkb", "P59594" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "1251", "1251", "Decrease in Golgi localization, and complete loss of COPI binding; when associated with A-1253.", "ECO_0000269", "K", "A", "protein_xref_pubmed", "17166901" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "452", "452", "90% loss of human ACE2 binding in vitro.", "ECO_0000269", "E", "A", "protein_xref_uniprotkb", "P59594" ], [ "P59594-1", "S", "Mutagenesis_Annotation", "452", "452", "90% loss of human ACE2 binding in vitro.", "ECO_0000269", "E", "A", "protein_xref_pubmed", "14670965" ] ] }, "readme": "Name\n - SARS-CoV1 Protein Site Annotation\n\nVersion\n - v-2.1.1\n\nCreated on\n - 2020-04-09T13:22:15.821413\n\nModified on\n - 2022-09-26T09:05:56.467926\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]\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 Site Annotation (UniProtKB) dataset contains sarscov1 [taxid:694009] site annotations for UniProtKB canonical accessions. The dataset contains information about UniProtKB annotations with their amino acid range. The dataset is derived form 2019-09 UniprotKB release. If you use this dataset please give proper attribution to UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - site annotation\n - amino acid range\n - UniProtKB\n\n Pipeline Steps\n - Step-1: The script extracts the site annotation triples from the triplestore for the UniProtKB canonical sequences and extracts as a dataset in a csv format. \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: sarscov1_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/sarscov1_protein_masterlist.csv\n Name: uniprot-proteome-sars-coronavirus.nt\n URI: /data/shared/glyds/downloads/ebi/2023_02/uniprot-proteome-sars-coronavirus.nt\n Output Subdomain\n Name: sarscov1_protein_site_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/sarscov1_protein_site_annotation_uniprotkb.csv\n Name: sarscov1_protein_site_annotation_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/sarscov1_protein_site_annotation_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"12\"\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: \"6\"\n Name: \"ann_type\"\n Description: \"Annotation Type\"\n Unique Values: \"6\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"239\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"242\"\n Name: \"annotation\"\n Description: \"Function annotation from UniProtKB|RefSeq database\"\n Unique Values: \"96\"\n Name: \"ecoid\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"4\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"44\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"34\"\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: \"39\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/sarscov1_protein_site_annotation_uniprotkb.csv" }