{ "bcoid": "GLY_000463", "title": "Human Literature Mutations", "description": "The Human Literature Mutation dataset contains human [taxid:9606] mutation data extracted from literature ...", "filename_list": "human_protein_mutation_literature.csv", "filename": "human_protein_mutation_literature.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Protein" ], "tag": [ "Literature Mutations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P31749-1...", "207..." ], [ "P18887-1...", "7515..." ] ], "headers": [ "uniprotkb_ca...", "entrez_id..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "entrez_id" }, { "type": "string", "label": "gene_mention" }, { "type": "string", "label": "doid" }, { "type": "string", "label": "do_name" }, { "type": "string", "label": "disease_mention" }, { "type": "string", "label": "mutation_type" }, { "type": "string", "label": "abstract_extraction" }, { "type": "string", "label": "sentence_number" }, { "type": "string", "label": "sentence_text" }, { "type": "string", "label": "extraction_method" }, { "type": "string", "label": "patient_control_counts" }, { "type": "string", "label": "is_meta" }, { "type": "string", "label": "is_review" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "ref_aa" }, { "type": "string", "label": "alt_aa" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" } ], [ "P31749-1", "207", "AKT1", "1612", "breast cancer", "breast cancer", "Amino acid", "Title", "0", "AKT1 (E17K) mutation profiling in breast cancer: prevalence, concurrent oncogenic alterations, and blood-based detection.", "", "600 samples", "1", "1", "17", "17", "E", "K", "protein_xref_pubmed", "27515171" ], [ "P18887-1", "7515", "XRCC1", "3070, 5076", "malignant glioma, mixed glioma", "glioma", "Amino acid", "Conclusion", "8", "This study demonstrates that the rs25489 (Arg280His) and Arg399Gln (rs25487) polymorphisms in XRCC1 gene might influence the risk of developing glioma in Chinese population.", "ASSOC", "368 patients, 346 controls", "1", "1", "280", "280", "R", "H", "protein_xref_pubmed", "25245010" ] ] }, "readme": "Name\n - Human Literature Mutations\n\nVersion\n - v-2.7.1\n\nCreated on\n - 2020-04-03T17:37:22.702254\n\nModified on\n - 2024-05-17T11:24:01.470Z\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 - The Human Literature Mutation dataset contains human [taxid:9606] mutation data extracted from literature using the DIMEX tool. The dataset contains only the mutations that have amino acid information and position in the mutation mention column.. If you use this dataset provide proper attribution to GlyGen and OncoMX.\n\nDescription Domain\n Keywords\n - single-nucleotide variations (nsSNVs)\n - literature mutations\n - dbSNP\n - disease\n - ClinVar\n\n Pipeline Steps\n - Step-1: The script extracts the mutation data only for the mutations that have amino acid information and position 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: aadict.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/misc/aadict.csv\n Name: human_cancer_mutation_literature.csv\n URI: https:/data.glygen.org/ln2downloads/biomuta/v-5.0/human_cancer_mutation_literature.csv\n Output Subdomain\n Name: human_protein_mutation_literature.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/human_protein_mutation_literature.csv\n Name: human_protein_mutation_literature.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/human_protein_mutation_literature.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"459\"\n Name: \"entrez_id\"\n Description: \"\"Unique\"\n Unique Values: \"463\"\n Name: \"gene_mention\"\n Description: \"Specific form/spelling of gene or transcript mentioned in the retrieved publication\"\n Unique Values: \"770\"\n Name: \"doid\"\n Description: \"Disease ID from Disease ontology database\"\n Unique Values: \"253\"\n Name: \"do_name\"\n Description: \"Disease Ontology term or name for the disease assigned to the Disease Ontology identifier\"\n Unique Values: \"253\"\n Name: \"disease_mention\"\n Description: \"Specific form/spelling of disease mentioned in the retrieved publication\"\n Unique Values: \"1169\"\n Name: \"mutation_type\"\n Description: \"Denotes whether mutation was reported with reference to amino acid or nucleotide\"\n Unique Values: \"2\"\n Name: \"abstract_extraction\"\n Description: \"Portion of the abstract from which sentence was extracted\"\n Unique Values: \"5\"\n Name: \"sentence_number\"\n Description: \"Number of sentence in abstract\"\n Unique Values: \"24\"\n Name: \"sentence_text\"\n Description: \"Text of sentence extracted\"\n Unique Values: \"6914\"\n Name: \"extraction_method\"\n Description: \"Denotes confidence in the reported association of the mutation and disease\"\n Unique Values: \"3\"\n Name: \"patient_control_counts\"\n Description: \"\"Counts of patients and controls reported in the publication\"\n Unique Values: \"2235\"\n Name: \"is_meta\"\n Description: \"Denotes whether the publication is a meta-analysis\"\n Unique Values: \"1\"\n Name: \"is_review\"\n Description: \"Denotes whether the publication is a review\"\n Unique Values: \"1\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"697\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"20\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"20\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"4559\"", "downloadurl": "/ln2data/releases/data/v-2.7.1/reviewed/human_protein_mutation_literature.csv" }