Merge pull request #458 from stitam/foodb

Implement access to FooDB

Author: stitam

.github/PULL_REQUEST_TEMPLATE.md

@@ -33,5 +33,6 @@ Brief description of the PR
 PR task list:
 - [ ] Update NEWS
 - [ ] Add tests (if appropriate)
+- [ ] Knit README.Rmd to update test coverage badge (optional, requires ~40 GB of local databases; if skipped, a maintainer will knit and commit the updated README before merge)
 - [ ] Update documentation with `devtools::document()`
 - [ ] Check package passed

.github/workflows/test-coverage.yaml

@@ -51,11 +51,15 @@ export(cts_convert)
 export(cts_from)
 export(cts_to)
 export(db_download_chembl)
+export(db_download_foodb)
 export(etox_basic)
 export(etox_targets)
 export(etox_tests)
 export(find_db)
 export(fn_percept)
+export(foodb_convert)
+export(foodb_list_compounds)
+export(foodb_query)
 export(get_chebiid)
 export(get_cid)
 export(get_csid)

NAMESPACE

@@ -2,6 +2,11 @@
 
 ## NEW FEATURES
 
+### NEW FEATURES
+
+* `webchem` can now access FooDB (https://foodb.ca/), a database of food constituents, chemistry and biology, implemented in offline mode. 
+* Added `db_download_foodb()` to download the database, `foodb_list_compounds()` to list all compounds, and `foodb_convert()` to convert between IDs and `foodb_query()` to query the database.
+
 ### OFFLINE ACCESS
 
 * `chembl_query()` can now perform both online queries (`mode = "ws"`, default) and offline retrievals (`mode = "offline"`) from a local ChEMBL database. Offline mode currently supports the following resources: `activity`, `assay`, `atc_class`, `binding_site`, `biotherapeutic`, `cell_line`, `chembl_id_lookup`, `compound_record`, `document`, `drug`,`drug_indication`, `drug_warning`, `go_slim`, `molecule`.