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@stitam stitam released this 14 Oct 13:26
· 1 commit to master since this release
v2.0.0
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Learn about vigilant mode.

This major release introduces offline access to ChEMBL, the EU Pesticides Database, and FooDB, enabling local database queries without relying on web services. PubChem access has been improved, with pc_sect() now supporting previously inaccessible sections.

NEW FEATURES

  • Added offline access to the EU Pesticides Database. Use db_download_eup() to download the database, eup_list_entries() to list all entries, eup_convert() to convert between identifiers, and eup_query() to query the database.
  • Added offline access to FooDB, a database of food constituents. Use db_download_foodb() to download the database, foodb_list_compounds() to list all compounds, foodb_convert() to convert between identifiers, and foodb_query() to query the database.
  • pc_sect() can now retrieve previously inaccessible PubChem sections, including spectral data and data from separate subsystems.
  • Added chembl_status() to retrieve status information about the ChEMBL webservice, including database version, release date, and entity counts.
  • Added chembl_atc_classes() to retrieve all available ATC classifications from ChEMBL.
  • Added chembl_img() for downloading SVG images from ChEMBL.

OFFLINE ACCESS TO CHEMBL

  • chembl_query() now supports both online queries (mode = "ws", default) and offline retrieval from a local ChEMBL database (mode = "offline"). Offline mode currently supports the following resources: "activity", "assay", "atc_class", "binding_site", "biotherapeutic", "cell_line", "chembl_id_lookup", "compound_record", "document", "drug", "drug_indication", "drug_warning", "go_slim", "and molecule".
  • Results for online and offline queries are identical for most resources. Where they differ, the offline version throws informative warnings.
  • Added db_download_chembl() for downloading ChEMBL for fully offline access. The function supports a version argument for downloading a specific version of ChEMBL.
  • Added chembl_check_db_version() to retrieve a pinned default ChEMBL database version from .Renviron or .Rprofile. An error is thrown if no version is configured. This can be used to work with pinned ChEMBL versions in offline mode.

MINOR IMPROVEMENTS

  • bcpc_query() now also looks for derivatives (esters and salts) of active compounds.
  • chembl_query() now returns a named list with improved formatting for nested output when output = "tidy".
  • chembl_query() now supports the "similarity" resource (currently limited to 20 results).
  • chembl_query() now supports the "compound_structural_alert" resource.
  • chembl_query() now retrieves the ChEMBL schema for each resource (once per session) and enforces it. Also NULL values are replaced with typed NA values.
  • Added new argument output to chembl_query() (values: "raw" or "tidy") to control output format. Raw format returns the full nested structure; tidy format attempts to flatten the results.
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