title: Oncotator: cancer variant annotation tool.
abstract: Oncotator is a tool for annotating genomic point mutations and short nucleotide insertions/deletions (indels) with variant- and gene-centric information relevant to cancer researchers. This information is drawn from 14 different publicly available resources that have been pooled and indexed, and we provide an extensible framework to add additional data sources. Annotations linked to variants range from basic information, such as gene names and functional classification (e.g. missense), to cancer-specific data from resources such as the Catalogue of Somatic Mutations in Cancer (COSMIC), the Cancer Gene Census, and The Cancer Genome Atlas (TCGA). For local use, Oncotator is freely available as a python module hosted on Github (https://github.com/broadinstitute/oncotator). Furthermore, Oncotator is also available as a web service and web application at http://www.broadinstitute.org/oncotator/.
authors.affiliation: Cancer Program, Broad Institute, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: Alex H
authors.initials: AH
authors.lastname: Ramos
authors.forename: Lee
authors.initials: L
authors.lastname: Lichtenstein
authors.forename: Manaswi
authors.initials: M
authors.lastname: Gupta
authors.forename: Michael S
authors.initials: MS
authors.lastname: Lawrence
authors.forename: Trevor J
authors.initials: TJ
authors.lastname: Pugh
authors.forename: Gordon
authors.initials: G
authors.lastname: Saksena
authors.forename: Matthew
authors.initials: M
authors.lastname: Meyerson
authors.forename: Gad
authors.initials: G
authors.lastname: Getz
mesh_terms: D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D014644:Genetic Variation; D023281:Genomics / Q000379:methods; D006801:Humans; D020407:Internet; D009369:Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000378:metabolism; D064878:Web Browser
keywords: TCGA; annotation; cancer; database; oncotator