webchem 1.0.0

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. [PR #241, added by @andschar]
• 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 [PR #226, fixed by stitam]
• get_chebiid() and chebi_comp_entity() fixed for invalid queries [PR #225, fixed by stitam]
• get_cid() returned the PubChem ID of sodium when the query was NA [PR #223, fixed by stitam]
• aw_query() returned a list for successful queries, NA for unsuccessful queries [PR #222, fixed by stitam]

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem 0.5.0

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 [contributed by @andschar].
• Retrieve retention indices from NIST (https://webbook.nist.gov) with nist_ri() [PR #154, contributed by @Aariq]
• Get record details from US EPA Substance Registry Services (https://cdxnodengn.epa.gov/cdx-srs-rest/) with srs_query() [PR #179]
• “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. [contributed by @Aariq]
• 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 [issue #148, reported and fixed by @stanstrup]
• pp_query() failed when compound present, but no properties [issue #151, reported and fixed by @stanstrup]
• ci_query() failed when missing table [issue #196, reported and fixed by @gjgetzinger]
• get_csid() failed because of a major change in the ChemSpider API [issue #149, PR #165, contributed by @stitam]
• multiple functions failed because of a major change in the ChemSpider API [issue #149, contributed by @stitam]
• cir_query() mistook NA for sodium [issue #158, reported and fixed by @Aariq]
• fixed functions that communicate with the ChemSpider API [issue #149, issue #160, fixed by @stitam]
• get_etoxid() printed incorrect results for certain match types [issue #201, fixed by @stitam]

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

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

• extr_num() did not work properly with decimal numbers [issue #136, reported and fixed by @stanstrup]
• cs_prop() failed when epi-suite data was not available [issue #139, reported and fixed by @stanstrup]
• cs_prop() failed with invalid html [issue #138, reported and fixed by @stanstrup]
• cs_prop() gave incorrect answer, if entries were not available [issue #142, reported and fixed by @stanstrup]
• cs_prop() did not parse scientific number correctly [issue #143, reported by @stanstrup, fixed by @EDiLD]
• is.smiles() failed because of changes in rcdk [PR #140, reported and fixed by @allaway]
• cir_query() failed with identifiers containing spaces (e.g. ‘acetic acid’) [issue #146, reported by Lars Nielsen]
• several other functions failed with identifiers containing spaces & returned wrong distance.

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

webchem 0.3.0

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 [issue #129, requested by @Aariq]
• cts_convert now returns NA if no matches are found.

BUG FIXES

• cs_prop() failed with some CSIDs [isse #127, reported by @Aariq]
• 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. [contributed by @Aariq]

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 (Issue #120, reported by @jranke)
• 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 predcitions (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

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() [contribution of @jranke]

webchem 0.0.2

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.