webchem: An R package to retrieve chemical information from the web.

Description

Chemical information from around the web. This package interacts with a suite of web APIs for chemical information.

Author(s)

Maintainer: Tamás Stirling stirling.tamas@gmail.com [contributor]

Authors:

• Eduard Szöcs

Other contributors:

• Robert Allaway [contributor]

• Daniel Muench [contributor]

• Johannes Ranke [contributor]

• Andreas Scharmüller [contributor]

• Eric R Scott [contributor]

• Jan Stanstrup [contributor]

• João Vitor F Cavalcante [contributor]

• Gordon Getzinger [contributor]

• Ethan Bass [contributor]

See Also

Useful links:

• https://docs.ropensci.org/webchem/

• https://github.com/ropensci/webchem

• Report bugs at https://github.com/ropensci/webchem/issues

Format numbers as CAS numbers

Description

This function attempts to format numeric (or character) vectors as character vectors of CAS numbers. If they cannot be converted to CAS format or don't pass is.cas, NA is returned

Usage

as.cas(x, verbose = getOption("verbose"))

Arguments

Value

character vector of valid CAS numbers

See Also

is.cas

Examples

x = c(58082, 123456, "hexenol")
as.cas(x)

Query https://pesticidecompendium.bcpc.org

Description

Query the BCPC Compendium of Pesticide Common Names https://pesticidecompendium.bcpc.org formerly known as Alan Woods Compendium of Pesticide Common Names

Usage

bcpc_query(
  query,
  from = c("name", "cas"),
  verbose = getOption("verbose"),
  type,
  ...
)

Arguments

Value

A list of eight entries: common-name, status, preferred IUPAC Name, IUPAC Name, cas, formula, activity, subactivity, inchikey, inchi and source url.

Note

for from = 'cas' only the first matched link is returned. Please respect Copyright, Terms and Conditions https://pesticidecompendium.bcpc.org/legal.html!

References

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). doi:10.18637/jss.v093.i13.

Examples

## Not run: 
bcpc_query('Fluazinam', from = 'name')
out <- bcpc_query(c('Fluazinam', 'Diclofop'), from = 'name')
out
# extract subactivity from object
sapply(out, function(y) y$subactivity[1])

# use CAS-numbers
bcpc_query("79622-59-6", from = 'cas')

## End(Not run)

Retrieve Complete Entity from ChEBI

Description

Returns a list of Complete ChEBI entities. ChEBI data are parsed as data.frames ("properties", "chebiid_snd", "synonyms", "iupacnames", "formulae", "regnumbers", "citations", "dblinks", "parents", "children", "comments", "origins") or as a list ("chem_structure") in the list. The SOAP protocol is used https://www.ebi.ac.uk/chebi/webServices.do.

Usage

chebi_comp_entity(chebiid, verbose = getOption("verbose"), ...)

Arguments

Value

returns a list of data.frames or lists containing a complete ChEBI entity

References

Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. (2016). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res.

Hastings, J., de Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., Muthukrishnan, V., Owen, G., Turner, S., Williams, M., and Steinbeck, C. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res.

de Matos, P., Alcantara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S., and Steinbeck, C. (2010) Chemical entities of biological interest: an update. Nucleic Acids Res. Degtyarenko, K., Hastings, J., de Matos, P., and Ennis, M. (2009). ChEBI: an open bioinformatics and cheminformatics resource. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis et al., Chapter 14.

Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M. and Ashburner, M. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344–D350.

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). doi:10.18637/jss.v093.i13.

Examples

## Not run: 
# might fail if API is not available
chebi_comp_entity('CHEBI:27744')

# multiple inputs
comp <- c('CHEBI:27744', 'CHEBI:27744')
chebi_comp_entity(comp)


## End(Not run)

Retrieve all ATC classes

Description

Retrieve all available classes within the Anatomical Therapeutic Chemical (ATC) classification system.

Usage

chembl_atc_classes(verbose = getOption("verbose"), test_service_down = FALSE)

Arguments

References

Gaulton, A., Bellis, L. J., Bento, A. P., Chambers, J., Davies, M., Hersey, A., ... & Overington, J. P. (2012). ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic acids research, 40(D1), D1100-D1107.

Examples

## Not run: 
# Might fail if API is not available

atc <- atc_classes()

## End(Not run)

Query ChEMBL using ChEMBL IDs

Description

Retrieve ChEMBL data using a vector of ChEMBL IDs.

Usage

chembl_query(
  query,
  resource = "molecule",
  cache_file = NULL,
  verbose = getOption("verbose"),
  test_service_down = FALSE
)

Arguments

Details

Each entry in ChEMBL has a unique ID. Data in ChEMBL is organized in databases called resources. An entry may or may not have a record in a particular resource. An entry may have a record in more than one resource, e.g. a compound may be present in both the "molecule" and the "drug" resource. This function queries a vector of ChEMBL IDs from a specific ChEMBL resource.

If you are unsure which ChEMBL resource contains your ChEMBL ID, use this function with the "chembl_id_lookup" resource to find the appropriate resource for a ChEMBL ID. Note that "chembl_id_lookup" is not a separate function but a resource used by chembl_query.

If cache_file is not NULL the function creates a cache directory in the working directory and a cache file in the cache directory. This file is used in subsequent calls of the function. The function first tries to retrieve query results from the cache file and only accesses the webservice if the ChEMBL ID cannot be found in the cache file. The cache file is extended as new ChEMBL ID-s are queried during the session.

Value

The function returns a list of lists, where each element of the list contains a list of respective query results. Results are simplified, if possible.

Note

Links to the webservice documentation:

• https://chembl.gitbook.io/chembl-interface-documentation,

• https://www.ebi.ac.uk/chembl/api/data/docs

References

Gaulton, A., Bellis, L. J., Bento, A. P., Chambers, J., Davies, M., Hersey, A., ... & Overington, J. P. (2012). ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic acids research, 40(D1), D1100-D1107.

Examples

## Not run: 
# Might fail if API is not available

# Search molecules
chembl_query("CHEMBL1082", resource = "molecule")
chembl_query(c("CHEMBL25", "CHEMBL1082"), resource = "molecule")

# Look up ChEMBL IDs in ChEMBL "resources", returns one resource per query.
chembl_query("CHEMBL771355", "chembl_id_lookup")

# Search assays
chembl_query("CHEMBL771355", resource = "assay")

## End(Not run)

List ChEMBL Resources

Description

Data in ChEMBL is organized in databases called resources. This function lists available ChEMBL resources.

Usage

chembl_resources()

Note

The list was compiled manually using the following url: https://chembl.gitbook.io/chembl-interface-documentation/web-services/chembl-data-web-services

References

Gaulton, A., Bellis, L. J., Bento, A. P., Chambers, J., Davies, M., Hersey, A., ... & Overington, J. P. (2012). ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic acids research, 40(D1), D1100-D1107.

Query Chemical Identifier Resolver Images

Description

A interface to the Chemical Identifier Resolver (CIR). (https://cactus.nci.nih.gov/chemical/structure_documentation).

Usage

cir_img(
  query,
  dir,
  format = c("png", "gif"),
  width = 500,
  height = 500,
  linewidth = 2,
  symbolfontsize = 16,
  bgcolor = NULL,
  antialiasing = TRUE,
  atomcolor = NULL,
  bondcolor = NULL,
  csymbol = c("special", "all"),
  hsymbol = c("special", "all"),
  hcolor = NULL,
  header = NULL,
  footer = NULL,
  frame = NULL,
  verbose = getOption("verbose"),
  ...
)

Arguments

Details

CIR can resolve can be of the following identifier: Chemical Names, IUPAC names, CAS Numbers, SMILES strings, IUPAC InChI/InChIKeys, NCI/CADD Identifiers, CACTVS HASHISY, NSC number, PubChem SID, ZINC Code, ChemSpider ID, ChemNavigator SID, eMolecule VID.

For an image with transparent background use ‘transparent’ as color name and switch off antialiasing (i.e. antialiasing = 0).

Value

image written to disk

Note

You can only make 1 request per second (this is a hard-coded feature).

References

cir relies on the great CIR web service created by the CADD Group at NCI/NIH!
https://cactus.nci.nih.gov/chemical/structure_documentation,
https://cactus.nci.nih.gov/blog/?cat=10,
https://cactus.nci.nih.gov/blog/?p=1386,
https://cactus.nci.nih.gov/blog/?p=1456,

Examples

## Not run: 
# might fail if API is not available
cir_img("CCO", dir = tempdir()) # SMILES

# multiple query strings and different formats
query = c("Glyphosate", "Isoproturon", "BSYNRYMUTXBXSQ-UHFFFAOYSA-N")
cir_img(query, dir = tempdir(), bgcolor = "transparent", antialising = 0)

# all parameters
query  = "Triclosan"
cir_img(query,
        dir = tempdir(),
        format = "png",
        width = 600,
        height = 600,
        linewidth = 5,
        symbolfontsize = 30,
        bgcolor = "red",
        antialiasing = FALSE,
        atomcolor = "green",
        bondcolor = "yellow",
        csymbol = "all",
        hsymbol = "all",
        hcolor = "purple",
        header = "My funky chemical structure..",
        footer = "..is just so awesome!",
        frame = 1,
        verbose = getOption("verbose"))

## End(Not run)

Query Chemical Identifier Resolver

Description

A interface to the Chemical Identifier Resolver (CIR). (https://cactus.nci.nih.gov/chemical/structure_documentation).

Usage

cir_query(
  identifier,
  representation = "smiles",
  resolver = NULL,
  match = c("all", "first", "ask", "na"),
  verbose = getOption("verbose"),
  choices = NULL,
  ...
)

Arguments

Details

CIR can resolve can be of the following identifier: Chemical Names, IUPAC names, CAS Numbers, SMILES strings, IUPAC InChI/InChIKeys, NCI/CADD Identifiers, CACTVS HASHISY, NSC number, PubChem SID, ZINC Code, ChemSpider ID, ChemNavigator SID, eMolecule VID.

cir_query() can handle only a part of all possible conversions of CIR. Possible representations are:

• 'smiles'(SMILES strings),

• 'names' (Names),

• 'cas' (CAS numbers),

• 'stdinchikey' (Standard InChIKey),

• 'stdinchi' (Standard InChI),

• 'ficts' (FICTS Identifier),

• 'ficus' (FICuS Indetifier),

• 'uuuuu' (uuuuu Identifier),

• 'mw' (Molecular weight),

• 'monoisotopic_mass' (Monoisotopic Mass),

• 'formula' (Chemical Formula),

• 'chemspider_id' (ChemSpider ID),

• 'pubchem_sid' (PubChem SID),

• 'chemnavigator_sid' (ChemNavigator SID),

• 'h_bond_donor_count' (Number of Hydrogen Bond Donors),

• 'h_bond_acceptor_count' (Number of Hydrogen Bond Acceptors),

• 'h_bond_center_count' (Number of Hydrogen Bond Centers),

• 'rule_of_5_violation_count' (Number of Rule of 5 Violations),

• 'rotor_count' (Number of Freely Rotatable Bonds),

• 'effective_rotor_count' (Number of Effectively Rotatable Bonds),

• 'ring_count' (Number of Rings),

• 'ringsys_count' (Number of Ring Systems),

• 'xlogp2' (octanol-water partition coefficient),

• 'aromatic' (is the compound aromatic),

• 'macrocyclic' (is the compound macrocyclic),

• 'heteroatom_count' (heteroatom count),

• 'hydrogen_atom_count' (H atom count),

• 'heavy_atom_count' ( Heavy atom count),

• 'deprotonable_group_count' (Number of deprotonable groups),

• 'protonable_group_count' (Number of protonable groups).

CIR first tries to determine the identifier type submitted and then uses 'resolvers' to look up the data. If no resolver is supplied, CIR tries different resolvers in turn till a hit is found. E.g. for names CIR tries first to look up in OPSIN and if this fails the local name index of CIR. However, it can be also specified which resolvers to use (if you know e.g. know your identifier type) Possible resolvers are:

• 'name_by_cir' (Lookup in name index of CIR),

• 'name_by_opsin' (Lookup in OPSIN),

• 'name_by_chemspider' (Lookup in ChemSpider, https://cactus.nci.nih.gov/blog/?p=1386),

• 'smiles' (Lookup SMILES),

• 'stdinchikey', 'stdinchi' (InChI),

• 'cas_number' (CAS Number),

• 'name_pattern' (Google-like pattern search (https://cactus.nci.nih.gov/blog/?p=1456) Note, that the pattern search can be combined with other resolvers, e.g. resolver = 'name_by_chemspider,name_pattern'.

Value

A tibble with a 'query' column and a column for the requested representation.

Note

You can only make 1 request per second (this is a hard-coded feature).

References

cir relies on the great CIR web service created by the CADD Group at NCI/NIH!
https://cactus.nci.nih.gov/chemical/structure_documentation,
https://cactus.nci.nih.gov/blog/?cat=10,
https://cactus.nci.nih.gov/blog/?p=1386,
https://cactus.nci.nih.gov/blog/?p=1456,

Examples

## Not run: 
# might fail if API is not available
cir_query("Triclosan", "cas")
cir_query("3380-34-5", "cas", match = "first")
cir_query("3380-34-5", "cas", resolver = "cas_number")
cir_query("3380-34-5", "smiles")
cir_query("Triclosan", "mw")

# multiple inputs
comp <- c("Triclosan", "Aspirin")
cir_query(comp, "cas", match = "first")


## End(Not run)

Retrieve ChemSpider API key

Description

Look for and retrieve ChemSpider API key stored in .Renviron or .Rprofile.

Usage

cs_check_key()

Details

To use the any of the functions in webchem that access the ChemSpider database, you'll need to obtain an API key. Register at https://developer.rsc.org/ for an API key. Please respect the Terms & Conditions https://developer.rsc.org/terms.

You can store your API key as CHEMSPIDER_KEY = <your key> in .Renviron or as options(chemspider_key = <your key>) in .Rprofile. This will allow you to use ChemSpider without adding your API key in the beginning of each session, and will also allow you to share your analysis without sharing your API key. Keeping your API key hidden is good practice.

Value

an API key

See Also

edit_r_environ edit_r_profile

Examples

## Not run: 
cs_check_key()

## End(Not run)

Retrieve record details by ChemSpider ID

Description

Submit a ChemSpider ID (CSID) and the fields you are interested in, and retrieve the record details for your query.

Usage

cs_compinfo(csid, fields, verbose = getOption("verbose"), apikey = NULL)

Arguments

Details

Valid values for fields are "SMILES", "Formula", "InChI", "InChIKey", "StdInChI", "StdInChIKey", "AverageMass", "MolecularWeight", "MonoisotopicMass", "NominalMass", "CommonName", "ReferenceCount", "DataSourceCount", "PubMedCount", "RSCCount", "Mol2D", "Mol3D". You can specify any number of fields.

Value

Returns a data frame.

Note

An API key is needed. Register at https://developer.rsc.org/ for an API key. Please respect the Terms & Conditions. The Terms & Conditions can be found at https://developer.rsc.org/terms.

References

https://developer.rsc.org/docs/compounds-v1-trial/1/overview

Examples

## Not run: 
cs_compinfo(171, c("SMILES", "CommonName"))
cs_compinfo(171:182, "SMILES")

## End(Not run)

Control ChemSpider API requests

Description

For some ChemSpider API requests, you can also specify various control options. This function is used to set these control options.

Usage

cs_control(
  datasources = vector(),
  order_by = "default",
  order_direction = "default",
  include_all = FALSE,
  complexity = "any",
  isotopic = "any"
)

Arguments

Details

The only function that currently uses databases is get_csid() and only when you query a CSID from a formula. This parameter is disregarded in all other queries.

Setting include_all to TRUE will consider records which contain all of the filter criteria specified in the request. Setting it to FALSE will consider records which contain any of the filter criteria.

A compound with a complexity of "multiple" has more than one disconnected system in it or a metal atom or ion.

Value

Returns a list of specified control options.

Note

This is a full list of all API control options. However, not all of these options are used in all functions. Each API uses a subset of these controls. The controls that are available for a given function are indicated within the documentation of the function.

References

https://developer.rsc.org/docs/compounds-v1-trial/1/overview

See Also

get_csid

Examples

cs_control()
cs_control(order_direction = "descending")

Convert identifiers using ChemSpider

Description

Submit one or more identifiers (CSID, SMILES, InChI, InChIKey or Mol) and return one or more identifiers in another format (CSID, SMILES, InChI, InChIKey or Mol).

Usage

cs_convert(query, from, to, verbose = getOption("verbose"), apikey = NULL)

Arguments

Details

Not all conversions are supported. Allowed conversions:

• CSID <-> InChI

• CSID <-> InChIKey

• CSID <-> SMILES

• CSID -> Mol file

• InChI <-> InChIKey

• InChI <-> SMILES

• InChI -> Mol file

• InChIKey <-> Mol file

Value

Returns a vector containing the converted identifier(s).

Note

An API key is needed. Register at https://developer.rsc.org/ for an API key. Please respect the Terms & Conditions. The Terms & Conditions can be found at https://developer.rsc.org/terms.

References

https://developer.rsc.org/docs/compounds-v1-trial/1/overview

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). doi:10.18637/jss.v093.i13.

Examples

## Not run: 
cs_convert("BQJCRHHNABKAKU-KBQPJGBKSA-N",
  from = "inchikey", to = "csid"
)
cs_convert("BQJCRHHNABKAKU-KBQPJGBKSA-N",
  from = "inchikey", to = "inchi"
)
cs_convert("BQJCRHHNABKAKU-KBQPJGBKSA-N",
  from = "inchikey", to = "mol"
)
cs_convert(160, from = "csid", to = "smiles")

## End(Not run)

Retrieve ChemSpider data sources

Description

The function returns a vector of available data sources used by ChemSpider. Some ChemSpider functions allow you to restrict which sources are used to lookup the requested query. Restricting the sources makes these queries faster.

Usage

cs_datasources(apikey = NULL, verbose = getOption("verbose"))

Arguments

Value

Returns a character vector.

Note

An API key is needed. Register at https://developer.rsc.org/ for an API key. Please respect the Terms & Conditions. The Terms & Conditions can be found at https://developer.rsc.org/terms.

References

https://developer.rsc.org/docs/compounds-v1-trial/1/overview

Examples

## Not run: 
cs_datasources()

## End(Not run)

Get extended record details by ChemSpider ID

Description

Get extended info from ChemSpider, see https://www.chemspider.com/

Usage

cs_extcompinfo(csid, token, verbose = getOption("verbose"), ...)

Arguments

Value

a data.frame with entries: 'csid', 'mf' (molecular formula), 'smiles', 'inchi' (non-standard), 'inchikey' (non-standard), 'average_mass', 'mw' (Molecular weight), 'monoiso_mass' (MonoisotopicMass), nominal_mass', 'alogp', 'xlogp', 'common_name' and 'source_url'

Note

A security token is needed. Please register at RSC https://www.rsc.org/rsc-id/register for a security token. Please respect the Terms & conditions https://www.rsc.org/help-legal/legal/terms-conditions/.

use cs_compinfo to retrieve standard inchikey.

See Also

get_csid to retrieve ChemSpider IDs, cs_compinfo for extended compound information.

Examples

## Not run: 
token <- "<redacted>"
csid <- get_csid("Triclosan")
cs_extcompinfo(csid, token)

csids <- get_csid(c('Aspirin', 'Triclosan'))
cs_compinfo(csids)

## End(Not run)

Download images from ChemSpider

Description

Retrieve images of substances from ChemSpider and export them in PNG format.

Usage

cs_img(
  csid,
  dir,
  overwrite = TRUE,
  apikey = NULL,
  verbose = getOption("verbose")
)

Arguments

Note

An API key is needed. Register at https://developer.rsc.org/ for an API key. Please respect the Terms & Conditions. The Terms & Conditions can be found at https://developer.rsc.org/terms.

References

https://developer.rsc.org/docs/compounds-v1-trial/1/overview

See Also

get_csid, cs_check_key

Examples

## Not run: 
cs_img(c(582, 682), dir = tempdir())

## End(Not run)

Get record details from Chemical Translation Service (CTS)

Description

Get record details from CTS, see http://cts.fiehnlab.ucdavis.edu/

Usage

cts_compinfo(
  query,
  from = "inchikey",
  verbose = getOption("verbose"),
  inchikey
)

Arguments

Value

a list of lists (for each supplied inchikey): a list of 7. inchikey, inchicode, molweight, exactmass, formula, synonyms and externalIds

References

Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Chemical Translation Service – a Web-Based Tool to Improve Standardization of Metabolomic Reports. Bioinformatics 26(20): 2647–2648.

Examples

## Not run: 
# might fail if API is not available
out <- cts_compinfo("XEFQLINVKFYRCS-UHFFFAOYSA-N")
# = Triclosan
str(out)
out[[1]][1:5]

### multiple inputs
inchikeys <- c("XEFQLINVKFYRCS-UHFFFAOYSA-N","BSYNRYMUTXBXSQ-UHFFFAOYSA-N" )
out2 <- cts_compinfo(inchikeys)
str(out2)
# a list of two
# extract molecular weight
sapply(out2, function(y) y$molweight)

## End(Not run)

Convert Ids using Chemical Translation Service (CTS)

Description

Convert Ids using Chemical Translation Service (CTS), see http://cts.fiehnlab.ucdavis.edu/

Usage

cts_convert(
  query,
  from,
  to,
  match = c("all", "first", "ask", "na"),
  verbose = getOption("verbose"),
  choices = NULL,
  ...
)

Arguments

Details

See also http://cts.fiehnlab.ucdavis.edu/ for possible values of from and to.

Value

a list of character vectors or if choices is used, then a single named vector.

References

Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Chemical Translation Service – a Web-Based Tool to Improve Standardization of Metabolomic Reports. Bioinformatics 26(20): 2647–2648.

See Also

cts_from for possible values in the 'from' argument and cts_to for possible values in the 'to' argument.

Examples

## Not run: 
# might fail if API is not available
cts_convert("XEFQLINVKFYRCS-UHFFFAOYSA-N", "inchikey", "Chemical Name")

### multiple inputs
keys <- c("XEFQLINVKFYRCS-UHFFFAOYSA-N", "VLKZOEOYAKHREP-UHFFFAOYSA-N")
cts_convert(keys, "inchikey", "cas")

## End(Not run)

Return a list of all possible ids

Description

Return a list of all possible ids that can be used in the 'from' argument

Usage

cts_from(verbose = getOption("verbose"))

Arguments

Details

See also http://cts.fiehnlab.ucdavis.edu/services

Value

a character vector.

References

Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Chemical Translation Service – a Web-Based Tool to Improve Standardization of Metabolomic Reports. Bioinformatics 26(20): 2647–2648.

See Also

cts_convert

Examples

## Not run: 
cts_from()

## End(Not run)

Return a list of all possible ids

Description

Return a list of all possible ids that can be used in the 'to' argument

Usage

cts_to(verbose = getOption("verbose"))

Arguments

Details

See also http://cts.fiehnlab.ucdavis.edu/services

Value

a character vector.

References

Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Chemical Translation Service – a Web-Based Tool to Improve Standardization of Metabolomic Reports. Bioinformatics 26(20): 2647–2648.

See Also

cts_convert

Examples

## Not run: 
cts_from()

## End(Not run)

Get basic information from a ETOX ID

Description

Query ETOX: Information System Ecotoxicology and Environmental Quality Targets https://webetox.uba.de/webETOX/index.do for basic information

Usage

etox_basic(id, verbose = getOption("verbose"))

Arguments

Value

a list with lists of four entries: cas (the CAS numbers), ec (the EC number), gsbl (the gsbl number), a data.frame synonys with synonyms and the source url.

Note

Before using this function, please read the disclaimer https://webetox.uba.de/webETOX/disclaimer.do.

References

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). doi:10.18637/jss.v093.i13.

See Also

get_etoxid to retrieve ETOX IDs, etox_basic for basic information, etox_targets for quality targets and etox_tests for test results

Examples

## Not run: 
id <- get_etoxid('Triclosan', match = 'best')
etox_basic(id$etoxid)

# Retrieve data for multiple inputs
ids <- c("20179", "9051")
out <- etox_basic(ids)
out

# extract cas numbers
sapply(out, function(y) y$cas)

## End(Not run)

Get Quality Targets from a ETOX ID

Description

Query ETOX: Information System Ecotoxicology and Environmental Quality Targets https://webetox.uba.de/webETOX/index.do for quality targets

Usage

etox_targets(id, verbose = getOption("verbose"))

Arguments

Value

A list of lists of two: res a data.frame with quality targets from the ETOX database, and source_url.

Note

Before using this function, please read the disclaimer https://webetox.uba.de/webETOX/disclaimer.do.

References

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). doi:10.18637/jss.v093.i13.

See Also

get_etoxid to retrieve ETOX IDs, etox_basic for basic information, etox_targets for quality targets and etox_tests for test results

Examples

## Not run: 
id <- get_etoxid('Triclosan', match = 'best')
out <- etox_targets(id$etoxid)
out[ , c('Substance', 'CAS_NO', 'Country_or_Region', 'Designation',
'Value_Target_LR', 'Unit')]
etox_targets( c("20179", "9051"))


## End(Not run)

Get Tests from a ETOX ID

Description

Query ETOX: Information System Ecotoxicology and Environmental Quality Targets https://webetox.uba.de/webETOX/index.do for tests

Usage

etox_tests(id, verbose = getOption("verbose"))

Arguments

Value

A list of lists of two: A data.frame with test results from the ETOX database and the source_url.

Note

Before using this function, please read the disclaimer https://webetox.uba.de/webETOX/disclaimer.do.

See Also

get_etoxid to retrieve ETOX IDs, etox_basic for basic information, etox_targets for quality targets and etox_tests for test results

Examples

## Not run: 
id <- get_etoxid('Triclosan', match = 'best')
out <- etox_tests(id$etoxid)
out[ , c('Organism', 'Effect', 'Duration', 'Time_Unit',
'Endpoint', 'Value', 'Unit')]
etox_tests( c("20179", "9051"))

## End(Not run)

Extract parts from webchem objects

Description

Extract parts from webchem objects

Usage

cas(x, ...)

inchikey(x, ...)

smiles(x, ...)

Arguments

Value

a vector.

References

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). doi:10.18637/jss.v093.i13.

Check data source coverage of compounds

Description

Checks if entries are found in (most) data sources included in webchem

Usage

find_db(
  query,
  from,
  sources = c("etox", "pc", "chebi", "cs", "bcpc", "fn", "srs"),
  plot = FALSE
)

Arguments

Value

a tibble of logical values where TRUE indicates that a data source contains a record for the query

Examples

## Not run: 
find_db("hexane", from = "name")

## End(Not run)

Retrieve flavor percepts from www.flavornet.org

Description

Retrieve flavor percepts from http://www.flavornet.org. Flavornet is a database of 738 compounds with odors perceptible to humans detected using gas chromatography olfactometry (GCO).

Usage

fn_percept(query, from = "cas", verbose = getOption("verbose"), CAS, ...)

Arguments

Value

A named character vector containing flavor percepts or NA's in the case of CAS numbers that are not found

Examples

## Not run: 
# might fail if website is not available
fn_percept("123-32-0")

CASs <- c("75-07-0",  "64-17-5",  "109-66-0", "78-94-4",  "78-93-3")
fn_percept(CASs)

## End(Not run)

Retrieve Lite Entity (identifiers) from ChEBI

Description

Returns a data.frame with a ChEBI entity ID (chebiid), a ChEBI entity name (chebiasciiname), a search score (searchscore) and stars (stars) using the SOAP protocol: https://www.ebi.ac.uk/chebi/webServices.do

Usage

get_chebiid(
  query,
  from = c("all", "chebi id", "chebi name", "definition", "name", "iupac name",
    "citations", "registry numbers", "manual xrefs", "automatic xrefs", "formula",
    "mass", "monoisotopic mass", "charge", "inchi", "inchikey", "smiles", "species"),
  match = c("all", "best", "first", "ask", "na"),
  max_res = 200,
  stars = c("all", "two only", "three only"),
  verbose = getOption("verbose"),
  ...
)

Arguments

Value

returns a list of data.frames containing a chebiid, a chebiasciiname, a searchscore and stars if matches were found. If not, data.frame(NA) is returned

References

Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. (2016). ChEBI in 2016: Improved services and an expanding collection of metabfolites. Nucleic Acids Res.

Hastings, J., de Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., Muthukrishnan, V., Owen, G., Turner, S., Williams, M., and Steinbeck, C. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res.

de Matos, P., Alcantara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S., and Steinbeck, C. (2010) Chemical entities of biological interest: an update. Nucleic Acids Res. Degtyarenko, K., Hastings, J., de Matos, P., and Ennis, M. (2009). ChEBI: an open bioinformatics and cheminformatics resource. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis et al., Chapter 14.

Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M. and Ashburner, M. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344–D350.

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). doi:10.18637/jss.v093.i13.

Examples

## Not run: 
# might fail if API is not available
get_chebiid('Glyphosate')
get_chebiid('BPGDAMSIGCZZLK-UHFFFAOYSA-N')

# multiple inputs
comp <- c('Iron', 'Aspirin', 'BPGDAMSIGCZZLK-UHFFFAOYSA-N')
get_chebiid(comp)


## End(Not run)

Retrieve Pubchem Compound ID (CID)

Description

Retrieve compound IDs (CIDs) from PubChem.

Usage

get_cid(
  query,
  from = "name",
  domain = c("compound", "substance", "assay"),
  match = c("all", "first", "ask", "na"),
  verbose = getOption("verbose"),
  arg = NULL,
  first = NULL,
  ...
)

Arguments

Details

Valid values for the from argument depend on the domain:

• compound: "name", "smiles", "inchi", "inchikey", "formula", "sdf", "cas" (an alias for "xref/RN"), <xref>, <structure search>, <fast search>.

• substance: "name", "sid", <xref>, "sourceid/<source id>" or "sourceall".

• assay: "aid", <assay target>.

<structure search> is assembled as "(substructure | superstructure | similarity | identity) / (smiles | inchi | sdf | cid)", e.g. from = "substructure/smiles".

<xref> is assembled as "xref/(RegistryID | RN | PubMedID | MMDBID | ProteinGI, NucleotideGI | TaxonomyID | MIMID | GeneID | ProbeID | PatentID)", e.g. from = "xref/RN" will query by CAS RN.

<fast search> is either fastformula or it is assembled as "(fastidentity | fastsimilarity_2d | fastsimilarity_3d | fastsubstructure | fastsuperstructure)/(smiles | smarts | inchi | sdf | cid)", e.g. from = "fastidentity/smiles".

<source id> is any valid PubChem Data Source ID. When from = "sourceid/<source id>", the query is the ID of the substance in the depositor's database.

If from = "sourceall" the query is one or more valid Pubchem depositor names. Depositor names are not case sensitive.

Depositor names and Data Source IDs can be found at https://pubchem.ncbi.nlm.nih.gov/sources/.

<assay target> is assembled as "target/(gi | proteinname | geneid | genesymbol | accession)", e.g. from = "target/geneid" will query by GeneID.

Value

a tibble.

Note

Please respect the Terms and Conditions of the National Library of Medicine, https://www.nlm.nih.gov/databases/download.html the data usage policies of National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/home/about/policies/, https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access, and the data usage policies of the indicidual data sources https://pubchem.ncbi.nlm.nih.gov/sources/.

References

Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public Information System for Analyzing Bioactivities of Small Molecules. Nucleic Acids Research 37: 623–633.

Kim, Sunghwan, Paul A. Thiessen, Evan E. Bolton, et al. 2016 PubChem Substance and Compound Databases. Nucleic Acids Research 44(D1): D1202–D1213.

Kim, S., Thiessen, P. A., Bolton, E. E., & Bryant, S. H. (2015). PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. Nucleic acids research, gkv396.

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). doi:10.18637/jss.v093.i13.

Examples

## Not run: 
# might fail if API is not available
get_cid("Triclosan")
get_cid("Triclosan", arg = "name_type=word")
# from SMILES
get_cid("CCCC", from = "smiles")
# from InChI
get_cid("InChI=1S/CH5N/c1-2/h2H2,1H3", from = "inchi")
# from InChIKey
get_cid("BPGDAMSIGCZZLK-UHFFFAOYSA-N", from = "inchikey")
# from formula
get_cid("C26H52NO6P", from = "formula")
# from CAS RN
get_cid("56-40-6", from = "xref/rn")
# similarity
get_cid(5564, from = "similarity/cid")
get_cid("CCO", from = "similarity/smiles")
# from SID
get_cid("126534046", from = "sid", domain = "substance")
# sourceid
get_cid("VCC957895", from = "sourceid/23706", domain = "substance")
# sourceall
get_cid("Optopharma Ltd", from = "sourceall", domain = "substance")
# from AID (CIDs of substances tested in the assay)
get_cid(170004, from = "aid", domain = "assay")
# from GeneID (CIDs of substances tested on the gene)
get_cid(25086, from = "target/geneid", domain = "assay")

# multiple inputs
get_cid(c("Triclosan", "Aspirin"))


## End(Not run)

ChemSpider ID from compound name, formula, SMILES, InChI or InChIKey

Description

Query one or more compunds by name, formula, SMILES, InChI or InChIKey and return a vector of ChemSpider IDs.

Usage

get_csid(
  query,
  from = c("name", "formula", "inchi", "inchikey", "smiles"),
  match = c("all", "first", "ask", "na"),
  verbose = getOption("verbose"),
  apikey = NULL,
  ...
)

Arguments

Details

Queries by SMILES, InChI or InChiKey do not use cs_control options. Queries by name use order_by and order_direction. Queries by formula also use datasources. See cs_control() for a full list of valid values for these control options.

formula can be expressed with and without LaTeX syntax.

Value

Returns a tibble.

Note

An API key is needed. Register at https://developer.rsc.org/ for an API key. Please respect the Terms & conditions: https://developer.rsc.org/terms.

References

https://developer.rsc.org/docs/compounds-v1-trial/1/overview

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). doi:10.18637/jss.v093.i13.

Examples

## Not run: 
get_csid("triclosan")
get_csid(c("carbamazepine", "naproxene","oxygen"))
get_csid("C2H6O", from = "formula")
get_csid("C_{2}H_{6}O", from = "formula")
get_csid("CC(O)=O", from = "smiles")
get_csid("InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)", from = "inchi")
get_csid("QTBSBXVTEAMEQO-UHFFFAOYAR", from = "inchikey")

## End(Not run)

Get ETOX ID

Description

Query ETOX: Information System Ecotoxicology and Environmental Quality Targets https://webetox.uba.de/webETOX/index.do for their substance ID

Usage

get_etoxid(
  query,
  from = c("name", "cas", "ec", "gsbl", "rtecs"),
  match = c("all", "best", "first", "ask", "na"),
  verbose = getOption("verbose")
)

Arguments

Value

a tibble with 3 columns: the query, the match, and the etoxID

Note

Before using this function, please read the disclaimer https://webetox.uba.de/webETOX/disclaimer.do.

References

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). doi:10.18637/jss.v093.i13.

See Also

etox_basic for basic information, etox_targets for quality targets and etox_tests for test results.

Examples

## Not run: 
# might fail if API is not available
get_etoxid("Triclosan")
# multiple inputs
comps <- c("Triclosan", "Glyphosate")
get_etoxid(comps)
get_etoxid(comps, match = "all")
get_etoxid("34123-59-6", from = "cas") # Isoproturon
get_etoxid("133483", from = "gsbl") # 3-Butin-1-ol
get_etoxid("203-157-5", from = "ec") # Paracetamol

## End(Not run)

Get Wikidata Item ID

Description

Search www.wikidata.org for wikidata item identifiers. Note that this search is currently not limited to chemical substances, so be sure to check your results.

Usage

get_wdid(
  query,
  match = c("best", "first", "all", "ask", "na"),
  verbose = getOption("verbose"),
  language = "en"
)

Arguments

Value

if match = 'all' a list with ids, otherwise a dataframe with 4 columns: id, matched text, string distance to match and the queried string

Note

Only matches in labels are returned.

Examples

## Not run: 
get_wdid('Triclosan', language = 'de')
get_wdid('DDT')
get_wdid('DDT', match = 'all')

# multiple inputs
comps <- c('Triclosan', 'Glyphosate')
get_wdid(comps)

## End(Not run)

Check if input is a valid CAS

Description

This function checks if a string is a valid CAS registry number. A valid CAS is 1) separated by two hyphes into three parts; 2) the first part consists from two up to seven digits; 3) the second of two digits; 4) the third of one digit (check digit); 5) the check digits corresponds the checksum. The checksum is found by taking the last digit (excluding the check digit) multiplyingit with 1, the second last multiplied with 2, the third-last multiplied with 3 etc. The modulo 10 of the sum of these is the checksum.

Usage

is.cas(x, verbose = getOption("verbose"))

Arguments

Value

a logical

Note

This function can only handle one CAS string

References

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). doi:10.18637/jss.v093.i13.

Examples

is.cas('64-17-5')
is.cas('64175')
is.cas('4-17-5')
is.cas('64-177-6')
is.cas('64-17-55')
is.cas('64-17-6')

Check if input is a valid inchikey

Description

This function checks if a string is a valid inchikey. Inchikey must fulfill the following criteria: 1) consist of 27 characters; 2) be all uppercase, all letters (no numbers); 3) contain two hyphens at positions 15 and 26; 4) 24th character (flag character) be 'S' (Standard InChI) or 'N' (non-standard) 5) 25th character (version character) must be 'A' (currently).

Usage

is.inchikey(
  x,
  type = c("format", "chemspider"),
  apikey = NULL,
  verbose = getOption("verbose")
)

Arguments

Value

a logical

Note

This function can handle only one inchikey string.

References

Heller, Stephen R., et al. "InChI, the IUPAC International Chemical Identifier." Journal of Cheminformatics 7.1 (2015): 23.

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). doi:10.18637/jss.v093.i13.

Examples

is.inchikey('BQJCRHHNABKAKU-KBQPJGBKSA-N')
is.inchikey('BQJCRHHNABKAKU-KBQPJGBKSA')
is.inchikey('BQJCRHHNABKAKU-KBQPJGBKSA-5')
is.inchikey('BQJCRHHNABKAKU-KBQPJGBKSA-n')
is.inchikey('BQJCRHHNABKAKU/KBQPJGBKSA/N')
is.inchikey('BQJCRHHNABKAKU-KBQPJGBKXA-N')
is.inchikey('BQJCRHHNABKAKU-KBQPJGBKSB-N')

Check if input is a valid inchikey using ChemSpider API

Description

Check if input is a valid inchikey using ChemSpider API

Usage

is.inchikey_cs(x, apikey = NULL, verbose = getOption("verbose"))

Arguments

Value

a logical

See Also

is.inchikey for a pure-R implementation.

Examples

## Not run: 
# might fail if API is not available
is.inchikey_cs('BQJCRHHNABKAKU-KBQPJGBKSA-N')
is.inchikey_cs('BQJCRHHNABKAKU-KBQPJGBKSA')
is.inchikey_cs('BQJCRHHNABKAKU-KBQPJGBKSA-5')
is.inchikey_cs('BQJCRHHNABKAKU-KBQPJGBKSA-n')
is.inchikey_cs('BQJCRHHNABKAKU/KBQPJGBKSA/N')
is.inchikey_cs('BQJCRHHNABKAKU-KBQPJGBKXA-N')
is.inchikey_cs('BQJCRHHNABKAKU-KBQPJGBKSB-N')

## End(Not run)

Check if input is a valid inchikey using format

Description

Inchikey must fulfill the following criteria: 1) consist of 27 characters; 2) be all uppercase, all letters (no numbers); 3) contain two hyphens at positions 15 and 26; 4) 24th character (flag character) be 'S' (Standard InChI) or 'N' (non-standard) 5) 25th character (version character) must be 'A' (currently).

Usage

is.inchikey_format(x, verbose = getOption("verbose"))

Arguments

Value

a logical

See Also

is.inchikey for a pure-R implementation.

Examples

## Not run: 
# might fail if API is not available
is.inchikey_format('BQJCRHHNABKAKU-KBQPJGBKSA-N')
is.inchikey_format('BQJCRHHNABKAKU-KBQPJGBKSA')
is.inchikey_format('BQJCRHHNABKAKU-KBQPJGBKSA-5')
is.inchikey_format('BQJCRHHNABKAKU-KBQPJGBKSA-n')
is.inchikey_format('BQJCRHHNABKAKU/KBQPJGBKSA/N')
is.inchikey_format('BQJCRHHNABKAKU-KBQPJGBKXA-N')
is.inchikey_format('BQJCRHHNABKAKU-KBQPJGBKSB-N')

## End(Not run)

Check if input is a SMILES string

Description

This function checks if a string is a valid SMILES by checking if (R)CDK can parse it. If it cannot be parsed by rcdk FALSE is returned, else TRUE.

Usage

is.smiles(x, verbose = getOption("verbose"))

Arguments

Value

a logical

Note

This function can handle only one SMILES string.

References

Egon Willighagen (2015). How to test SMILES strings in Supplementary Information. https://chem-bla-ics.blogspot.nl/2015/10/how-to-test-smiles-strings-in.html

Examples

## Not run: 
# might fail if rcdk is not working properly
is.smiles('Clc(c(Cl)c(Cl)c1C(=O)O)c(Cl)c1Cl')
is.smiles('Clc(c(Cl)c(Cl)c1C(=O)O)c(Cl)c1ClJ')

## End(Not run)

Organic plant protection products in the river Jagst / Germany in 2013

Description

This dataset comprises environmental monitoring data of organic plant protection products in the year 2013 in the river Jagst, Germany. The data is publicly available and can be retrieved from the LUBW Landesanstalt für Umwelt, Messungen und Naturschutz Baden-Württemberg. It has been preprocessed and comprises measurements of 34 substances. Substances without detects have been removed. on 13 sampling occasions. Values are given in ug/L.

Usage

jagst

Format

A data frame with 442 rows and 4 variables:

date

sampling data

substance

substance names

value

concentration in ug/L

qual

qualifier, indicating values < LOQ

Source

https://udo.lubw.baden-wuerttemberg.de/public/

Acute toxicity data from U.S. EPA ECOTOX

Description

This dataset comprises acute ecotoxicity data of 124 insecticides. The data is publicly available and can be retrieved from the EPA ECOTOX database (https://cfpub.epa.gov/ecotox/) It comprises acute toxicity data (D. magna, 48h, Laboratory, 48h) and has been preprocessed (remove non-insecticides, aggregate multiple value, keep only numeric data etc).

Usage

lc50

Format

A data frame with 124 rows and 2 variables:

cas

CAS registry number

value

LC50value

Source

https://cfpub.epa.gov/ecotox/

Retrieve retention indices from NIST

Description

This function scrapes NIST for literature retention indices given a query or vector of queries as input. The query can be a cas number, IUPAC name, or International Chemical Identifier (inchikey), according to the value of the from argument. Retention indices are stored in tables by type, polarity and temperature program (temp_prog). The function can take multiple arguments for these parameters and will return any retention times matching the specified criteria in a single table.

If a non-cas query is provided, the function will try to resolve the query by searching the NIST WebBook for a corresponding CAS number. If from == "name", phonetic spellings of Greek stereo-descriptors (e.g. "alpha", "beta", "gamma") will be automatically converted to the corresponding letters to match the form used by NIST. If a CAS number is found, it will be returned in a tibble with the corresponding information from the NIST retention index database.

Usage

nist_ri(
  query,
  from = c("cas", "inchi", "inchikey", "name"),
  type = c("kovats", "linear", "alkane", "lee"),
  polarity = c("polar", "non-polar"),
  temp_prog = c("isothermal", "ramp", "custom"),
  cas = NULL,
  verbose = getOption("verbose")
)

Arguments

Details

The types of retention indices included in NIST include Kovats ("kovats"), Van den Dool and Kratz ("linear"), normal alkane ("alkane"), and Lee ("lee"). Details about how these are calculated are available on the NIST website: https://webbook.nist.gov/chemistry/gc-ri/

Value

returns a tibble of literature RIs with the following columns:

• query is the query provided to the NIST server

• cas is the CAS number or unique record identified used by NIST

• RI is retention index

• type is the type of RI (e.g. "kovats", "linear", "alkane", or "lee")

• polarity is the polarity of the column (either "polar" or "non-polar")

• temp_prog is the type of temperature program (e.g. "isothermal", "ramp", or "custom")

• column is the column type, e.g. "capillary"

• phase is the stationary phase (column phase)

• length is column length in meters

• gas is the carrier gas used

• substrate

• diameter is the column diameter in mm

• thickness is the phase thickness in µm

• program. various columns depending on the value of temp_prog

• reference is where this retention index was published

• comment. I believe this denotes the database these data were aggregated from

Note

Copyright for NIST Standard Reference Data is governed by the Standard Reference Data Act, https://www.nist.gov/srd/public-law.

References

NIST Mass Spectrometry Data Center, William E. Wallace, director, "Retention Indices" in NIST Chemistry WebBook, NIST Standard Reference Database Number 69, Eds. P.J. Linstrom and W.G. Mallard, National Institute of Standards and Technology, Gaithersburg MD, 20899, doi:10.18434/T4D303.

See Also

is.cas as.cas

Examples

## Not run: 
myRIs <-
  nist_ri(
    c("78-70-6", "13474-59-4"),
    from = "cas",
    type = c("linear", "kovats"),
    polarity = "non-polar",
    temp_prog = "ramp"
  )
myRIs
## End(Not run)

OPSIN web interface

Description

Query the OPSIN (Open Parser for Systematic IUPAC nomenclature) web service https://www.ebi.ac.uk/opsin.

Usage

opsin_query(query, verbose = getOption("verbose"), ...)

Arguments

Value

a tibble with six columnns: "query", inchi", "stdinchi", "stdinchikey", "smiles", "message", and "status"

References

Lowe, D. M., Corbett, P. T., Murray-Rust, P., & Glen, R. C. (2011). Chemical Name to Structure: OPSIN, an Open Source Solution. Journal of Chemical Information and Modeling, 51(3), 739–753. doi:10.1021/ci100384d

Examples

## Not run: 
opsin_query('Cyclopropane')
opsin_query(c('Cyclopropane', 'Octane'))
opsin_query(c('Cyclopropane', 'Octane', 'xxxxx'))

## End(Not run)

Parse Molfile (as returned by ChemSpider) into a R-object.

Description

Parse Molfile (as returned by ChemSpider) into a R-object.

Usage

parse_mol(string)

Arguments

Value

A list with of four entries: header (eh), counts line (cl), atom block (ab) and bond block (bb).

header: a = number of atoms, b = number of bonds, l = number of atom lists, f = obsolete, c = chiral flag (0=not chiral, 1 = chiral), s = number of stext entries, x, r, p, i = obsolete, m = 999, v0 version

atom block: x, y, z = atom coordinates, a = mass difference, c= charge, s= stereo parity, h = hydrogen count 1, b = stereo care box, v = valence, h = h0 designator, r, i = not used, m = atom-atom mapping number, n = inversion/retention flag, e = exact change flag

bond block: 1 = first atom, 2 = second atom, t = bond type, s = stereo type, x = not used, r = bond typology, c = reacting center status.

References

Grabner, M., Varmuza, K., & Dehmer, M. (2012). RMol: a toolset for transforming SD/Molfile structure information into R objects. Source Code for Biology and Medicine, 7, 12. doi:10.1186/1751-0473-7-12

Retrieve compound properties from a pubchem CID

Description

Retrieve compound information from pubchem CID, see https://pubchem.ncbi.nlm.nih.gov/

Usage

pc_prop(cid, properties = NULL, verbose = getOption("verbose"), ...)

Arguments

Value

a tibble; each row is a queried CID, each column is a requested property.

Note

Please respect the Terms and Conditions of the National Library of Medicine, https://www.nlm.nih.gov/databases/download.html the data usage policies of National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/home/about/policies/, https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access, and the data usage policies of the indicidual data sources https://pubchem.ncbi.nlm.nih.gov/sources/.

References

Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public Information System for Analyzing Bioactivities of Small Molecules. Nucleic Acids Research 37: 623–633.

Kim, Sunghwan, Paul A. Thiessen, Evan E. Bolton, et al. 2016 PubChem Substance and Compound Databases. Nucleic Acids Research 44(D1): D1202–D1213.

Kim, S., Thiessen, P. A., Bolton, E. E., & Bryant, S. H. (2015). PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. Nucleic acids research, gkv396.

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). doi:10.18637/jss.v093.i13.

See Also

get_cid, pc_sect

Examples

## Not run: 
# might fail if API is not available
pc_prop(5564)

###
# multiple CIDS
comp <- c("Triclosan", "Aspirin")
cids <- get_cid(comp)
pc_prop(cids$cid, properties = c("MolecularFormula", "MolecularWeight",
"SMILES"))

## End(Not run)

Retrieve data from PubChem content pages

Description

When you search for an entity at https://pubchem.ncbi.nlm.nih.gov/, e.g. a compound or a substance, and select the record you are interested in, you will be forwarded to a PubChem content page. When you look at a PubChem content page, you can see that chemical information is organised into sections, subsections, etc. The chemical data live at the lowest levels of these sections. Use this function to retrieve the lowest level information from PubChem content pages.

Usage

pc_sect(
  id,
  section,
  domain = c("compound", "substance", "assay", "gene", "protein", "patent"),
  verbose = getOption("verbose")
)

Arguments

Details

section is not case sensitive but it is sensitive to typing errors and it requires the full name of the section as it is printed on the content page. The PubChem Table of Contents Tree can also be found at https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72.

Value

Returns a tibble of query results. In the returned tibble, SourceName is the name of the depositor, and SourceID is the ID of the search term within the depositor's database. You can browse https://pubchem.ncbi.nlm.nih.gov/sources/ for more information about the depositors.

Note

Please respect the Terms and Conditions of the National Library of Medicine, https://www.nlm.nih.gov/databases/download.html the data usage policies of National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/home/about/policies/, https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access, and the data usage policies of the individual data sources https://pubchem.ncbi.nlm.nih.gov/sources/.

References

Kim, S., Thiessen, P.A., Cheng, T. et al. PUG-View: programmatic access to chemical annotations integrated in PubChem. J Cheminform 11, 56 (2019). doi:10.1186/s13321-019-0375-2.

See Also

get_cid, pc_prop

Examples

# might fail if API is not available
## Not run: 
pc_sect(176, "Dissociation Constants")
pc_sect(c(176, 311), "density")
pc_sect(2231, "depositor-supplied synonyms", "substance")
pc_sect(780286, "modify date", "assay")
pc_sect(9023, "Ensembl ID", "gene")
pc_sect("1ZHY_A", "Sequence", "protein")

## End(Not run)

Search synonyms in pubchem

Description

Search synonyms using PUG-REST, see https://pubchem.ncbi.nlm.nih.gov/.

Usage

pc_synonyms(
  query,
  from = c("name", "cid", "sid", "aid", "smiles", "inchi", "inchikey"),
  match = c("all", "first", "ask", "na"),
  verbose = getOption("verbose"),
  arg = NULL,
  choices = NULL,
  ...
)

Arguments

Value

a named list.

Note

Please respect the Terms and Conditions of the National Library of Medicine, https://www.nlm.nih.gov/databases/download.html the data usage policies of National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/home/about/policies/, https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access, and the data usage policies of the indicidual data sources https://pubchem.ncbi.nlm.nih.gov/sources/.

References

Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public Information System for Analyzing Bioactivities of Small Molecules. Nucleic Acids Research 37: 623–633.

Kim, Sunghwan, Paul A. Thiessen, Evan E. Bolton, et al. 2016 PubChem Substance and Compound Databases. Nucleic Acids Research 44(D1): D1202–D1213.

Kim, S., Thiessen, P. A., Bolton, E. E., & Bryant, S. H. (2015). PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. Nucleic acids research, gkv396.

Examples

## Not run: 
pc_synonyms("Aspirin")
pc_synonyms(c("Aspirin", "Triclosan"))
pc_synonyms(5564, from = "cid")
pc_synonyms(c("Aspirin", "Triclosan"), match = "ask")

## End(Not run)

Ping an API used in webchem to see if it's working.

Description

Ping an API used in webchem to see if it's working.

Usage

ping_service(
  service = c("bcpc", "chebi", "chembl", "cs", "cs_web", "cir", "cts", "etox", "fn",
    "nist", "opsin", "pc", "srs", "wd"),
  apikey = NULL
)

Arguments

Value

A logical, TRUE if the service is available or FALSE if it isn't

Examples

## Not run: 
ping_service("chembl")

## End(Not run)

Get record details from U.S. EPA Substance Registry Servives (SRS)

Description

Get record details from SRS, see https://cdxnodengn.epa.gov/cdx-srs-rest/

Usage

srs_query(
  query,
  from = c("itn", "cas", "epaid", "tsn", "name"),
  verbose = getOption("verbose"),
  ...
)

Arguments

Value

a list of lists (for each supplied query): a list of 22. subsKey, internalTrackingNumber, systematicName, epaIdentificationNumber, currentCasNumber, currentTaxonomicSerialNumber, epaName, substanceType, categoryClass, kingdomCode, iupacName, pubChemId, molecularWeight, molecularFormula, inchiNotation, smilesNotation, classifications, characteristics, synonyms, casNumbers, taxonomicSerialNumbers, relationships

Examples

## Not run: 
# might fail if API is not available
srs_query(query = '50-00-0', from = 'cas')

### multiple inputs
casrn <- c('50-00-0', '67-64-1')
srs_query(query = casrn, from = 'cas')

## End(Not run)

Retrieve identifiers from Wikidata

Description

Retrieve identifiers from Wikidata

Usage

wd_ident(id, verbose = getOption("verbose"))

Arguments

Value

A data.frame of identifiers. Currently these are 'smiles', 'cas', 'cid', 'einecs', 'csid', 'inchi', 'inchikey', 'drugbank', 'zvg', 'chebi', 'chembl', 'unii', 'lipidmaps', 'swisslipids' and source_url.

Note

Only matches in labels are returned. If more than one unique hit is found, only the first is returned.

References

Willighagen, E., 2015. Getting CAS registry numbers out of WikiData. The Winnower. doi:10.15200/winn.142867.72538

Mitraka, Elvira, Andra Waagmeester, Sebastian Burgstaller-Muehlbacher, et al. 2015 Wikidata: A Platform for Data Integration and Dissemination for the Life Sciences and beyond. bioRxiv: 031971.

See Also

get_wdid

Examples

## Not run: 
 id <- c("Q408646", "Q18216")
 wd_ident(id)

## End(Not run)

Defunct function(s) in the webchem package

Description

These functions are defunct and no longer available.

Usage

ppdb_query()

ppdb_parse()

ppdb()

cir()

pp_query()

cs_prop()

ci_query()

pan_query()

Deprecated function(s) in the webchem package

Description

These functions are provided for compatibility with older version of the webchem package. They may eventually be completely removed.

Usage

cid_compinfo(...)

aw_query(...)

Arguments

Details

Deprecated functions are:

Auto-translate identifiers and search databases

Description

Supply a query of any type (e.g. SMILES, CAS, name, InChI, etc.) along with any webchem function that has query and from arguments. If the function doesn't accept the type of query you've supplied, this will try to automatically translate it using CTS and run the query.

Usage

with_cts(query, from, .f, .verbose = getOption("verbose"), ...)

Arguments

Value

returns results from .f

Note

During the translation step, only the first hit from CTS is used. Therefore, using this function to translate on the fly is not foolproof and care should be taken to verify the results.

Examples

## Not run: 
with_cts("XDDAORKBJWWYJS-UHFFFAOYSA-N", from = "inchikey", .f = "get_etoxid")

## End(Not run)

Export a Chemical Structure in .mol Format.

Description

Some webchem functions return character strings that contain a chemical structure in Mol format. This function exports a character string as a .mol file so it can be imported with other chemistry software.

Usage

write_mol(x, file = "")

Arguments

Examples

## Not run: 
# export Mol file
csid <- get_csid("bergapten")
mol3d <- cs_compinfo(csid$csid, field = "Mol3D")
write_mol(mol3d$mol3D, file = mol3d$id)

# export multiple Mol files
csids <- get_csid(c("bergapten", "xanthotoxin"))
mol3ds <- cs_compinfo(csids$csid, field = "Mol3D")
mapply(function(x, y) write_mol(x, y), x = mol3ds$mol3D, y = mol3ds$id)

## End(Not run)