fixed metadata and platin-bug

sigven · Oct 18, 2023 · aa8b1d7 · aa8b1d7
1 parent 938f7dd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pharmOncoX
 Type: Package
 Title: Molecularly targeted cancer drugs and biomarkers
 Version: 1.4.5
-Date: 2023-10-06
+Date: 2023-10-18
 Authors@R: 
     c(person(given = "Sigve",
              family = "Nakken",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# Version 1.4.6 (October 18th 2023)
+
+* Fixed metadata
+* Fixed out-dated version descriptions (GH site)
+* Do not exclude compounds with missing drug action type (platins etc.)
+
 # Version 1.4.5 (October 6th 2023)
 
 * Updated NCI Thesaurus - 23.09d
@@ -11,81 +17,5 @@
 * Updated Mitelman database (20230803)
 * `get_biomarkers()` now exported as a main function
 
-# Version 1.4.3 (August 7th 2023)
-
-* NCI Thesaurus 23.07e
-
-# Version 1.4.2 (August 1st 2023)
-
-* Added biomarker aliases
-* Updated CIViC data
-
-# Version 1.4.1 (July 23rd 2023)
-
-* Added missing biomarker aliases for synonymous variants
-
-# Version 1.4.0 (July 11th 2023)
-
-* Updated metadata
-* Updated CIViC
-
-# Version 1.3.8 (July 5th 2023)
-
-* Cleaned biomarker data (CIViC)
-
-# Version 1.3.7 (June 28th 2023)
-
-* Updated NCI Thesaurus (23.06d release)
-* Updated biomarker data (CIViC)
-* Updated Open Targets Platform (2023.06)
-
-# Version 1.3.6 (June 1st 2023)
-
-* Updated NCI Thesaurus (23.05d release)
-* Cleaned biomarker alteration types
-
-# Version 1.3.5 (May 24th 2023)
-
-* Removed general words from drug alias list
-* Fixed bug in biomarker alias parsing
-
-# Version 1.3.3 (May 15th 2023)
-
-* Added additional drug entries (primary indication non-cancer)
-* Fixed a bug in parsing of drugs from Open Targets Platform
-
-# Version 1.3.0 (May 10th 2023)
-
-* Updated NCI Thesaurus (23.04d release)
-* Drugs are now provided with [ATC](https://www.whocc.no/atc_ddd_index/) classification labels
-* Major changes/revision to input arguments in `get_drugs()`
-   - all arguments for filtering towards specific inhibitors etc are now removed (e.g. `is_alkylating_agent`,`is_angiogenesis_inhibitor` etc.), such filtering can be performed by the user, e.g. by considering the drug class labels from ATC or the drug targets
-   - Other naming changes to arguments for `get_drugs()`
-       * `drug_is_targeted` -> `drug_targeted_agent`
-       * `inhibitor_only` -> `drug_action_inhibition`
-       * `drug_approved_later_than` -> `drug_approval_year`
-       * `source_opentargets_only` -> `drug_source_opentargets`
-   - The `drug_targeted_agent` option has been improved basd on ATC labeling
-   - New arguments for `get_drugs()`:
-       * `drug_cancer_indication` - logical indicating if resulting drug records 
-should be for those indicated for cancer conditions only (i.e. from approved 
-conditions, listed in clinical trials etc.) - defaults to TRUE
-       * `drug_classified_cancer` - logical indicating if resulting drug 
-records should be for those classified only in the "L" class of ATC (
-"ANTINEOPLASTIC AND IMMUNOMODULATING AGENTS") - defaults to TRUE
-
-
-# Version 1.2.0 (April 26th 2023)
-
-* Using [sigven/phenOncoX](https://github.com/sigven/phenOncoX) v0.5.8
-  for cancer phenotype matching
-* Updated NCI Thesaurus (23.03d release)
-* New helper function to retrieve drug biomarkers (`pharmOncoX:::get_biomarkers`)
-
-# Version 1.1.9 (March 1st 2023)
-
-* Updated NCI Thesaurus (23.02d release)
-* Updated biomarker data (CIViC)
-* Updated Open Targets Platform (2023.02)
 
 
diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/data-raw/data-raw.R b/data-raw/data-raw.R
@@ -74,7 +74,7 @@ drug_sets <- list()
 ## Get all anticancer drugs, NCI thesaurus + DGIdb
 drug_sets[['nci']] <- get_nci_drugs(
   nci_db_release = nci_db_release,
-  overwrite = T,
+  overwrite = F,
   path_data_raw = path_data_raw,
   path_data_processed = path_data_tmp_processed)
 
@@ -133,7 +133,8 @@ if(NROW(dup_chembl_ids) > 0){
     dplyr::inner_join(dup_chembl_ids) |> 
     dplyr::select(
       drug_name, molecule_chembl_id, 
-      nci_cd_name, drug_cancer_relevance)
+      nci_cd_name, drug_cancer_relevance) |>
+    dplyr::distinct()
 }
 
 ####--- Cancer drug aliases ----#####

diff --git a/data-raw/drug_name_black_list.txt b/data-raw/drug_name_black_list.txt
@@ -22,4 +22,16 @@ Tetradecanoylphorbol Acetate
 4-DEMETHYL-4-CHOLESTERYLOXYCARBONYLPENCLOMEDINE
 Nitrofurantoin Monohydrate
 Pentamidine Mesylate
+Fertirelin Acetate
+Dimethicone
+Alpha Galactosylceramide
+THIOUREA, N-(5-BROMO-2-PYRIDINYL)-N'-(2-(2-CHLORO-3-ETHOXY-6-FLUOROPHENYL)ETHYL)-
+CG-200745
+KZR-616
+CYC-065
+Recombinant Fibroblast Growth Factor 1
+NIS-793
+CBS-9106
+PF-06865571
+
 
diff --git a/data-raw/drug_utilities.R b/data-raw/drug_utilities.R
@@ -270,7 +270,7 @@ get_chembl_pubchem_compound_xref <- function(datestamp = '20220906',
 ### TARGETED ANTICANCER COMPOUNDS FROM OPEN TARGETS
 get_opentargets_cancer_drugs <-
   function(path_data_raw = NULL,
-           ot_version = "2023.02"){
+           ot_version = "2023.09"){
 
     cancer_terms <- list()
     cancer_terms[['all']] <- phenOncoX::get_terms(
@@ -359,10 +359,17 @@ get_opentargets_cancer_drugs <-
         as.character(drug_cancer_relevance)
       )
     ) |>
-    dplyr::filter(
-      !is.na(drug_action_type)
+    dplyr::mutate(
+      drug_type = dplyr::if_else(
+        drug_type == "unknown",
+        "Unknown",
+        as.character(drug_type)
+      )
     ) |>
     # dplyr::filter(
+    #   !is.na(drug_action_type)
+    # ) |>
+    # dplyr::filter(
     #   !stringr::str_detect(
     #     tolower(drug_action_type),
     #     "allosteric|modulator|substrate|releasing|opener"

diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
@@ -11,7 +11,6 @@ template:
          window.dataLayer = window.dataLayer || [];
          function gtag(){dataLayer.push(arguments);}
          gtag('js', new Date());
-
          gtag('config', 'G-K1KDXWGEWK');
        </script>
 authors:
@@ -25,7 +24,6 @@ navbar:
     get_started:
       text: Getting started
       href: articles/pharmOncoX.html
-
 home:
   sidebar:
     structure: [links, license, community, citation, authors, dev]
@@ -34,4 +32,4 @@ home:
           title: Citation
           text: "[Citing pharmOncoX](authors.html#citation)"
 news:
-  one_page: true
+  one_page: true
diff --git a/pkgdown/index.md b/pkgdown/index.md
@@ -10,12 +10,12 @@ Drug-target associations from the Open Targets Platform have furthermore been in
 
 We provide anti-cancer drugs in **pharmOncoX** with drug class labeling from [Anatomical Therapeutic Chemical (ATC) Classification System](https://www.whocc.no/atc_ddd_index/), enabling a filtering of drugs according to their main mechanisms of action.
 
-Currently (as of late April 2023), `pharmOncoX` is built upon the following 
+Currently (as of late October 2023), `pharmOncoX` is built upon the following 
 releases of external databases:
 
- - Open Targets Platform (2023.02)
- - ChEMBL (v31)
- - NCI Thesaurus (23.04d)
+ - Open Targets Platform (2023.09)
+ - ChEMBL (v33)
+ - NCI Thesaurus (23.09d)
 
 ### Getting started