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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,
    name,
    nameLabel=None,
    nameLong=None,
    srcUrl=None,
    baseIdUrl=None,
    description=None,
    UCICount=None,
    created=None,
    lastChecked=None,
    srcLastUpdated=None,
    srcDetails=None,
    updateComments=None,
    private=None,
)

Database known to UniChem, see the sources endpoint of the web service.

Only sourceID and name are required. UniChem adds and removes the descriptive fields without notice, so they are optional, and UnichemSource.from_dict ignores fields which are not declared here.

Attributes:

Name Type Description
sourceID int

id of the source in UniChem
name str

unique name of the source in UniChem, always lower case
nameLabel str | None

name suitable as label of the source, in the case used by the source
nameLong str | None

full name of the source, as defined by the source
srcUrl str | None

home page of the source
baseIdUrl str | None

base url for links to a compound in the source; the identifier of the compound is appended or replaces {$id}
description str | None

description of the content of the source
UCICount int | None

number of UniChem compound identifiers in the source
created str | None

date the source was added to UniChem
lastChecked str | None

date UniChem checked the source for an update
srcLastUpdated str | None

date of the last update of the source
srcDetails str | None

details on the source
updateComments str | None

comments on the update of the source
private bool | None

the source is not public

from_dict classmethod 

from_dict(data)

Create a source from a source of the web service or of the cache.

Parameters:

Name Type Description Default
data dict[str, Any]

fields of the source, fields unknown to UnichemSource are ignored

 required

Returns:

Type Description
UnichemSource

The source.

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.

Parameters:

Name Type Description Default
inchikey str

InChIKey of the structure, e.g., AAOVKJBEBIDNHE-UHFFFAOYSA-N, case is ignored

 required

Returns:

Type Description
list[CrossReference]

One cross reference per database which contains the structure,
list[CrossReference]

empty for an invalid InChIKey.