{
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  "Package": "biomaRt",
  "Title": "Interface to BioMart databases (i.e. Ensembl)",
  "Version": "2.69.0",
  "Authors@R": "c(\nperson(\"Steffen\", \"Durinck\", , \"biomartdev@gmail.com\", role = \"aut\"),\nperson(\"Wolfgang\", \"Huber\", role = \"aut\"),\nperson(\"Sean\", \"Davis\", , \"sdavis2@mail.nih.gov\", role = \"ctb\"),\nperson(\"Francois\", \"Pepin\", role = \"ctb\"),\nperson(\"Vince S\", \"Buffalo\", role = \"ctb\"),\nperson(\"Mike\", \"Smith\", , \"grimbough@gmail.com\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-7800-3848\")),\nperson(\"Hugo\", \"Gruson\", , \"hugo.gruson@embl.de\", role = c(\"ctb\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4094-1476\")),\nperson(\"German Network for Bioinformatics Infrastructure - de.NBI\", role = \"fnd\")\n)",
  "Description": "In recent years a wealth of biological data has become\navailable in public data repositories. Easy access to these\nvaluable data resources and firm integration with data analysis\nis needed for comprehensive bioinformatics data analysis.\nbiomaRt provides an interface to a growing collection of\ndatabases implementing the BioMart software suite\n(<https://www.ensembl.org/info/data/biomart/index.html>). The\npackage enables retrieval of large amounts of data in a uniform\nway without the need to know the underlying database schemas or\nwrite complex SQL queries.  The most prominent examples of\nBioMart databases are maintained by Ensembl, which provides\nbiomaRt users direct access to a diverse set of data and\nenables a wide range of powerful online queries from gene\nannotation to database mining.",
  "License": "Artistic-2.0",
  "URL": "https://github.com/Huber-group-EMBL/biomaRt,\nhttps://huber-group-embl.github.io/biomaRt/",
  "BugReports": "https://github.com/Huber-group-EMBL/biomaRt/issues",
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  "biocViews": "Annotation",
  "Config/Needs/website": "xfun",
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  "NeedsCompilation": "no",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "Collate": "'biomaRt-package.R' 'biomaRtClasses.R' 'methods-Mart.R'\n'biomaRt.R' 'caching.R' 'ensembl.R' 'ensembl_wrappers.R'\n'ensembl_ssl_settings.R' 'utilityFunctions.R'\n'non-biomart-utils.R' 'exportFASTA.R' 'NP2009code.R'",
  "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:30:57 UTC",
  "RemoteUrl": "https://github.com/bioc/biomaRt",
  "RemoteRef": "HEAD",
  "RemoteSha": "0b83a479a1b2eef36f95579324e4ac0404976707",
  "Packaged": {
    "Date": "2026-05-29 08:39:01 UTC",
    "User": "root"
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  "Author": "Steffen Durinck [aut],\nWolfgang Huber [aut],\nSean Davis [ctb],\nFrancois Pepin [ctb],\nVince S Buffalo [ctb],\nMike Smith [ctb] (ORCID: <https://orcid.org/0000-0002-7800-3848>),\nHugo Gruson [ctb, cre] (ORCID: <https://orcid.org/0000-0002-4094-1476>),\nGerman Network for Bioinformatics Infrastructure - de.NBI [fnd]",
  "Maintainer": "Hugo Gruson <hugo.gruson@embl.de>",
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  "_realowner": "bioc",
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  "_exports": [
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    "biomartCacheClear",
    "biomartCacheInfo",
    "columns",
    "exportFASTA",
    "filterOptions",
    "filterType",
    "getBM",
    "getGene",
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    "getSequence",
    "keys",
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    "listDatasets",
    "listEnsembl",
    "listEnsemblArchives",
    "listEnsemblGenomes",
    "listFilterOptions",
    "listFilters",
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    "searchAttributes",
    "searchDatasets",
    "searchFilterOptions",
    "searchFilters",
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    "useDataset",
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    "useEnsemblGenomes",
    "useMart"
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      "page": "attributePages",
      "title": "Gives a summary of the attribute pages",
      "topics": [
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      ]
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      "title": "Deprecated and defunct functions in package 'biomaRt'",
      "topics": [
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        "filterOptions",
        "listFilterValues",
        "searchFilterValues"
      ]
    },
    {
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      "title": "'biomaRt' result caching",
      "topics": [
        "biomartCache",
        "biomartCacheClear",
        "biomartCacheInfo"
      ]
    },
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      "title": "Exports getSequence results to FASTA format",
      "topics": [
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      ]
    },
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      "title": "Displays the filter type",
      "topics": [
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      "title": "Retrieves information from the BioMart database",
      "topics": [
        "getBM"
      ]
    },
    {
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      "title": "Retrieves gene annotation information given a vector of identifiers",
      "topics": [
        "getGene"
      ]
    },
    {
      "page": "getHomologs",
      "title": "List homologous genes between two species.",
      "concept": [
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      ],
      "topics": [
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      ]
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      "title": "Retrieves information from two linked datasets",
      "topics": [
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    },
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      "title": "Retrieves sequences",
      "topics": [
        "getSequence"
      ]
    },
    {
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      "title": "lists the attributes available in the selected dataset",
      "topics": [
        "listAttributes",
        "searchAttributes"
      ]
    },
    {
      "page": "listDatasets",
      "title": "List or search the datasets available in the selected BioMart database",
      "topics": [
        "listDatasets",
        "searchDatasets"
      ]
    },
    {
      "page": "listEnsembl",
      "title": "lists the available BioMart databases hosted by Ensembl",
      "topics": [
        "listEnsembl",
        "listEnsemblGenomes"
      ]
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      "title": "Lists the available archived versions of Ensembl",
      "topics": [
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      ]
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      "page": "listFilters",
      "title": "List or search the filters available in the selected dataset",
      "topics": [
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        "searchFilters"
      ]
    },
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      "title": "lists the available BioMart databases",
      "topics": [
        "listMarts"
      ]
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      "title": "Display the analysis code from the 2009 Nature protocols paper",
      "topics": [
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      "topics": [
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        "searchFilterOptions"
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    },
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      "title": "Retrieve information from the BioMart databases",
      "topics": [
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        "columns,Mart-method",
        "keys",
        "keys,Mart-method",
        "keytypes",
        "keytypes,Mart-method",
        "select",
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        "select-methods"
      ]
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      "title": "Save system specific SSL settings for contacting Ensembl",
      "topics": [
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      "title": "Class Mart",
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        "show,Mart-method"
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      "title": "Select a dataset to use and updates Mart object",
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      "title": "Connects to the selected BioMart database and dataset hosted by Ensembl",
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        "useEnsemblGenomes"
      ]
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      "title": "Connects to the selected BioMart database and dataset",
      "topics": [
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      "title": "Accessing Ensembl annotation with biomaRt",
      "author": "Mike L. Smith, Steffen Durinck, Wolfgang Huber",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Selecting an Ensembl BioMart database and dataset",
        "Step1: Identifying the database you need",
        "Step 2: Choosing a dataset",
        "Ensembl mirror sites",
        "Using archived versions of Ensembl",
        "Using Ensembl Genomes",
        "How to build a biomaRt query",
        "Searching for filters and attributes",
        "Using predefined filter values",
        "Finding out more information on filters",
        "filterType",
        "Attribute Pages",
        "Using select()",
        "Result Caching",
        "biomaRt helper functions",
        "exportFASTA",
        "Examples of biomaRt queries",
        "Annotate a set of Affymetrix identifiers with HUGO symbol and chromosomal locations of corresponding genes",
        "Annotate a set of EntrezGene identifiers with GO annotation",
        "Retrieve all HUGO gene symbols of genes that are located on chromosomes 17,20 or Y, and are associated with specific GO terms",
        "Annotate set of idenfiers with INTERPRO protein domain identifiers",
        "Select all Affymetrix identifiers on the hgu133plus2 chip and Ensembl gene identifiers for genes located on chromosome 16 between basepair 1100000 and 1250000.",
        "Retrieve all EntrezGene identifiers and HUGO gene symbols of genes which have a \"MAP kinase activity\" GO term associated with it.",
        "Given a set of EntrezGene identifiers, retrieve 100bp upstream promoter sequences",
        "Retrieve all 5' UTR sequences of all genes that are located on chromosome 3 between the positions 185,514,033 and 185,535,839",
        "Retrieve protein sequences for a given list of EntrezGene identifiers",
        "Retrieve known SNPs located on the human chromosome 8 between positions 148350 and 148400",
        "Given the human gene TP53, retrieve the human chromosomal location of this gene and also retrieve the chromosomal location and RefSeq id of its homolog in mouse.",
        "Connection troubleshooting",
        "r BiocStyle::Biocpkg(\"biomaRt\") specific solutions",
        "Global connection settings",
        "Error: \"SSL certificate problem\"",
        "Error: \"sslv3 alert handshake failure\"",
        "Session Info"
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      "created": "2020-01-30 13:17:54",
      "modified": "2025-09-29 13:08:59",
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      "filename": "accessing_other_marts.html",
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      "author": "Steffen Durinck, Wolfgang Huber, Mike Smith",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Using a BioMart other than Ensembl",
        "Wormbase",
        "Phytozome",
        "Version 12",
        "Version 13",
        "Session Info"
      ],
      "created": "2020-11-10 09:30:57",
      "modified": "2025-09-29 13:09:43",
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