webservices.unichem¶

Substance cross references from UniChem.

UniChem maps a structure, identified by its InChIKey, to the entries of many chemistry databases, which gives cross references for a substance without having to query every database separately.

from pymetadata.webservices.unichem import UnichemQuery

query = UnichemQuery()
xrefs = query.query_xrefs_for_inchikey("AAOVKJBEBIDNHE-UHFFFAOYSA-N")

See https://www.ebi.ac.uk/unichem/info/webservices.

UnichemSource `dataclass` ¶

UnichemSource(
    sourceID,
    srcUrl,
    name,
    nameLabel,
    nameLong,
    UCICount,
    baseIdUrl,
    description,
    created,
    lastUpdated,
    srcDetails,
    srcReleaseDate,
    srcReleaseNumber,
    updateComments,
    private,
)

Unichem source.

src_id (the src_id for this source), src_url (the main home page of the source), name (the unique name for the source in UniChem, always lower case), name_long (the full name of the source, as defined by the source), name_label (A name for the source suitable for use as a 'label' for the source within a web-page. Correct case setting for source, and always less than 30 characters), description (a description of the content of the source), base_id_url_available (an flag indicating whether this source provides a valid base_id_url for creating cpd-specific links [1=yes, 0=no]). base_id_url (the base url for constructing hyperlinks to this source [append an identifier from this source to the end of this url to create a valid url to a specific page for this cpd], unless aux_for_url=1), aux_for_url (A flag to indicate whether the aux_src field should be used to create hyperlinks instead of the src_compound_id [1=yes, 0=no]

UnichemQuery ¶

UnichemQuery(cache_path=None, cache=None)

Queries against the UniChem web service.

The sources of UniChem are retrieved once and shared by all instances. Responses are cached on disk for CACHE_DURATION_ONTOLOGY hours, see pymetadata.CACHE_USE. If UniChem cannot be reached, cached content is used however old it is.

Initialize the query.

Parameters:

Name	Type	Description	Default
`cache_path`	`Path \| None`	directory for cached responses, defaults to `pymetadata.CACHE_PATH`	`None`
`cache`	`bool \| None`	cache responses, defaults to `pymetadata.CACHE_USE`	`None`

get_sources ¶

get_sources()

Get the databases known to UniChem, from the cache or the service.

Returns:

Type	Description
`dict[int, UnichemSource]`	The sources by their UniChem source id.

Raises:

Type	Description
`WebserviceError`	if the sources are neither cached nor retrievable

query_xrefs_for_inchikey ¶

query_xrefs_for_inchikey(inchikey)

Get the cross references for a structure.