pc_sect: Retrieve data from PubChem content pages

In ropensci/webchem: Chemical Information from the Web

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

id	numeric or character; a vector of PubChem identifiers to search for.
section	character; the section of the content page to be imported.
domain	character; the query domain. Can be one of "compound", "substance", "assay", "gene", "protein" or "patent".
verbose	logical; should a verbose output be printed on the console?

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). \Sexpr[results=rd]{tools:::Rd_expr_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)

ropensci/webchem documentation built on Dec. 27, 2024, 2:19 a.m.