{
  "_id": "6ad35d266fd9391477c95ac8",
  "Package": "drugTargetInteractions",
  "Type": "Package",
  "Title": "drugTargetInteractions: Mining the Druggable Genome",
  "Version": "1.21.15",
  "Date": "2026-10-13",
  "Authors@R": "c(\nperson(\"Thomas\", \"Girke\", email=\"thomas.girke@ucr.edu\", role=c(\"cre\", \"aut\"), comment=c(ORCID=\"0000-0003-0710-3777\")),\nperson(\"Kevin\", \"Horan\", role=\"ctb\"))",
  "Description": "Utilities for identifying known drug-target interactions\nfor sets of query drug and/or target protein (gene)\nidentifiers. The interaction information is obtained from a\nseries of drug and target databases, including ChEMBL, PubChem,\nDGIdb, Open Targets, the Therapeutic Target Database, the Broad\nInstitute Drug Repurposing Hub and the IUPHAR/BPS Guide to\nPHARMACOLOGY. Each source can be queried on its own, or several\nof them combined into a single table anchored on HGNC gene\nidentifiers. Identifier translation utilities map query\nidentifiers onto the native identifier types each source\nexpects.",
  "VignetteBuilder": "knitr",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "NeedsCompilation": "no",
  "URL": "https://github.com/girke-lab/drugTargetInteractions",
  "biocViews": "Cheminformatics, BiomedicalInformatics, Pharmacogenetics,\nPharmacogenomics, Proteomics, Metabolomics, GeneTarget, Network",
  "Config/testthat/edition": "3",
  "BugReports": "https://github.com/girke-lab/drugTargetInteractions",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-17 02:36:23 UTC",
  "RemoteUrl": "https://github.com/bioc/drugTargetInteractions",
  "RemoteRef": "HEAD",
  "RemoteSha": "bf6616552e125642ac04d795dec153c00ca63000",
  "Packaged": {
    "Date": "2026-10-17 11:03:48 UTC",
    "User": "root"
  },
  "Author": "Thomas Girke [cre, aut] (ORCID:\n<https://orcid.org/0000-0003-0710-3777>),\nKevin Horan [ctb]",
  "Maintainer": "Thomas Girke <thomas.girke@ucr.edu>",
  "_user": "bioc",
  "_type": "src",
  "_file": "drugTargetInteractions_1.21.15.tar.gz",
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  "_expires": "2027-01-25T11:33:56.000Z",
  "_created": "2026-10-17T11:03:48.000Z",
  "_published": "2026-10-17T11:33:58.142Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39026617241",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 10
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  "_upstream": "https://github.com/bioc/drugTargetInteractions",
  "_commit": {
    "id": "bf6616552e125642ac04d795dec153c00ca63000",
    "author": "tgirke <tgirke@citrus.ucr.edu>",
    "committer": "tgirke <tgirke@citrus.ucr.edu>",
    "message": "Add runnable examples to the two hand-written man pages\n\ndownloadChemblDb.Rd and getUniprotIDs.Rd are among the 15 man pages\nwritten by hand rather than generated from roxygen, so the pass that\nadded runnable examples to the other pages never reached them.\n\ndownloadChemblDb() now shows where the download is cached and that a\nsmall sample of the same database ships with the package, which is what\nthe examples of the functions querying it use - so trying those needs no\ndownload. That also surfaces the \"this is a very large file\" warning\nthat was previously only an Rd comment, invisible to readers.\n\ngetUniprotIDs() shows the shape of its two result tables from the\nsnapshot already shipped in inst/extdata, which is useful on its own\ngiven the live UNIREF path depends on UniProt being reachable. The live\nquery stays under \\donttest.\n\nExported-object man pages with a runnable example: 57 of 64 (89%), up\nfrom 55. The threshold BiocCheck errors below is 80%, so this widens the\nmargin from three pages to five. The remaining seven are REST getters\nwith no local data to demonstrate on.\n",
    "time": 1792204583
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  "_maintainer": {
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    "email": "thomas.girke@ucr.edu",
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  "_topics": [
    "cheminformatics",
    "biomedicalinformatics",
    "pharmacogenetics",
    "pharmacogenomics",
    "proteomics",
    "metabolomics",
    "genetarget",
    "network"
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
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    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/girke-lab/drugtargetinteractions",
  "_realowner": "bioc",
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  "_exports": [
    "addCommonIds",
    "assembleMoaTable",
    "assembleMoaTargets",
    "broadRepurposingHubAnnot",
    "buildBroadRepurposingHubDb",
    "buildGenomeWideDrugTargetTable",
    "buildGtoPdbDb",
    "buildHgncSymbolMap",
    "buildMoaMasterTable",
    "buildTtdDb",
    "buildUnichemDb",
    "cmpIdMapping",
    "combineDrugTargets",
    "combineGenomeWideDrugTargets",
    "downloadBroadRepurposingHub",
    "downloadChemblDb",
    "downloadGtoPdb",
    "downloadHgncTable",
    "downloadTTD",
    "downloadUniChem",
    "downloadUnichemTables",
    "drugTargetAnnot",
    "drugTargetAnnotTable",
    "drugTargetBioactivity",
    "drugTargetColumnMap",
    "genConfig",
    "getChemblBioactivities",
    "getChemblBioassay",
    "getChemblDrugTarget",
    "getChemblMolecule",
    "getChemblTarget",
    "getDgidbDrugs",
    "getDgidbDrugTarget",
    "getDgidbTargets",
    "getDrugTarget",
    "getEnsemblOrthologs",
    "getEnsemblParalogs",
    "getHgncGeneTable",
    "getOpenTargetsDrugIds",
    "getOpenTargetsDrugs",
    "getOpenTargetsDrugTarget",
    "getOpenTargetsIds",
    "getOpenTargetsTargets",
    "getParalogs",
    "getPubchemDrugs",
    "getPubchemDrugTarget",
    "getPubchemTargets",
    "getSymEnsUp",
    "getUnichemMapping",
    "getUniprotIDs",
    "getUniprotMapping",
    "gtoPdbTargetAnnot",
    "listBioassayFields",
    "listDrugTargetFields",
    "listMoaSources",
    "mergeDrugTargets",
    "moaWide",
    "normalizeGeneSymbols",
    "processDrugage",
    "queryDrugTargets",
    "queryMoa",
    "runDrugTarget_Annot_Bioassay",
    "transformTTD",
    "ttdTargetAnnot"
  ],
  "_help": [
    {
      "page": "drugTargetInteraction-package",
      "title": "drugTargetInteractions: Mining the Druggable Genome",
      "topics": [
        "drugTargetInteractions-package",
        "drugTargetInteractions"
      ]
    },
    {
      "page": "addCommonIds",
      "title": "Add shared gene and compound identifiers to per-source result tables",
      "topics": [
        "addCommonIds"
      ]
    },
    {
      "page": "assembleMoaTable",
      "title": "Assemble a drug -> mechanism-of-action table",
      "topics": [
        "assembleMoaTable"
      ]
    },
    {
      "page": "assembleMoaTargets",
      "title": "Assemble the link from a MOA term to the target(s) it acts through",
      "topics": [
        "assembleMoaTargets"
      ]
    },
    {
      "page": "broadRepurposingHubAnnot",
      "title": "Query Broad Repurposing Hub drug-target annotations bidirectionally",
      "topics": [
        "broadRepurposingHubAnnot"
      ]
    },
    {
      "page": "buildBroadRepurposingHubDb",
      "title": "Build (or fetch a cached) local SQLite database of Repurposing Hub drug-target annotations",
      "topics": [
        "buildBroadRepurposingHubDb"
      ]
    },
    {
      "page": "buildGenomeWideDrugTargetTable",
      "title": "Genome-wide, checkpointed drug-target annotation build across the six annotation sources, anchored on an HGNC gene table",
      "topics": [
        "buildGenomeWideDrugTargetTable"
      ]
    },
    {
      "page": "buildGtoPdbDb",
      "title": "Build (or fetch a cached) local SQLite database of GtoPdb drug-target interactions",
      "topics": [
        "buildGtoPdbDb"
      ]
    },
    {
      "page": "buildHgncSymbolMap",
      "title": "Build a prev/alias-symbol -> current-symbol normalization map",
      "topics": [
        "buildHgncSymbolMap"
      ]
    },
    {
      "page": "buildMoaMasterTable",
      "title": "Build a drug-centric master table of mechanisms of action",
      "topics": [
        "buildMoaMasterTable"
      ]
    },
    {
      "page": "buildTtdDb",
      "title": "Build (or fetch a cached) local SQLite database of TTD interactions",
      "topics": [
        "buildTtdDb"
      ]
    },
    {
      "page": "buildUnichemDb",
      "title": "Build (or fetch a cached) local SQLite of UniChem compound cross-references",
      "topics": [
        "buildUnichemDb"
      ]
    },
    {
      "page": "cmpIdMapping",
      "title": "cmpIdMapping",
      "topics": [
        "cmpIdMapping"
      ]
    },
    {
      "page": "combineDrugTargets",
      "title": "Combine 'queryDrugTargets' results into one table",
      "topics": [
        "combineDrugTargets"
      ]
    },
    {
      "page": "combineGenomeWideDrugTargets",
      "title": "Append a genome-wide build's per-source tables into one table",
      "topics": [
        "combineGenomeWideDrugTargets"
      ]
    },
    {
      "page": "downloadBroadRepurposingHub",
      "title": "Download the Broad Repurposing Hub drug/sample annotation flat files",
      "topics": [
        "downloadBroadRepurposingHub"
      ]
    },
    {
      "page": "downloadChemblDb",
      "title": "downloadChemblDb",
      "topics": [
        "downloadChemblDb"
      ]
    },
    {
      "page": "downloadGtoPdb",
      "title": "Download GtoPdb's bulk interactions and HGNC mapping data",
      "topics": [
        "downloadGtoPdb"
      ]
    },
    {
      "page": "downloadHgncTable",
      "title": "Download (and cache) an HGNC complete-gene-set TSV snapshot",
      "topics": [
        "downloadHgncTable"
      ]
    },
    {
      "page": "downloadTTD",
      "title": "Download the TTD flat files needed for target-drug mapping",
      "topics": [
        "downloadTTD"
      ]
    },
    {
      "page": "downloadUniChem",
      "title": "downloadUniChem",
      "topics": [
        "downloadUniChem"
      ]
    },
    {
      "page": "downloadUnichemTables",
      "title": "Download the UniChem table dumps needed for compound cross-referencing",
      "topics": [
        "downloadUnichemTables"
      ]
    },
    {
      "page": "drugTargetAnnot",
      "title": "drugTargetAnnot",
      "topics": [
        "drugTargetAnnot",
        "queryBy"
      ]
    },
    {
      "page": "drugTargetAnnotTable",
      "title": "drugTargetAnnotTable",
      "topics": [
        "drugTargetAnnotTable"
      ]
    },
    {
      "page": "drugTargetBioactivity",
      "title": "drugTargetBioactivity",
      "topics": [
        "drugTargetBioactivity"
      ]
    },
    {
      "page": "drugTargetColumnMap",
      "title": "Column mapping used to append per-source tables into one table",
      "topics": [
        "drugTargetColumnMap"
      ]
    },
    {
      "page": "genConfig",
      "title": "genConfig",
      "topics": [
        "genConfig"
      ]
    },
    {
      "page": "getChemblBioactivities",
      "title": "Retrieve bioactivity measurements from the ChEMBL REST API",
      "topics": [
        "getChemblBioactivities"
      ]
    },
    {
      "page": "getChemblBioassay",
      "title": "Query raw ChEMBL bioassay measurements via the queryBy interface",
      "topics": [
        "getChemblBioassay"
      ]
    },
    {
      "page": "getChemblDrugTarget",
      "title": "Query known drug-target annotations via the ChEMBL REST API",
      "topics": [
        "getChemblDrugTarget"
      ]
    },
    {
      "page": "getChemblMolecule",
      "title": "Retrieve molecule records from the ChEMBL REST API",
      "topics": [
        "getChemblMolecule"
      ]
    },
    {
      "page": "getChemblTarget",
      "title": "Search ChEMBL for a target by gene symbol or name",
      "topics": [
        "getChemblTarget"
      ]
    },
    {
      "page": "getDgidbDrugs",
      "title": "Retrieve DGIdb drug interactions for one or more genes",
      "topics": [
        "getDgidbDrugs"
      ]
    },
    {
      "page": "getDgidbDrugTarget",
      "title": "Query DGIdb interaction data via the uniform queryBy interface",
      "topics": [
        "getDgidbDrugTarget"
      ]
    },
    {
      "page": "getDgidbTargets",
      "title": "Retrieve DGIdb target interactions for one or more drugs",
      "topics": [
        "getDgidbTargets"
      ]
    },
    {
      "page": "getDrugTarget",
      "title": "getDrugTarget",
      "topics": [
        "getDrugTarget"
      ]
    },
    {
      "page": "getEnsemblOrthologs",
      "title": "Retrieve cross-species orthologs for one or more genes from Ensembl",
      "topics": [
        "getEnsemblOrthologs"
      ]
    },
    {
      "page": "getEnsemblParalogs",
      "title": "Retrieve within-species paralogs for one or more genes from Ensembl",
      "topics": [
        "getEnsemblParalogs"
      ]
    },
    {
      "page": "getHgncGeneTable",
      "title": "Load the HGNC complete gene set as a gene-centric data.frame",
      "topics": [
        "getHgncGeneTable"
      ]
    },
    {
      "page": "getOpenTargetsDrugIds",
      "title": "Resolve many drug names to ChEMBL IDs in batched GraphQL requests",
      "topics": [
        "getOpenTargetsDrugIds"
      ]
    },
    {
      "page": "getOpenTargetsDrugs",
      "title": "Retrieve known drugs / clinical candidates for one or more targets from Open Targets (target -> drug)",
      "topics": [
        "getOpenTargetsDrugs"
      ]
    },
    {
      "page": "getOpenTargetsDrugTarget",
      "title": "Query Open Targets drug/target data via the uniform queryBy interface",
      "topics": [
        "getOpenTargetsDrugTarget"
      ]
    },
    {
      "page": "getOpenTargetsIds",
      "title": "Resolve many gene symbols to Ensembl IDs in batched GraphQL requests",
      "topics": [
        "getOpenTargetsIds"
      ]
    },
    {
      "page": "getOpenTargetsTargets",
      "title": "Retrieve targets for one or more drugs from Open Targets (drug -> target)",
      "topics": [
        "getOpenTargetsTargets"
      ]
    },
    {
      "page": "getParalogs",
      "title": "getParalogs",
      "topics": [
        "getParalogs"
      ]
    },
    {
      "page": "getPubchemDrugs",
      "title": "Retrieve PubChem bioactivities for one or more genes (target -> drug)",
      "topics": [
        "getPubchemDrugs"
      ]
    },
    {
      "page": "getPubchemDrugTarget",
      "title": "Query PubChem bioactivity data via the uniform queryBy interface",
      "topics": [
        "getPubchemDrugTarget"
      ]
    },
    {
      "page": "getPubchemTargets",
      "title": "Retrieve PubChem bioactivities for one or more drugs (drug -> target)",
      "topics": [
        "getPubchemTargets"
      ]
    },
    {
      "page": "getSymEnsUp",
      "title": "Gene to Protein ID Mappings",
      "topics": [
        "getSymEnsUp"
      ]
    },
    {
      "page": "getUnichemMapping",
      "title": "Translate compound identifiers between databases via a local UniChem SQLite",
      "topics": [
        "getUnichemMapping"
      ]
    },
    {
      "page": "getUniprotIDs",
      "title": "Retrieve UniProt IDs via ID and Cluster Mappings",
      "topics": [
        "getUniprotIDs"
      ]
    },
    {
      "page": "getUniprotMapping",
      "title": "Map identifiers between databases via the UniProt REST ID Mapping API",
      "topics": [
        "getUniprotMapping"
      ]
    },
    {
      "page": "gtoPdbTargetAnnot",
      "title": "Query GtoPdb drug-target interactions bidirectionally",
      "topics": [
        "gtoPdbTargetAnnot"
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    {
      "page": "listBioassayFields",
      "title": "List the fields available from a bioassay source under 'fields = \"all\"'",
      "topics": [
        "listBioassayFields"
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    },
    {
      "page": "listDrugTargetFields",
      "title": "List the fields available from a drug-target source under 'fields = \"all\"'",
      "topics": [
        "listDrugTargetFields"
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    {
      "page": "listMoaSources",
      "title": "Which sources carry mechanism-of-action terms, and what the others store",
      "topics": [
        "listMoaSources"
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    },
    {
      "page": "mergeDrugTargets",
      "title": "Join the per-source tables side by side, one row per gene-drug pair",
      "topics": [
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      "page": "moaWide",
      "title": "Collapse a MOA table to one row per drug",
      "topics": [
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    },
    {
      "page": "normalizeGeneSymbols",
      "title": "Normalize gene symbols to their current HGNC-approved form",
      "topics": [
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    {
      "page": "processDrugage",
      "title": "processDrugage",
      "topics": [
        "processDrugage"
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    },
    {
      "page": "queryDrugTargets",
      "title": "Query drug-target interactions across multiple sources from any recognised starting identifier",
      "topics": [
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    {
      "page": "queryMoa",
      "title": "Query the MOA-carrying sources and assemble their MOA table in one call",
      "topics": [
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      "page": "runDrugTarget_Annot_Bioassay",
      "title": "runDrugTarget_Annot_Bioassay",
      "topics": [
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      "page": "transformTTD",
      "title": "transformTTD",
      "topics": [
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    {
      "page": "ttdTargetAnnot",
      "title": "Query TTD target-drug interactions bidirectionally",
      "topics": [
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  "_vignettes": [
    {
      "source": "drugTargetInteractions.Rmd",
      "filename": "drugTargetInteractions.html",
      "title": "drugTargetInteractions: Mining the Druggable Genome",
      "author": "Authors: Kevin Horan, Brandon Le, Brendan Gongol, Desmond Cairo, Mohammad Afsharinia, Tandis Salem, Dan Evans, Nicholas Schork and Thomas Girke",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Overview",
        "Data Sources at a Glance",
        "Install Package",
        "Load Package and Access Help",
        "Quick Start",
        "One Source, One Call",
        "Many Sources, One Call",
        "One Table",
        "Data Sources in Detail",
        "ChEMBL",
        "DGIdb",
        "Open Targets",
        "Requesting Additional Fields",
        "TTD (Therapeutic Target Database)",
        "Broad Repurposing Hub (CLUE)",
        "GtoPdb (IUPHAR/BPS Guide to PHARMACOLOGY)",
        "Bioassay Queries",
        "PubChem",
        "ID Translation Layer",
        "Protein/Gene IDs",
        "Paralogs and Orthologs",
        "Compound IDs",
        "Cross-Source Queries",
        "Querying One or All Sources",
        "Performance Considerations",
        "Combining Results",
        "Shared Identifiers for Merging",
        "Stacking Sources Versus Placing Them Side by Side",
        "Mechanism of Action",
        "Which sources report mechanisms",
        "A Master Table of Mechanisms",
        "Genome-Wide Master Table",
        "The HGNC Gene Table (the Anchor)",
        "Building the Table, With Checkpointing",
        "Assembling the Build Into One Table",
        "Adjusting the Column Mapping",
        "Supplement",
        "Local ChEMBL SQLite Workflow",
        "UniProt.ws-Based ID Mapping",
        "biomaRt-Based Paralogs",
        "ensembldb-Based ID Mapping",
        "Static UniChem Mirror",
        "Putting It Together",
        "Session Info",
        "References"
      ],
      "created": "2020-11-30 16:24:41",
      "modified": "2026-10-14 02:45:32",
      "commits": 38
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