Package: PubChemR 3.0.0

PubChemR: Interface to the 'PubChem' Database for Chemical Data Retrieval

Provides an interface to the 'PubChem' database via the PUG REST <https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest> and PUG View <https://pubchem.ncbi.nlm.nih.gov/docs/pug-view> services. This package allows users to automatically access chemical and biological data from 'PubChem', including compounds, substances, assays, and various other data types. Functions are available to retrieve data in different formats, perform searches, and access detailed annotations.

Authors:Selcuk Korkmaz [aut, cre], Bilge Eren Yamasan [aut], Dincer Goksuluk [aut]

PubChemR_3.0.0.tar.gz
PubChemR_3.0.0.zip(r-4.7)PubChemR_3.0.0.zip(r-4.6)PubChemR_3.0.0.zip(r-4.5)
PubChemR_3.0.0.tgz(r-4.6-any)PubChemR_3.0.0.tgz(r-4.5-any)
PubChemR_3.0.0.tar.gz(r-4.7-any)PubChemR_3.0.0.tar.gz(r-4.6-any)
PubChemR_3.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
PubChemR/json (API)

# Install 'PubChemR' in R:
install.packages('PubChemR', repos = c('https://selcukorkmaz.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/selcukorkmaz/pubchemr/issues

On CRAN:

Conda:

5.90 score 4 stars 40 scripts 304 downloads 55 exports 28 dependencies

Last updated from:5461d52a55. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK148
source / vignettesOK222
linux-release-x86_64OK143
macos-release-arm64OK98
macos-oldrel-arm64OK93
windows-develOK93
windows-releaseOK100
windows-oldrelOK90
wasm-releaseOK111

Exports:AIDsCIDsdownloadget_aidsget_all_sourcesget_assaysget_biological_test_resultsget_cidsget_compoundsget_propertiesget_pug_restget_pug_viewget_sdfget_sidsget_substancesget_synonymsinstancepc_activity_matrixpc_activity_outcome_mappc_assaypc_assay_activity_longpc_batchpc_benchmarkpc_benchmark_harnesspc_cache_clearpc_cache_infopc_collectpc_compoundpc_configpc_cross_domain_joinpc_export_model_datapc_feature_tablepc_identifier_mappc_lifecycle_policypc_model_matrixpc_pollpc_profilepc_propertypc_requestpc_responsepc_resume_batchpc_sdq_bioactivitypc_similarity_searchpc_submitpc_substancepc_to_chemminerpc_to_rcdkproperty_mappubChemDatarequest_argsretrievesectionsectionListSIDssynonyms

Dependencies:askpassclicpp11curldplyrgenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigpurrrR6RJSONIOrlangstringistringrsystibbletidyrtidyselectutf8vctrswithr

Phase 4 Analysis Layer: Similarity to Model-Ready Export
1) Similar compounds from a seed structure | 2) Fetch assay activity in long format | 3) Build activity matrix (compound x assay) | 4) Add chemical features and prepare model matrix | 5) Export model-ready artifact
Rendered fromphase4-analysis-layer-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-02-25
Started: 2026-02-23

Advanced Next-Generation Workflows in PubChemR
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
Rendered fromadvanced-nextgen-workflows.Rmdusingknitr::rmarkdown

Last update: 2026-02-24
Started: 2026-02-24

Compound-to-Assay Workflow With pc_* API
Step 1: Name to CID | Step 2: CID to AID | Step 3: Assay summary retrieval
Rendered fromcompound-to-assay-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-02-23
Started: 2026-02-23

PubChemR Workflow: Retrieval to Modeling Table
1) Resolve CIDs from names | 2) Retrieve a compact property panel | 3) Prepare a modeling-ready table | 4) Convert to model matrix form | 5) Benchmark harness for scale and CI gates
Rendered frompubchemr-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-02-23
Started: 2026-02-23

Reproducible Cached Retrieval and Batching
Configure defaults | Clear cache for a clean run | Cached property retrieval | Chunked batch execution
Rendered fromreproducible-cached-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-02-23
Started: 2026-02-23

Readme and manuals

Help Manual

Help pageTopics
Assay, Compound, and Substance IdentifiersAIDs AIDs-SIDs-CIDs AIDs.PubChemInstance_AIDs CIDs CIDs.PubChemInstance_CIDs SIDs SIDs.PubChemInstance_SIDs
Download Content from PubChem and Save to a Filedownload
Retrieve Assay IDs (AIDs) from PubChemget_aids
Retrieve All Sources from PubChemget_all_sources
Retrieve Assays from PubChemget_assays
Retrieve "Biological Test Results" Section from PubChem Contentsget_biological_test_results
Retrieve Compound IDs (CIDs) from PubChemget_cids
Retrieve Compounds from PubChemget_compounds
Retrieve Compound Properties from PubChemget_properties property_map
Retrieve Data from PubChem PUG REST APIget_pug_rest
Retrieve PUG View Data from PubChemget_pug_view
Retrieve/Save SDF Data from PubChemget_sdf
Retrieve Substance IDs (SIDs) from PubChemget_sids
Retrieve Substances from PubChemget_substances
Retrieve Synonyms from PubChemget_synonyms
Retrieve Information for Requested Instancesinstance instance.PubChemInstanceList
Build an Assay Activity Matrixpc_activity_matrix
Harmonize Activity Outcome Labelspc_activity_outcome_map
Query Assay Records via the Next-Generation APIpc_assay
Convert PubChem Assay Summary to Long Activity Tablepc_assay_activity_long
Batch-Orchestrate PubChem Workflowspc_batch
Benchmark Chunked PubChem Workflowspc_benchmark
Benchmark Harness for Scale Scenariospc_benchmark_harness
Clear PubChemR Request Cachepc_cache_clear
Cache Diagnostics for PubChemRpc_cache_info
Collect Results From an Async PubChem Querypc_collect
Query Compound Records via the Next-Generation APIpc_compound
Configure PubChemR Next-Gen API Defaultspc_config
Join Compound, Substance, Assay, and Target Tablespc_cross_domain_join
Export Model-Ready Datapc_export_model_data
Build a Modeling-Ready Feature Tablepc_feature_table
Map Identifiers via the Next-Generation APIpc_identifier_map
Versioning and Deprecation Policypc_lifecycle_policy
Convert Feature Tables to Model Matrix Formpc_model_matrix
Poll an Asynchronous PubChem ListKeypc_poll
Apply a Predefined Execution Profilepc_profile
Query Compound Properties via the Next-Generation APIpc_property
Unified Transport Layer for PubChem Requestspc_request
Normalize an HTTP Response Into a Typed PubChem Resultpc_response
Resume a Checkpointed Batch Workflowpc_resume_batch
Retrieve Full Biological Test Results from PubChem SDQpc_sdq_bioactivity
Similarity-Driven Identifier Searchpc_similarity_search
Submit an Asynchronous PubChem Querypc_submit
Query Substance Records via the Next-Generation APIpc_substance
Convert PubChem Tables to ChemmineR SDF Objectspc_to_chemminer
Convert PubChem Tables to rcdk Moleculespc_to_rcdk
Retrieve Raw Data from PUG REST ObjectpubChemData pubChemData.PugRestInstance
'PubChemInstanceList' and 'PubChemInstance' ClassesPubChemR-classes
Classes for Pug View RequestPugView-classes
Retrieve Function Inputsrequest_args
Retrieve Information from PubChem Instancesretrieve retrieve.PC_Substance retrieve.PubChemInstance retrieve.PubChemInstanceList retrieve.PugViewInstance retrieve.PugViewSection
Extract Sections from Pug View Requestsection section.PugViewInstance section.PugViewSection section.PugViewSectionList
List Available Section/SubsectionssectionList sectionList.PugViewInstance sectionList.PugViewSection sectionList.PugViewSectionList
Getter function for 'Synonyms'synonyms synonyms.PubChemInstance_Synonyms