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  "Title": "Interface to the 'PubChem' Database for Chemical Data Retrieval",
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  "Author": "Selcuk Korkmaz [aut, cre]\n(<https://orcid.org/0000-0003-4632-6850>), Bilge Eren Yamasan\n[aut] (<https://orcid.org/0000-0002-6525-2503>), Dincer\nGoksuluk [aut] (<https://orcid.org/0000-0002-2752-7668>)",
  "Maintainer": "Selcuk Korkmaz <selcukorkmaz@gmail.com>",
  "Description": "Provides an interface to the 'PubChem' database via the\nPUG REST <https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest> and\nPUG View <https://pubchem.ncbi.nlm.nih.gov/docs/pug-view>\nservices. This package allows users to automatically access\nchemical and biological data from 'PubChem', including\ncompounds, substances, assays, and various other data types.\nFunctions are available to retrieve data in different formats,\nperform searches, and access detailed annotations.",
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  "Date/Publication": "2026-02-27 13:36:11 UTC",
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    "AIDs",
    "CIDs",
    "download",
    "get_aids",
    "get_all_sources",
    "get_assays",
    "get_biological_test_results",
    "get_cids",
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    "get_properties",
    "get_pug_rest",
    "get_pug_view",
    "get_sdf",
    "get_sids",
    "get_substances",
    "get_synonyms",
    "instance",
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    "pc_activity_outcome_map",
    "pc_assay",
    "pc_assay_activity_long",
    "pc_batch",
    "pc_benchmark",
    "pc_benchmark_harness",
    "pc_cache_clear",
    "pc_cache_info",
    "pc_collect",
    "pc_compound",
    "pc_config",
    "pc_cross_domain_join",
    "pc_export_model_data",
    "pc_feature_table",
    "pc_identifier_map",
    "pc_lifecycle_policy",
    "pc_model_matrix",
    "pc_poll",
    "pc_profile",
    "pc_property",
    "pc_request",
    "pc_response",
    "pc_resume_batch",
    "pc_sdq_bioactivity",
    "pc_similarity_search",
    "pc_submit",
    "pc_substance",
    "pc_to_chemminer",
    "pc_to_rcdk",
    "property_map",
    "pubChemData",
    "request_args",
    "retrieve",
    "section",
    "sectionList",
    "SIDs",
    "synonyms"
  ],
  "_help": [
    {
      "page": "AIDs-SIDs-CIDs",
      "title": "Assay, Compound, and Substance Identifiers",
      "topics": [
        "AIDs",
        "AIDs-SIDs-CIDs",
        "AIDs.PubChemInstance_AIDs",
        "CIDs",
        "CIDs.PubChemInstance_CIDs",
        "SIDs",
        "SIDs.PubChemInstance_SIDs"
      ]
    },
    {
      "page": "download",
      "title": "Download Content from PubChem and Save to a File",
      "topics": [
        "download"
      ]
    },
    {
      "page": "get_aids",
      "title": "Retrieve Assay IDs (AIDs) from PubChem",
      "topics": [
        "get_aids"
      ]
    },
    {
      "page": "get_all_sources",
      "title": "Retrieve All Sources from PubChem",
      "topics": [
        "get_all_sources"
      ]
    },
    {
      "page": "get_assays",
      "title": "Retrieve Assays from PubChem",
      "topics": [
        "get_assays"
      ]
    },
    {
      "page": "get_biological_test_results",
      "title": "Retrieve \"Biological Test Results\" Section from PubChem Contents",
      "topics": [
        "get_biological_test_results"
      ]
    },
    {
      "page": "get_cids",
      "title": "Retrieve Compound IDs (CIDs) from PubChem",
      "topics": [
        "get_cids"
      ]
    },
    {
      "page": "get_compounds",
      "title": "Retrieve Compounds from PubChem",
      "topics": [
        "get_compounds"
      ]
    },
    {
      "page": "get_properties",
      "title": "Retrieve Compound Properties from PubChem",
      "topics": [
        "get_properties",
        "property_map"
      ]
    },
    {
      "page": "get_pug_rest",
      "title": "Retrieve Data from PubChem PUG REST API",
      "topics": [
        "get_pug_rest"
      ]
    },
    {
      "page": "get_pug_view",
      "title": "Retrieve PUG View Data from PubChem",
      "topics": [
        "get_pug_view"
      ]
    },
    {
      "page": "get_sdf",
      "title": "Retrieve/Save SDF Data from PubChem",
      "topics": [
        "get_sdf"
      ]
    },
    {
      "page": "get_sids",
      "title": "Retrieve Substance IDs (SIDs) from PubChem",
      "topics": [
        "get_sids"
      ]
    },
    {
      "page": "get_substances",
      "title": "Retrieve Substances from PubChem",
      "topics": [
        "get_substances"
      ]
    },
    {
      "page": "get_synonyms",
      "title": "Retrieve Synonyms from PubChem",
      "topics": [
        "get_synonyms"
      ]
    },
    {
      "page": "instance",
      "title": "Retrieve Information for Requested Instances",
      "topics": [
        "instance",
        "instance.PubChemInstanceList"
      ]
    },
    {
      "page": "pc_activity_matrix",
      "title": "Build an Assay Activity Matrix",
      "topics": [
        "pc_activity_matrix"
      ]
    },
    {
      "page": "pc_activity_outcome_map",
      "title": "Harmonize Activity Outcome Labels",
      "topics": [
        "pc_activity_outcome_map"
      ]
    },
    {
      "page": "pc_assay",
      "title": "Query Assay Records via the Next-Generation API",
      "topics": [
        "pc_assay"
      ]
    },
    {
      "page": "pc_assay_activity_long",
      "title": "Convert PubChem Assay Summary to Long Activity Table",
      "topics": [
        "pc_assay_activity_long"
      ]
    },
    {
      "page": "pc_batch",
      "title": "Batch-Orchestrate PubChem Workflows",
      "topics": [
        "pc_batch"
      ]
    },
    {
      "page": "pc_benchmark",
      "title": "Benchmark Chunked PubChem Workflows",
      "topics": [
        "pc_benchmark"
      ]
    },
    {
      "page": "pc_benchmark_harness",
      "title": "Benchmark Harness for Scale Scenarios",
      "topics": [
        "pc_benchmark_harness"
      ]
    },
    {
      "page": "pc_cache_clear",
      "title": "Clear PubChemR Request Cache",
      "topics": [
        "pc_cache_clear"
      ]
    },
    {
      "page": "pc_cache_info",
      "title": "Cache Diagnostics for PubChemR",
      "topics": [
        "pc_cache_info"
      ]
    },
    {
      "page": "pc_collect",
      "title": "Collect Results From an Async PubChem Query",
      "topics": [
        "pc_collect"
      ]
    },
    {
      "page": "pc_compound",
      "title": "Query Compound Records via the Next-Generation API",
      "topics": [
        "pc_compound"
      ]
    },
    {
      "page": "pc_config",
      "title": "Configure PubChemR Next-Gen API Defaults",
      "topics": [
        "pc_config"
      ]
    },
    {
      "page": "pc_cross_domain_join",
      "title": "Join Compound, Substance, Assay, and Target Tables",
      "topics": [
        "pc_cross_domain_join"
      ]
    },
    {
      "page": "pc_export_model_data",
      "title": "Export Model-Ready Data",
      "topics": [
        "pc_export_model_data"
      ]
    },
    {
      "page": "pc_feature_table",
      "title": "Build a Modeling-Ready Feature Table",
      "topics": [
        "pc_feature_table"
      ]
    },
    {
      "page": "pc_identifier_map",
      "title": "Map Identifiers via the Next-Generation API",
      "topics": [
        "pc_identifier_map"
      ]
    },
    {
      "page": "pc_lifecycle_policy",
      "title": "Versioning and Deprecation Policy",
      "topics": [
        "pc_lifecycle_policy"
      ]
    },
    {
      "page": "pc_model_matrix",
      "title": "Convert Feature Tables to Model Matrix Form",
      "topics": [
        "pc_model_matrix"
      ]
    },
    {
      "page": "pc_poll",
      "title": "Poll an Asynchronous PubChem ListKey",
      "topics": [
        "pc_poll"
      ]
    },
    {
      "page": "pc_profile",
      "title": "Apply a Predefined Execution Profile",
      "topics": [
        "pc_profile"
      ]
    },
    {
      "page": "pc_property",
      "title": "Query Compound Properties via the Next-Generation API",
      "topics": [
        "pc_property"
      ]
    },
    {
      "page": "pc_request",
      "title": "Unified Transport Layer for PubChem Requests",
      "topics": [
        "pc_request"
      ]
    },
    {
      "page": "pc_response",
      "title": "Normalize an HTTP Response Into a Typed PubChem Result",
      "topics": [
        "pc_response"
      ]
    },
    {
      "page": "pc_resume_batch",
      "title": "Resume a Checkpointed Batch Workflow",
      "topics": [
        "pc_resume_batch"
      ]
    },
    {
      "page": "pc_sdq_bioactivity",
      "title": "Retrieve Full Biological Test Results from PubChem SDQ",
      "topics": [
        "pc_sdq_bioactivity"
      ]
    },
    {
      "page": "pc_similarity_search",
      "title": "Similarity-Driven Identifier Search",
      "topics": [
        "pc_similarity_search"
      ]
    },
    {
      "page": "pc_submit",
      "title": "Submit an Asynchronous PubChem Query",
      "topics": [
        "pc_submit"
      ]
    },
    {
      "page": "pc_substance",
      "title": "Query Substance Records via the Next-Generation API",
      "topics": [
        "pc_substance"
      ]
    },
    {
      "page": "pc_to_chemminer",
      "title": "Convert PubChem Tables to ChemmineR SDF Objects",
      "topics": [
        "pc_to_chemminer"
      ]
    },
    {
      "page": "pc_to_rcdk",
      "title": "Convert PubChem Tables to rcdk Molecules",
      "topics": [
        "pc_to_rcdk"
      ]
    },
    {
      "page": "pubChemData",
      "title": "Retrieve Raw Data from PUG REST Object",
      "topics": [
        "pubChemData",
        "pubChemData.PugRestInstance"
      ]
    },
    {
      "page": "PubChemR-classes",
      "title": "'PubChemInstanceList' and 'PubChemInstance' Classes",
      "topics": [
        "PubChemR-classes"
      ]
    },
    {
      "page": "PugView-classes",
      "title": "Classes for Pug View Request",
      "topics": [
        "PugView-classes"
      ]
    },
    {
      "page": "request_args",
      "title": "Retrieve Function Inputs",
      "topics": [
        "request_args"
      ]
    },
    {
      "page": "retrieve",
      "title": "Retrieve Information from PubChem Instances",
      "topics": [
        "retrieve",
        "retrieve.PC_Substance",
        "retrieve.PubChemInstance",
        "retrieve.PubChemInstanceList",
        "retrieve.PugViewInstance",
        "retrieve.PugViewSection"
      ]
    },
    {
      "page": "section",
      "title": "Extract Sections from Pug View Request",
      "topics": [
        "section",
        "section.PugViewInstance",
        "section.PugViewSection",
        "section.PugViewSectionList"
      ]
    },
    {
      "page": "sectionList",
      "title": "List Available Section/Subsections",
      "topics": [
        "sectionList",
        "sectionList.PugViewInstance",
        "sectionList.PugViewSection",
        "sectionList.PugViewSectionList"
      ]
    },
    {
      "page": "synonyms",
      "title": "Getter function for 'Synonyms'",
      "topics": [
        "synonyms",
        "synonyms.PubChemInstance_Synonyms"
      ]
    }
  ],
  "_readme": "https://github.com/selcukorkmaz/pubchemr/raw/HEAD/README.md",
  "_rundeps": [
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    "cli",
    "cpp11",
    "curl",
    "dplyr",
    "generics",
    "glue",
    "httr",
    "jsonlite",
    "lifecycle",
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    "mime",
    "openssl",
    "pillar",
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  "_vignettes": [
    {
      "source": "advanced-nextgen-workflows.Rmd",
      "filename": "advanced-nextgen-workflows.html",
      "title": "Advanced Next-Generation Workflows in PubChemR",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1) Typed result contract",
        "2) Runtime policy and transport controls",
        "3) Unified request layer and typed wrappers",
        "4) Caching and offline replay",
        "5) Async listkey workflows (pc_submit -> pc_poll -> pc_collect)",
        "6) Checkpointed batching and resume",
        "7) Benchmarking and threshold gates",
        "8) Analysis-layer helpers for assay modeling",
        "8.1 Similarity retrieval and long assay activity table",
        "8.2 Activity matrix (dense or sparse)",
        "8.3 Feature table, matrix conversion, and export",
        "9) Optional ecosystem bridges",
        "10) Targeted PUG View helper for bio test sections",
        "11) Lifecycle policy (legacy vs nextgen)",
        "12) Recommended production pattern"
      ],
      "created": "2026-02-24 18:52:41",
      "modified": "2026-02-24 18:52:41",
      "commits": 1
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