NEWS

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webchem 1.3.0 (2023-06-09)

NEW FEATURES

• The nist_ri function now returns a column with the CAS number to facilitate querying of multiple retention index tables.
• The nist_ri function can now take multiple arguments for type, polarity and temp_prog.
• CAS numbers are automatically reformatted using as.cas in bcpc_query, cts_convert, get_etoxid, fn_percept, get_cid, and srs_query.
• The as.cas function now has a verbose argument.

DEFUNCT FUNCTIONS

• ci_query() has been removed from the package because NLM had retired ChemIDplus.
• pan_query() has been removed from the package because PAN no longer supports programmatic access.

BUG FIXES

• nist_ri() failed because the behaviour of a dependency had changed. This has been fixed.
• pc_sect() failed when query response was valid but the content was NA. This has been fixed.

webchem 1.2.0 (2022-11-02)

NEW FEATURES

• webchem can now access ChEMBL (https://www.ebi.ac.uk/chembl/) with chembl_*() functions. ChEMBL is a manually curated database of bioactive molecules with drug-like properties.

BUG FIXES

• ChemSpider functions did not include time delays between queries. This has been fixed.
• Multiple ChemSpider functions failed when the API key was provided during function call. This has been fixed.
• Minor change in NIST retention index tables was causing nist_ri() to fail. This has been fixed.

webchem 1.1.3 (2022-06-15)

NEW FEATURES

• cir_query() now returns a tibble instead of a list to be consistent with other translator functions. This is a potentially breaking change for users.

BUG FIXES

• cts_convert() now accepts numeric input as well e.g. PubChem CID.
• get_cid() became more robust to smiles queries with special characters.
• bcpc_query now correctly parses the activity in cases that two activities are given (e.g. "herbicides" and "plant growth regulators").

webchem 1.1.2 (2021-12-06)

NEW FEATURES

• Export chemical structures in Mol format with write_mol().

BUG FIXES

• ci_query() can no longer query chemicals by name.
• Non-exported function ping_pubchem_pw() was incorrectly reporting that PUG VIEW was down. This has been fixed.
• is.cas() now catches whitespaces correctly.
• aw_query() was renamed and adapted to bcpc_query, as the alanwood site has moved.

MINOR IMPROVEMENTS

• webchem functions now default to global options regarding verbose messages.

webchem 1.1.1 (2021-02-07)

NEW FEATURES

• Fetch LIPID MAPS and SwissLipids identifiers from Wikidata.

BUG FIXES

• Fix get_csid() so it doesn't break when a query is invalid.

webchem 1.1.0 (2020-10-02)

NEW FEATURES

• Download images of substances from Chemical Identifier Resolver (CIR) with cir_img().
• Download images of substances from ChemSpider with cs_img().
• find_db() checks if a query gets a hit in most databases integrated in webchem. Useful for deciding which of several databases to focus on given a set of chemicals.

MINOR IMPROVEMENTS

• Most functions now use httr::RETRY() to access webservices.
• Verbose messages are now harmonized.
• The "type" argument in ci_query() and aw_query() has been changed to "from" for consistency with other functions.
• fn_percept() and cts_compinfo() now have "query" and "from" arguments for consistency with other functions.
• Possible values for "from" have been made more consistent across functions.
• pc_synonyms(), cts_convert(), cir_query() have been changed to use the match argument instead of choices for consistency with other functions.
• get_etoxid() output changed slightly so that the matched chemical name string no longer includes the etoxid in parentheses.
• is.cas() is now vectorized.

BUG FIXES

• Fix URL encoding so SMILES queries don't fail on some special characters.

webchem 1.0.0 (2020-05-28)

NEW FEATURES

• get_cid() now can search by registry IDs (e.g. CAS RN), and can handle more complex requests like searching for similar compounds.
• Retrieve chemical data from PubChem content pages with pc_sect().
• get_etoxid() now can search by CAS, EC, GSBL and RTECS numbers. Added from = argument.
• nist_ri() now can search by name, InChI, InChIKey, or CAS. The cas argument is deprecated. Use query instead with from = "cas".

MINOR IMPROVEMENTS

• All get_*() functions now output tibbles with a column for the query and a column for the retrieved ID.
• Changes to arguments in get_*() functions to make them more consistent.
• aw_idx.rda is no longer included in the package as a data set. Instead, it is built by build_aw_idx() to tempdir().

BUG FIXES

• nist_ri() returned malformed tables or errored if there was only one entry for a query.
• get_csid() now returns all csids when queried from formula.
• get_csid() returned an error when query was NA.
• get_chebiid() and chebi_comp_entity() fixed for invalid queries.
• get_cid() returned the PubChem ID of sodium when the query was NA.
• aw_query() returned a list for successful queries, NA for unsuccessful queries.

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem 0.5.0 (2020-03-02)

NEW FEATURES

• Retrieve data from ChEBI (https://www.ebi.ac.uk/chebi/) webservice with get_chebiid() and chebi_comp_entity(). ChEBI comprises a rich data base on chemicals with bilogical interest.
• Retrieve retention indices from NIST (https://webbook.nist.gov) with nist_ri().
• Get record details from US EPA Substance Registry Services (https://cdxnodengn.epa.gov/cdx-srs-rest/) with srs_query().
• "first" argument in cts_convert() and cir_query() and "interactive" argument in pc_synonyms() deprecated. Use "choices" instead to return either a list of all results, only the first result, or an interactive menu to choose a result to return.
• ChemSpider functions now look for an API token stored in .Renviron or .Rprofile by default so you can keep them hidden more easily.

MINOR IMPROVEMENTS

• as.cas() added.
• Removed documentation files for non-exported functions that were only used internally.

BUG FIXES

• cs_prop() failed with duplicated return values.
• pp_query() failed when compound present, but no properties.
• ci_query() failed when missing table.
• get_csid() failed because of a major change in the ChemSpider API.
• multiple functions failed because of a major change in the ChemSpider API.
• cir_query() mistook NA for sodium.
• fixed functions that communicate with the ChemSpider API.
• get_etoxid() printed incorrect results for certain match types.

DEPRECATED FUNCTIONS

• cs_extcompinfo() cannot be fixed as there is no equivalent in the new ChemSpider API yet.

DEFUNCT FUNCTIONS

• ppdb_parse() has been removed. webchem no longer offers any support for PPDB.
• pp_query() has been removed. Physprop API is no longer active.
• cs_prop() has been removed.

webchem 0.4.0 (2018-04-07)

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

• extr_num() did not work properly with decimal numbers.
• cs_prop() failed when epi-suite data was not available.
• cs_prop() failed with invalid html.
• cs_prop() gave incorrect answer, if entries were not available.
• cs_prop() did not parse scientific number correctly.
• is.smiles() failed because of changes in rcdk.
• cir_query() failed with identifiers containing spaces (e.g. 'acetic acid').
• Aeveral other functions failed with identifiers containing spaces & returned wrong distance.

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem 0.3.0 (2017-10-20)

NEW FEATURES

MINOR IMPROVEMENTS

• cs_prop() now also return experimental data for Boiling and Melting Points.
• pc_synonyms gained an argument 'interactive' to enter an interactive mode for selecting synonyms.
• cts_convert now returns NA if no matches are found.

BUG FIXES

• cs_prop() failed with some CSIDs.
• wd_ident() failed if multiple entries where found. Now returns the first hit only.
• ci_query() did not return fully cleaned smiles and inchi.

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem 0.2.0

NEW FEATURES

• fn_percept() extracts flavor percepts using CAS numbers from www.flavornet.org. Flavornet is a database of 738 compounds with human-detectible odors.

MINOR IMPROVEMENTS

BUG FIXES

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem 0.1.1

NEW FEATURES

• Added ping_pubchem() to check whether pubchem is up & running.
• Added cs_web_ping () to check whether the chemspider webpage is functional.

MINOR IMPROVEMENTS

• Updated allan wood index.

BUG FIXES

• pc_prop() returned to many rows if last cid supplied was NA.
• Switched to https for NCBI, chemspider & chemid.
• get_wdid() failed if non-ascii characters where returned by wikipedia.
• rcdk:parse.smiles() now returns NA if a SMILES string could not be parsed. => broke is.smiles

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem 0.1.0

NEW FEATURES

• Added cts_to() and cts_from() to retrieve possible ids that can be queried.
• cts_(), pp_query(), cir_query(), get_cid(), get_etoxid(), etox_(), pan_query() get_wdid(), aw_query(), get_csid(), cs_prop(), cs_compinfo() and ci_query() can handle multiple inputs.
• pc_prop() queries properties and pc_synonmy() synonyms from PUG-REST.
• Added extractors for webchem objects: cas(), inchikey() and smiles().

MINOR IMPROVEMENTS

• Rewrite of pubchem functions using PUG-REST.
• ChemSpider: better use of NA in input (=return NA).
• More robust matching in get_etoxid.

BUG FIXES

• pan_query() did not return numeric values.
• get_cid() failed with multiple results.

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

• ppdb_query() has been removed due to copyright issues. The new ppdb_parse() parses only a html, but does not interact with the database.
• pan()
• alanwood()
• get_cid()
• cid_compinfo()
• chemid()
• physprop()

webchem 0.0.5

NEW FEATURES

• is.smiles() checks SMILES strings, by parsing via (R)CDK.
• get_wdid() and wd_indent() to retrieve information from wikidata.
• get_etoxid() can handle multi inputs (interactive mode, best match, first match, NA and all matches).
• ci_query() can handle multi inputs (interactive mode, best match, first match and NA).
• cs_prop() queries predictions (ACD and EPiSuite) from ChemSpider.

MINOR IMPROVEMENTS

• webchem uses exclusively xml2 (instead of XML).
• All function return source_url for (micro-)attribution of sources.
• cs_compinfo(): names of returned list changed.
• cs_extcompinfo():
  • names of returned list changed.
  • result is numeric where appropriate.
• cir(): result is numeric where appropriate.
• Unified naming scheme of functions.
• is.inchikey_cs() has been integrated into is.inchikey().
• aw_query() returns multiple inchikey if found.
• pan() now returns chemical name and matched synonym.

BUG FIXES

• Utility functions are not vectorized and throw an error.
• chemid() did mot work with inchikey as input.
• ppdb_idx returned duplicated CAS values, which caused ppdb() to fail.
• ppdb() failed in some cases because of false encoding.
• etox_*() functions are more robust.
• ci_query() failed if multi hits were found. Now returns first hit.
• aw_fuery() failed if inchikey was not found.

DEPRECATED FUNCTIONS

• pan_query() replaces pan().
• aw_query() replaces alanwood().
• get_pcid() replaces get_cid().
• pc_compinfo() replaces cid_compinfo().
• ci_query() replaces chemid().
• pp_query() replaces physprop().

DEFUNCT FUNCTIONS

• csid_compinfo()
• csid_extcompinfo()

webchem 0.0.4

NEW FEATURES

• chemid() to query ChemIDplus http://chem.sis.nlm.nih.gov/chemidplus/.
• is.inchikey() and is.cas() to check if a string is valid inchikey or CAS registry number.
• parse_mol(): A simple molfile parser.
• Functions to work with ChemSpider InChI API:
  • cs_csid_mol() : convert csid to mol.
  • cs_inchikey_csid() : convert inchikey to csid.
  • cs_inchikey_inchi() : convert inchikey to inchi.
  • cs_inchikey_mol() : convert inchikey to Molfile.
  • cs_inchi_csid() : convert inchi to csid.
  • cs_inchi_inchikey : convert inchi to inchikey.
  • cs_inchi_mol() : convert inchi to molfile.
  • cs_inchi_smiles() : convert inchi to smiles.
  • cs_smiles_inchi() : convert smiles to inchi.
  • These are all wrapped into cs_convert().
  • is.inchikey_cs() : Check via ChemSpider if inchikey is valid.
• webchem has now a zenodo doi, please cite if you use it.

MINOR IMPROVEMENTS

• cts_compinfo() checks if input is a inchikey (via exported function is.inchikey()).
• cts_compinfo() is now more robust and verbose, if problems are encountered.
• alanwood() returns separate inchi and ichikeys in case of isomers.
• alanwood() returns also subactvity (e.g. $Fluazinam$activity [1] "fungicides" and $Fluazinam$subactivity [1] "pyridine fungicides").
• physprop() also returns boiling and melting points. Moreover, values are now numeric.

BUG FIXES

• alanwood() returns only results for first match in case of multiple links found.
• physprop() stopped working after change of SRC to https, fixed now.
• Changed etox_* functions to https.

DEPRECATED FUNCTIONS

• ppdb() replaces ppdb_query() and accepts individual index as created by ppdb_buildidx().
• cir() replaces cir_query().
• cs_compinfo() replaces csid_compinfo().
• cs_extcompinfo() replaces csid_extcompinfo().

DEFUNCT FUNCTIONS

• allanwood()

webchem 0.0.3 (2015-09-25)

NEW FEATURES

• Query SRC PHYSPROP Database with physprop().
• Query the ETOX ID with get_etoxid(); query basic information with etox_basic(); quality targets with etox_targets() and test results with etox_tests().
• Query PPDB with ppdb_query().

MINOR IMPROVEMENTS

• Added exceptions/checks to tests.
• Improved robustness of cir_query().

BUG FIXES

• Correct the spelling of Alan Wood and rename function allanwood() to alanwood().

webchem 0.0.2 (2015-08-15)

NEW FEATURES

• Query the PAN Pesticides Database with pan().
• Query Allan Woods Compendium of Pesticide Common Names with allanwood().

MINOR IMPROVEMENTS

• Added checks for user input.
• Fixed documentation, added example for bulk processing.
• cts_convert() returns NA if no result was found.
• Set 'verbose = TRUE' as default for all functions.
• Added unit tests.
• All functions return silently NA, if API is not reachable.

BUG FIXES

• cts_convert() does not ignore 'first' argument.
• get_csid() did not return NA, if there was a problem with the API.
• Many functions returned 'NA2+' if NA was given - now return NA by default.
• Many fixes in NA handling, e.g. when no hit was found.