{ "bcoid": "GLY_000024", "title": "Human Cancer Mutation", "description": "The Human Cancer Mutation dataset contains Homo sapiens [taxid:9606] mutation data from the BioMuta database ...", "filename_list": "human_protein_mutation_cancer.csv", "filename": "human_protein_mutation_cancer.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Protein" ], "tag": [ "Somatic Cancer Mutations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ], "file_category": [ "mutation_" ] }, "minitable": { "content": [ [ "P42345-1...", "2327..." ], [ "P42345-1...", "2215..." ] ], "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": "ref_aa" }, { "type": "string", "label": "alt_aa" }, { "type": "string", "label": "chr_id" }, { "type": "string", "label": "chr_start_pos" }, { "type": "string", "label": "chr_end_pos" }, { "type": "string", "label": "ref_nt" }, { "type": "string", "label": "alt_nt" }, { "type": "string", "label": "patients_positive" }, { "type": "string", "label": "patients_tested" }, { "type": "string", "label": "mut_freq" }, { "type": "string", "label": "data_source" }, { "type": "string", "label": "do_id" }, { "type": "string", "label": "do_name" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "filter_flags" }, { "type": "string", "label": "glyco_annotation" }, { "type": "string", "label": "mim_id" }, { "type": "string", "label": "somatic_status" }, { "type": "string", "label": "minor_allelic_frequency" }, { "type": "string", "label": "protein_class" } ], [ "P42345-1", "2327", "M", "I", "1", "11117039", "11117039", "C", "A", "0", "0", "0.0", "civic", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "P42345", "Somatic mutation passed 1 out of 6 filters: num. of cancers (6).", "glycancount:0, pmidcount:0", "", "1", "", "none" ], [ "P42345-1", "2215", "S", "Y", "1", "11124516", "11124516", "G", "T", "0", "0", "0.0", "civic", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "P42345", "Somatic mutation passed 1 out of 6 filters: num. of cancers (7).", "glycancount:0, pmidcount:0", "", "1", "", "none" ] ] }, "readme": "Name\n - Human Cancer Mutation\n\nVersion\n - v-2.12.1\n\nCreated on\n - 2019-01-23T17:21:05.891293\n\nModified on\n - 2026-07-08T10:52:25.123Z\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], Mariia Kim [maria.kim@gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Human Cancer Mutation dataset contains Homo sapiens [taxid:9606] mutation data from the BioMuta database (https://hive.biochemistry.gwu.edu/biomuta). The BioMuta pipeline documentation can be found on the HIVE Lab Wiki: https://hivelab.biochemistry.gwu.edu/wiki/BioMuta_pipeline_README.\n - The current version of BioMuta contains only nonsynonymous single-nucleotide variations (nsSNVs) associated with cancer.\n - BioMuta is a single-nucleotide variation (SNV) and disease association database where variations are mapped to genomes and NCBI RefSeq nucleotide entries, and unified through UniProtKB/Swiss-Prot positional coordinates.\n - The dataset is imported and contributed by BioMuta and processed by GlyGen. If you use this dataset, please provide proper attribution to BioMuta and GlyGen.\n - Note that the mutations in GlyGen are annotated based on passing of one or more filter criteria.\n - Filter criterion 1 - Positive Patients Frequency Ratio \u2265 1.0%\n - Filter criterion 2 - Presence of mutation in \u2265 3 cancer types\n - Filter criterion 3 - Positive Patients count \u2265 10 patients\n - Filter criterion 4 - Mutation reported and annotated in number of databases\n - Filter criterion 5 - Mutation mined from literature using literature mining tools (human_protein_mutation_literature.csv)\n - Filter criterion 6 - At least one glyco-relevant mutation effect i.e. N-glycosylation sequon loss, N-glycosylation sequon gain or O-glycosylation site loss.\n - If there is also a germline mutation reported in dbSNP, the rsid is also shown\n - Two different DO child terms are merged into one single entry showing the parent cancer DO term from the DO cancer slim.\n\nDescription Domain\n Keywords\n - single-nucleotide variations (nsSNVs)\n - cancer mutations\n - BioMuta\n - disease\n\n Pipeline Steps\n - Step-1: The script extracts the mutation data from the BioMuta and maps the UniProtKB accession to the UniProtKB canonical accessions as per the criterias\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: human_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_masterlist.csv\n Name: human_protein_mutation_literature.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_mutation_literature.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: biomuta.csv\n URI: https:/data.glygen.org/ln2downloads/biomuta/2025_05_27/biomuta.csv\n Name: clinical_information.csv\n URI: https:/data.glygen.org/ln2downloads/biomuta/2025_05_27/clinical_information.csv\n Name: dbSNP-homo-sapiens.tsv\n URI: https:/data.glygen.org/ln2downloads/ebi/2026_06_13/dbSNP-homo-sapiens.tsv\n Output Subdomain\n Name: human_protein_mutation_cancer.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_mutation_cancer.csv\n Name: human_protein_mutation_cancer.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_mutation_cancer.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\"\n Description: \"\"\n Unique Values: \"19268\"", "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/human_protein_mutation_cancer.csv" }