fix: list FDA drugs on genes-and-drugs page

PharmGKB · May 16, 2024 · cbb58c6 · cbb58c6
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diff --git a/docs/Genes-and-Drugs.md b/docs/Genes-and-Drugs.md
@@ -14,7 +14,7 @@ The following tables list genes used by PharmCAT to find drug recommendation, al
 
 The `Named Allele Matcher` will search the given sample file for locations associated with these genes and attempt to match them to known allele definitions.
 
-| Gene | CPIC | PharmGKB-DPWG |
+| Gene | CPIC | DPWG |
 | :--- | :---: | :---: |
 | [ABCG2](/Phenotypes-List#abcg2) | :heavy_check_mark: | :heavy_check_mark: |
 | [CACNA1S](/Phenotypes-List#cacna1s) | :heavy_check_mark: |  |
@@ -48,7 +48,7 @@ See [Outside Call Format](/using/Outside-Call-Format) for formatting details and
 [Calling CYP2D6](/using/Calling-CYP2D6) or [Calling HLA](/using/Calling-HLA) for how to obtain CYP2D6 or
 HLA calls, respectively, using sequencing data.
 
-| Gene | CPIC | PharmGKB-DPWG |
+| Gene | CPIC | DPWG |
 | :--- | :---: | :---: |
 | [CYP2D6](/Phenotypes-List#cyp2d6) | :heavy_check_mark: | :heavy_check_mark: |
 | [HLA-A](/Phenotypes-List#hla-a) | :heavy_check_mark: | :heavy_check_mark: |
@@ -63,107 +63,182 @@ HLA calls, respectively, using sequencing data.
 
 The following table lists drugs for which PharmCAT has recommendations for, along with their sources. 
 
-| Drug | CPIC | PharmGKB-DPWG |
-| :--- | :---: | :---: |
-| abacavir | :heavy_check_mark: | :heavy_check_mark: |
-| acenocoumarol |  | :heavy_check_mark: |
-| allopurinol | :heavy_check_mark: | :heavy_check_mark: |
-| amikacin | :heavy_check_mark: |  |
-| amitriptyline | :heavy_check_mark: | :heavy_check_mark: |
-| aripiprazole |  | :heavy_check_mark: |
-| atazanavir | :heavy_check_mark: |  |
-| atomoxetine | :heavy_check_mark: | :heavy_check_mark: |
-| atorvastatin | :heavy_check_mark: | :heavy_check_mark: |
-| azathioprine | :heavy_check_mark: | :heavy_check_mark: |
-| brexpiprazole |  | :heavy_check_mark: |
-| capecitabine | :heavy_check_mark: | :heavy_check_mark: |
-| carbamazepine | :heavy_check_mark: | :heavy_check_mark: |
-| celecoxib | :heavy_check_mark: |  |
-| citalopram | :heavy_check_mark: | :heavy_check_mark: |
-| clomipramine | :heavy_check_mark: | :heavy_check_mark: |
-| clopidogrel | :heavy_check_mark: | :heavy_check_mark: |
-| codeine | :heavy_check_mark: | :heavy_check_mark: |
-| dapsone | :heavy_check_mark: |  |
-| desflurane | :heavy_check_mark: |  |
-| desipramine | :heavy_check_mark: |  |
-| dexlansoprazole | :heavy_check_mark: |  |
-| doxepin | :heavy_check_mark: | :heavy_check_mark: |
-| efavirenz | :heavy_check_mark: | :heavy_check_mark: |
-| eliglustat |  | :heavy_check_mark: |
-| enflurane | :heavy_check_mark: |  |
-| escitalopram | :heavy_check_mark: | :heavy_check_mark: |
-| flecainide |  | :heavy_check_mark: |
-| flucloxacillin |  | :heavy_check_mark: |
-| flucytosine |  | :heavy_check_mark: |
-| fluorouracil | :heavy_check_mark: | :heavy_check_mark: |
-| flurbiprofen | :heavy_check_mark: |  |
-| fluvastatin | :heavy_check_mark: |  |
-| fluvoxamine | :heavy_check_mark: |  |
-| fosphenytoin | :heavy_check_mark: |  |
-| gentamicin | :heavy_check_mark: |  |
-| haloperidol |  | :heavy_check_mark: |
-| halothane | :heavy_check_mark: |  |
-| hydrocodone | :heavy_check_mark: |  |
-| ibuprofen | :heavy_check_mark: |  |
-| imipramine | :heavy_check_mark: | :heavy_check_mark: |
-| irinotecan |  | :heavy_check_mark: |
-| isoflurane | :heavy_check_mark: |  |
-| ivacaftor | :heavy_check_mark: |  |
-| kanamycin | :heavy_check_mark: |  |
-| lamotrigine |  | :heavy_check_mark: |
-| lansoprazole | :heavy_check_mark: | :heavy_check_mark: |
-| lornoxicam | :heavy_check_mark: |  |
-| lovastatin | :heavy_check_mark: |  |
-| meloxicam | :heavy_check_mark: |  |
-| mercaptopurine | :heavy_check_mark: | :heavy_check_mark: |
-| methoxyflurane | :heavy_check_mark: |  |
-| methylene blue | :heavy_check_mark: |  |
-| metoprolol |  | :heavy_check_mark: |
-| nitrofurantoin | :heavy_check_mark: |  |
-| nortriptyline | :heavy_check_mark: | :heavy_check_mark: |
-| omeprazole | :heavy_check_mark: | :heavy_check_mark: |
-| ondansetron | :heavy_check_mark: |  |
-| oxcarbazepine | :heavy_check_mark: | :heavy_check_mark: |
-| pantoprazole | :heavy_check_mark: | :heavy_check_mark: |
-| paromomycin | :heavy_check_mark: |  |
-| paroxetine | :heavy_check_mark: | :heavy_check_mark: |
-| peginterferon alfa-2a | :heavy_check_mark: |  |
-| peginterferon alfa-2b | :heavy_check_mark: |  |
-| pegloticase | :heavy_check_mark: |  |
-| phenprocoumon |  | :heavy_check_mark: |
-| phenytoin | :heavy_check_mark: | :heavy_check_mark: |
-| pimozide |  | :heavy_check_mark: |
-| piroxicam | :heavy_check_mark: |  |
-| pitavastatin | :heavy_check_mark: |  |
-| plazomicin | :heavy_check_mark: |  |
-| pravastatin | :heavy_check_mark: |  |
-| primaquine | :heavy_check_mark: |  |
-| propafenone |  | :heavy_check_mark: |
-| quetiapine |  | :heavy_check_mark: |
-| rasburicase | :heavy_check_mark: |  |
-| ribavirin | :heavy_check_mark: |  |
-| risperidone |  | :heavy_check_mark: |
-| rosuvastatin | :heavy_check_mark: |  |
-| sertraline | :heavy_check_mark: | :heavy_check_mark: |
-| sevoflurane | :heavy_check_mark: |  |
-| simvastatin | :heavy_check_mark: | :heavy_check_mark: |
-| siponimod |  | :heavy_check_mark: |
-| streptomycin | :heavy_check_mark: |  |
-| succinylcholine | :heavy_check_mark: |  |
-| tacrolimus | :heavy_check_mark: | :heavy_check_mark: |
-| tafenoquine | :heavy_check_mark: |  |
-| tamoxifen | :heavy_check_mark: | :heavy_check_mark: |
-| tegafur |  | :heavy_check_mark: |
-| tenoxicam | :heavy_check_mark: |  |
-| thioguanine | :heavy_check_mark: | :heavy_check_mark: |
-| tobramycin | :heavy_check_mark: |  |
-| toluidine blue | :heavy_check_mark: |  |
-| tramadol | :heavy_check_mark: | :heavy_check_mark: |
-| trimipramine | :heavy_check_mark: |  |
-| tropisetron | :heavy_check_mark: |  |
-| venlafaxine | :heavy_check_mark: | :heavy_check_mark: |
-| voriconazole | :heavy_check_mark: | :heavy_check_mark: |
-| vortioxetine | :heavy_check_mark: |  |
-| warfarin | :heavy_check_mark: | :heavy_check_mark: |
-| zuclopenthixol |  | :heavy_check_mark: |
+| Drug | CPIC | DPWG | FDA Label | FDA PGx Assoc |
+| :--- | :---: | :---: | :---: | :---: |
+| Ascorbic acid (vitamin C), combinations |  |  | :heavy_check_mark: |  |
+| Ascorbic acid (vitamin C), plain |  |  | :heavy_check_mark: |  |
+| abacavir | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| abrocitinib |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| acenocoumarol |  | :heavy_check_mark: |  |  |
+| acetaminophen / caffeine / dihydrocodeine |  |  | :heavy_check_mark: |  |
+| allopurinol | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| amikacin | :heavy_check_mark: |  |  |  |
+| amitriptyline | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| amoxapine |  |  |  | :heavy_check_mark: |
+| amphetamine |  |  |  | :heavy_check_mark: |
+| aripiprazole |  | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| aripiprazole lauroxil |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| articaine / epinephrine |  |  | :heavy_check_mark: |  |
+| atazanavir | :heavy_check_mark: |  |  |  |
+| atomoxetine | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| atorvastatin | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| avatrombopag |  |  |  | :heavy_check_mark: |
+| azathioprine | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| belinostat |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| belzutifan |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| brexpiprazole |  | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| brivaracetam |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| capecitabine | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| carbamazepine | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| carisoprodol |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| carvedilol |  |  |  | :heavy_check_mark: |
+| ceftriaxone |  |  | :heavy_check_mark: |  |
+| celecoxib | :heavy_check_mark: |  | :heavy_check_mark: | :heavy_check_mark: |
+| cevimeline |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| chloroquine |  |  | :heavy_check_mark: |  |
+| chlorpropamide |  |  | :heavy_check_mark: |  |
+| citalopram | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| clobazam |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| clomipramine | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| clopidogrel | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| clozapine |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| codeine | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| dapsone | :heavy_check_mark: |  |  |  |
+| darifenacin |  |  |  | :heavy_check_mark: |
+| desflurane | :heavy_check_mark: |  | :heavy_check_mark: |  |
+| desipramine | :heavy_check_mark: |  |  | :heavy_check_mark: |
+| deutetrabenazine |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| dexlansoprazole | :heavy_check_mark: |  |  | :heavy_check_mark: |
+| dextromethorphan / quinidine |  |  | :heavy_check_mark: |  |
+| dextromethorphan hydrobromide / bupropion hydrochloride |  |  | :heavy_check_mark: |  |
+| diazepam |  |  |  | :heavy_check_mark: |
+| dolutegravir |  |  |  | :heavy_check_mark: |
+| donepezil |  |  |  | :heavy_check_mark: |
+| doxepin | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| dronabinol |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| efavirenz | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| elagolix |  |  |  | :heavy_check_mark: |
+| eliglustat |  | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| enflurane | :heavy_check_mark: |  |  |  |
+| erdafitinib |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| escitalopram | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| esomeprazole |  |  |  | :heavy_check_mark: |
+| fesoterodine |  |  |  | :heavy_check_mark: |
+| flecainide |  | :heavy_check_mark: |  |  |
+| flibanserin |  |  |  | :heavy_check_mark: |
+| flucloxacillin |  | :heavy_check_mark: |  |  |
+| flucytosine |  | :heavy_check_mark: |  |  |
+| fluorouracil | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| flurbiprofen | :heavy_check_mark: |  | :heavy_check_mark: | :heavy_check_mark: |
+| fluvastatin | :heavy_check_mark: |  |  |  |
+| fluvoxamine | :heavy_check_mark: |  |  | :heavy_check_mark: |
+| fosphenytoin | :heavy_check_mark: |  | :heavy_check_mark: | :heavy_check_mark: |
+| galantamine |  |  |  | :heavy_check_mark: |
+| gefitinib |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| gentamicin | :heavy_check_mark: |  |  |  |
+| glimepiride |  |  | :heavy_check_mark: |  |
+| glipizide |  |  | :heavy_check_mark: |  |
+| glyburide |  |  | :heavy_check_mark: |  |
+| haloperidol |  | :heavy_check_mark: |  |  |
+| halothane | :heavy_check_mark: |  |  |  |
+| hormonal contraceptives for systemic use |  | :heavy_check_mark: |  |  |
+| hydrocodone | :heavy_check_mark: |  |  |  |
+| hydroxychloroquine |  |  | :heavy_check_mark: |  |
+| ibuprofen | :heavy_check_mark: |  |  | :heavy_check_mark: |
+| iloperidone |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| imipramine | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| irinotecan |  | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| isoflurane | :heavy_check_mark: |  | :heavy_check_mark: |  |
+| ivacaftor | :heavy_check_mark: |  | :heavy_check_mark: |  |
+| kanamycin | :heavy_check_mark: |  |  |  |
+| lamotrigine |  | :heavy_check_mark: |  |  |
+| lansoprazole | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| lesinurad |  |  | :heavy_check_mark: |  |
+| lidocaine and tetracaine |  |  | :heavy_check_mark: |  |
+| lofexidine |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| lornoxicam | :heavy_check_mark: |  |  |  |
+| lovastatin | :heavy_check_mark: |  |  |  |
+| mavacamten |  |  |  | :heavy_check_mark: |
+| meclizine |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| meloxicam | :heavy_check_mark: |  | :heavy_check_mark: | :heavy_check_mark: |
+| mepivacaine |  |  | :heavy_check_mark: |  |
+| mercaptopurine | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| methoxyflurane | :heavy_check_mark: |  |  |  |
+| methylene blue | :heavy_check_mark: |  | :heavy_check_mark: |  |
+| metoclopramide |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| metoprolol |  | :heavy_check_mark: |  | :heavy_check_mark: |
+| mirabegron |  |  |  | :heavy_check_mark: |
+| moviprep |  |  | :heavy_check_mark: |  |
+| nalidixic acid |  |  | :heavy_check_mark: |  |
+| nateglinide |  |  |  | :heavy_check_mark: |
+| nebivolol |  |  |  | :heavy_check_mark: |
+| nilotinib |  |  |  | :heavy_check_mark: |
+| nitrofurantoin | :heavy_check_mark: |  |  |  |
+| nortriptyline | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| oliceridine |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| omeprazole | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| ondansetron | :heavy_check_mark: |  |  |  |
+| oxcarbazepine | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| oxymetazoline and tetracaine |  |  | :heavy_check_mark: |  |
+| pantoprazole | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| paromomycin | :heavy_check_mark: |  |  |  |
+| paroxetine | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| pazopanib |  |  |  | :heavy_check_mark: |
+| peginterferon alfa-2a | :heavy_check_mark: |  |  |  |
+| peginterferon alfa-2b | :heavy_check_mark: |  |  |  |
+| pegloticase | :heavy_check_mark: |  | :heavy_check_mark: |  |
+| perphenazine |  |  |  | :heavy_check_mark: |
+| phenprocoumon |  | :heavy_check_mark: |  |  |
+| phenytoin | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| pimozide |  | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| piroxicam | :heavy_check_mark: |  | :heavy_check_mark: | :heavy_check_mark: |
+| pitavastatin | :heavy_check_mark: |  |  |  |
+| pitolisant |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| plazomicin | :heavy_check_mark: |  |  |  |
+| pravastatin | :heavy_check_mark: |  |  |  |
+| primaquine | :heavy_check_mark: |  | :heavy_check_mark: |  |
+| propafenone |  | :heavy_check_mark: |  | :heavy_check_mark: |
+| propranolol |  |  |  | :heavy_check_mark: |
+| protriptyline |  |  |  | :heavy_check_mark: |
+| quetiapine |  | :heavy_check_mark: |  |  |
+| rabeprazole |  |  |  | :heavy_check_mark: |
+| raltegravir |  |  |  | :heavy_check_mark: |
+| rasburicase | :heavy_check_mark: |  | :heavy_check_mark: |  |
+| ribavirin | :heavy_check_mark: |  |  |  |
+| risperidone |  | :heavy_check_mark: |  | :heavy_check_mark: |
+| rosuvastatin | :heavy_check_mark: |  |  | :heavy_check_mark: |
+| sacituzumab govitecan |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| sertraline | :heavy_check_mark: | :heavy_check_mark: |  |  |
+| sevoflurane | :heavy_check_mark: |  | :heavy_check_mark: |  |
+| simvastatin | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| siponimod |  | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| sodium ascorbate |  |  | :heavy_check_mark: |  |
+| sodium nitrite |  |  | :heavy_check_mark: |  |
+| streptomycin | :heavy_check_mark: |  |  |  |
+| succinylcholine | :heavy_check_mark: |  | :heavy_check_mark: |  |
+| sulfasalazine |  |  | :heavy_check_mark: |  |
+| tacrolimus | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| tafenoquine | :heavy_check_mark: |  | :heavy_check_mark: |  |
+| tamoxifen | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| tamsulosin |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| tegafur |  | :heavy_check_mark: |  |  |
+| tenoxicam | :heavy_check_mark: |  |  |  |
+| tetrabenazine |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| thioguanine | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| thioridazine |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| tobramycin | :heavy_check_mark: |  |  |  |
+| tolazamide |  |  | :heavy_check_mark: |  |
+| tolbutamide |  |  | :heavy_check_mark: |  |
+| tolterodine |  |  |  | :heavy_check_mark: |
+| toluidine blue | :heavy_check_mark: |  |  |  |
+| tramadol | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| trimipramine | :heavy_check_mark: |  |  | :heavy_check_mark: |
+| tropisetron | :heavy_check_mark: |  |  |  |
+| valbenazine |  |  | :heavy_check_mark: | :heavy_check_mark: |
+| venlafaxine | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| viloxazine |  |  |  | :heavy_check_mark: |
+| voriconazole | :heavy_check_mark: | :heavy_check_mark: |  | :heavy_check_mark: |
+| vortioxetine | :heavy_check_mark: |  | :heavy_check_mark: | :heavy_check_mark: |
+| warfarin | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
+| zuclopenthixol |  | :heavy_check_mark: |  |  |
 
diff --git a/src/main/java/org/pharmgkb/pharmcat/reporter/PgkbGuidelineCollection.java b/src/main/java/org/pharmgkb/pharmcat/reporter/PgkbGuidelineCollection.java
@@ -83,10 +83,10 @@ public Set<GuidelinePackage> getGuidelinesFromSource(PrescribingGuidanceSource s
         .collect(Collectors.toSet());
   }
 
-  public Set<String> getChemicalsUsedInSource(DataSource source) {
+  public Set<String> getChemicalsUsedInSource(PrescribingGuidanceSource source) {
     return f_guidelineMap.values().stream()
         .map(GuidelinePackage::getGuideline)
-        .filter(g -> g.getSource().equalsIgnoreCase(source.getPharmgkbName()))
+        .filter(g -> g.getSource().equalsIgnoreCase(source.getPgkbSource().getPharmgkbName()) && g.getObjCls().equalsIgnoreCase(source.getPgkbObjectType()))
         .flatMap(g -> g.getRelatedChemicals().stream())
         .map(AccessionObject::getName)
         .collect(Collectors.toSet());