{ "bcoid": "GLY_001533", "title": "All Human Somatic Mutations", "description": "This Human Somatic Mutation dataset contains all Homo sapiens [taxid:9606] somatic mutation data from ...", "filename_list": "human_protein_mutation_somatic_all.csv", "filename": "human_protein_mutation_somatic_all.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Protein" ], "tag": [ "Somatic Mutations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ], "file_category": [ "mutation_" ] }, "minitable": { "content": [ [ "Q9H0G5-1...", "180..." ], [ "Q9H0G5-1...", "180..." ] ], "headers": [ "uniprotkb_ca...", "aa_pos..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "aa_pos" }, { "type": "string", "label": "dbsnp_id" }, { "type": "string", "label": "cosmic_id" }, { "type": "string", "label": "description" }, { "type": "string", "label": "cytogenic_band" }, { "type": "string", "label": "chr_id" }, { "type": "string", "label": "chr_pos" }, { "type": "string", "label": "ref_nt" }, { "type": "string", "label": "alt_nt" }, { "type": "string", "label": "ref_aa" }, { "type": "string", "label": "alt_aa" }, { "type": "string", "label": "begin_aa_pos" }, { "type": "string", "label": "end_aa_pos" }, { "type": "string", "label": "minor_allelic_frequency" }, { "type": "string", "label": "mutation_type" }, { "type": "string", "label": "polyphen_score" }, { "type": "string", "label": "polyphen_prediction" }, { "type": "string", "label": "sift_score" }, { "type": "string", "label": "sift_prediction" }, { "type": "string", "label": "somatic_status" }, { "type": "string", "label": "disease" }, { "type": "string", "label": "disease_description" }, { "type": "string", "label": "disease_xrefs" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "mim_id" }, { "type": "string", "label": "do_id" }, { "type": "string", "label": "filter_flags" }, { "type": "string", "label": "glyco_annotation" }, { "type": "string", "label": "protein_class" } ], [ "Q9H0G5-1", "180", "rs1189713038", "", "[NCI-TCGA]: Variant assessed as Somatic; MODERATE impact.", "17q11.2", "17", "30184697", "A", "null", "L", "I", "180", "180", "", "missense", "0.024", "benign", "0.11", "tolerated", "1", "Adenomas and Adenocarcinomas", "From tissue: Endometrium", "", "protein_xref_dbsnp", "rs1189713038", "", "", "No filters applied", "glycancount:0, pmidcount:0", "none" ], [ "Q9H0G5-1", "180", "rs1189713038", "", "[NCI-TCGA]: Variant assessed as Somatic; MODERATE impact.", "17q11.2", "17", "30184697", "A", "null", "L", "I", "180", "180", "", "missense", "0.024", "benign", "0.11", "tolerated", "1", "Adenomas and Adenocarcinomas", "From tissue: Endometrium", "", "protein_xref_gnomad", "rs1189713038", "", "", "No filters applied", "glycancount:0, pmidcount:0", "none" ] ] }, "readme": "Name\n - All Human Somatic Mutations\n\nVersion\n - v-2.12.1\n\nModified on\n - 2026-03-23T18:08:19.453Z\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 - This Human Somatic Mutation dataset contains all Homo sapiens [taxid:9606] somatic mutation data from EBI Variant Data API. Only nonsynonymous single-nucleotide variations (nsSNVs) somatic mutations are integrated. If you use this dataset provide proper attribution to GlyGen and EBI-EMBL-UniProtKB.\n\nDescription Domain\n Keywords\n - single-nucleotide variations (nsSNVs)\n - somatic mutations\n - dbSNP\n - disease\n - ClinVar\n\n Pipeline Steps\n - Step-1: The script extracts the somatic (somatic_staus = 1) mutation data from the input file and maps the UniProtKB accession 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: glycan_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/glycan_masterlist.csv\n Name: human_protein_gene_groups.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_gene_groups.csv\n Name: protein_disease_idmap.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/protein_disease_idmap.csv\n Name: aadict.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/misc/aadict.csv\n Name: dbSNP-homo-sapiens.tsv\n URI: https:/data.glygen.org/ln2downloads/ebi/2026_01_31/dbSNP-homo-sapiens.tsv\n Name: homo-sapiens-cosmic.tsv\n URI: https:/data.glygen.org/ln2downloads/ebi/2026_01_31/homo-sapiens-cosmic.tsv\n Output Subdomain\n Name: human_protein_mutation_somatic_all.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_mutation_somatic_all.csv\n Name: human_protein_mutation_somatic_all.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_mutation_somatic_all.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\"\n Description: \"\"\n Unique Values: \"17681\"", "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/human_protein_mutation_somatic_all.csv" }