{ "bcoid": "GLY_000327", "title": "Mouse Protein Site Annotation", "description": "The Mouse Protein Site Annotation (UniProtKB) dataset contains mouse [taxid:10090] site annotations for ...", "filename": "mouse_protein_site_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Mus musculus", "molecule": "Protein", "tags": "site annotation", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q8BH24-1...", "Tm9sf4..." ], [ "Q8BH24-1...", "Tm9sf4..." ] ], "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": 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"ECO_0007744", "S", "", "protein_xref_uniprotkb", "Q5EBH1" ], [ "Q5EBH1-1", "Rassf5", "Modified_Residue_Annotation", "177", "177", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "21183079" ], [ "Q5EBH1-1", "Rassf5", "Modified_Residue_Annotation", "274", "274", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "Q5EBH1" ], [ "Q5EBH1-1", "Rassf5", "Modified_Residue_Annotation", "274", "274", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_pubmed", "Q8WWW0" ], [ "Q5EBH1-1", "Rassf5", "Modified_Residue_Annotation", "347", "347", "Phosphothreonine", "ECO_0000250", "T", "", "protein_xref_uniprotkb", "Q5EBH1" ], [ "Q5EBH1-1", "Rassf5", "Modified_Residue_Annotation", "347", "347", "Phosphothreonine", "ECO_0000250", "T", "", "protein_xref_pubmed", "Q8WWW0" ], [ "Q5EBH1-1", "Rassf5", "Mutagenesis_Annotation", "220", "220", "Reduced interaction with HRAS.", "ECO_0000269", "C", "A", "protein_xref_uniprotkb", "Q5EBH1" ], [ "Q5EBH1-1", "Rassf5", "Mutagenesis_Annotation", "220", "220", "Reduced interaction with HRAS.", "ECO_0000269", "C", "A", "protein_xref_pubmed", "18596699" ], [ "Q5EBH1-1", "Rassf5", "Mutagenesis_Annotation", "302", "302", "Reduced specificity for HRAS and diminished discrimination between HRAS and RAP1A.", "ECO_0000269", "K", "D", "protein_xref_uniprotkb", "Q5EBH1" ], [ "Q5EBH1-1", "Rassf5", "Mutagenesis_Annotation", "302", "302", "Reduced specificity for HRAS and diminished discrimination between HRAS and RAP1A.", "ECO_0000269", "K", "D", "protein_xref_pubmed", "18596699" ] ] }, "readme": "Name\n - Mouse Protein Site Annotation\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-12-04T12:16:57.929402\n\nModified on\n - 2022-01-12T16:35:17.794615\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.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 Mouse Protein Site Annotation (UniProtKB) dataset contains mouse [taxid:10090] 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 it as a dataset in a csv format\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: mouse_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-1.12.3/reviewed/mouse_protein_masterlist.csv\n Name: uniprot-proteome-mus-musculus.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2021_04/uniprot-proteome-mus-musculus.nt\n Output Subdomain\n Name: mouse_protein_site_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-1.12.3/reviewed/mouse_protein_site_annotation_uniprotkb.csv\n Name: mouse_protein_site_annotation_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-1.12.3/reviewed/mouse_protein_site_annotation_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"13459\"\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: \"13366\"\n Name: \"ann_type\"\n Description: \"Annotation Type\"\n Unique Values: \"13\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"3323\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"3322\"\n Name: \"annotation\"\n Description: \"Function annotation from UniProtKB|RefSeq database\"\n Unique Values: \"8345\"\n Name: \"ecoid\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"10\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"4046\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"368\"\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: \"28145\"", "downloadurl": "/ln2data/releases/data/v-1.12.3/reviewed/mouse_protein_site_annotation_uniprotkb.csv" }