Skip to contents

Batch lookup via CTS-Lite

Source: R/cts_lite_lookup_class.R
cts_lite_lookup.Rd

Uses the CTS-Lite batch REST API to match InChIKeys against a curated subset of PubChem, returning the matched PubChem entry plus literature/patent annotation counts.

Usage

cts_lite_lookup(
  query_column,
  suffix = "_cts",
  columns = ".all",
  top_hit_only = TRUE,
  first_block_matches = TRUE,
  rdkit_conversion = TRUE,
  cache = NULL,
  cache_mode = "update",
  ...
)

Arguments

query_column

(character) The name of a column in the annotation table containing InChIKeys (or InChI, SMILES, molecular formula or PubChem CID values - CTS-Lite auto-detects the query type).

suffix

(character) A suffix appended to all column names in the returned result. The default is "_cts".

columns

(character) The columns to include in the result. One or more of "query_type", "found_match", "match_level", "pubchem_cid", "inchikey", "inchi", "smiles", "compound_name", "molecular_formula", "exact_mass", "literature_count", "patent_count", "annotation_type_count". Keyword ".all" (the default) returns every column. The default is ".all".

top_hit_only

(logical) If TRUE (the default), CTS-Lite returns only the single best-ranked match per query (by literature/patent count). If FALSE, a query may return multiple matches, producing one row per match. The default is TRUE.

first_block_matches

(logical) If TRUE (the default), an InChIKey (or converted SMILES) query with no exact match may still match on its first 14 characters (the connectivity/skeleton block), reported as match_level = "First Block". If FALSE, only exact matches are returned. The default is TRUE.

rdkit_conversion

(logical) If TRUE (the default), a SMILES query that fails to match directly is converted to an InChIKey with RDKit and retried. Has no effect for InChIKey queries. The default is TRUE.

cache

(annotation_database, NULL) A struct cache object (e.g. rds_cache()) that stores results of previous CTS-Lite queries, keyed by query value. Values already present in the cache are not requeried. If not using a cache then set to NULL. The default is NULL.

cache_mode

(character) Cache mode. Allowed values are limited to the following:

  • "update": The normal mode: values already in cache are used as-is, anything missing is queried live and the result added to the cache.

  • "offline": Never query the live CTS-Lite API - only values already present in cache are returned, and everything else is left as NA. A warning lists how many query values are not covered by the cache when this happens.

  • "rebuild": Ignore any existing cached value and query the live CTS-Lite API for every value, overwriting the corresponding entry in cache.

The default is "update".

...

Additional slots and values passed to struct_class.

Value

A cts_lite_lookup object with the following output slots:

updated(annotation_source) The annotation_source after adding data returned by CTS-Lite.

Details

CTS-Lite (the Fiehn Lab's successor to the original, now-closed Chemical Translation Service) matches an InChIKey (or InChI, SMILES, molecular formula or PubChem CID - the query type is auto-detected) against a curated subset of PubChem, returning the matched PubChem entry plus literature/patent annotation counts that can be used as a rough confidence signal. It does not support name-based translation - see mwb_refmet_lookup() or chebi_lookup() for that. Its REST API (POST .../match) is batch-based - every query value is submitted in a single request, rather than one request per value - so, unlike MetMashR's other REST API lookups, this object is not built on the rest_api base class.

Inheritance

A cts_lite_lookup object inherits the following struct classes:

[cts_lite_lookup] -> [model] -> [struct_class]

See also

Other REST API's: classyfire_batch_lookup(), classyfire_lookup(), kegg_lookup(), lipidmaps_lookup(), mwb_compound_lookup(), mwb_refmet_lookup(), pubchem_id_exchange(), rest_api()

Examples

M <- cts_lite_lookup(
        query_column = character(0),
        suffix = "_cts",
        columns = ".all",
        top_hit_only = FALSE,
        first_block_matches = FALSE,
        rdkit_conversion = FALSE,
        base_url = "https://cts-lite.metabolomics.us/match",
        cache = NULL,
        cache_mode = "update")