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https://github.com/wherrera10/rxnav.jl

Julia interface to the National Library of Medicine's online pharmaceutical RxNav API
https://github.com/wherrera10/rxnav.jl
health medicine pharmacology rest-api
Last synced: about 1 month ago
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Julia interface to the National Library of Medicine's online pharmaceutical RxNav API
Host: GitHub
URL: https://github.com/wherrera10/rxnav.jl
Owner: wherrera10
License: bsd-2-clause
Created: 2021-06-22T17:25:06.000Z (over 3 years ago)
Default Branch: main
Last Pushed: 2021-07-20T06:19:45.000Z (over 3 years ago)
Last Synced: 2024-11-10T20:11:55.022Z (about 2 months ago)
Topics: health, medicine, pharmacology, rest-api
Language: Julia
Homepage:
Size: 131 KB
Stars: 6
Watchers: 3
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE
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README

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# RxNav.jl

Julia interface to the National Library of Medicine's online pharmaceutical RxNav API



## Examples




    

    julia> using RxNav

    

    julia> for i in interact("fentanyl", "selegiline")

               if i.severity == "high"

                   println(i.description)

               end

           end

    Narcotic analgesics - monoamine oxidase (MAO) inhibitors

    

    julia> println(RxNav.getSpellingSuggestions("nortriptelene"))

    ["nortriptyline", "Nortriptylina"]

    

    julia> RxNav.prescribable(true)

    true

    

    julia> println(RxNav.getSpellingSuggestions("nortriptelene"))

    ["nortriptyline"]

    

    julia> interact("1191", "warfarin", "vitamin K")

    3-element Vector{NamedTuple}:

     (drug1 = "aspirin", drug2 = "vitamin K", severity = "N/A", description = "Acetylsalicylic acid may decrease the excretion rate of Phylloquinone which could result in a higher serum level.")

     (drug1 = "aspirin", drug2 = "warfarin", severity = "N/A", description = "Acetylsalicylic acid may increase the anticoagulant activities of Warfarin.")

     (drug1 = "vitamin K", drug2 = "warfarin", severity = "N/A", description = "The therapeutic efficacy of Warfarin can be decreased when used in combination with Phylloquinone.")

    

    julia> filter(x -> occursin("Pediatric", x), drugs("riboflavin"))

    2-element Vector{String}:

     "alpha-tocopherol acetate 1.4 MG/ML / ascorbic acid 16 MG/ML / biotin 0.004 MG/ML / dexpanthenol 1 MG/ML / ergocalciferol 0.002 MG/ML / folic acid 0.028 MG/ML / niacinamide 3.4 MG/ML / pyridoxine hydrochloride 0.2 MG/ML / riboflavin 0.28 MG/ML / thiamine hydrochloride 0.24 MG/ML / vitamin A 0.14 MG/ML / vitamin B12 0.0002 MG/ML / vitamin K1 0.04 MG/ML Injectable Solution [MVI Pediatric]"

     "alpha-tocopherol acetate 1.4 UNT/ML / ascorbic acid 16 MG/ML / biotin 0.004 MG/ML / cholecalciferol 80 UNT/ML / dexpanthenol 1 MG/ML / folic acid 0.028 MG/ML / niacinamide 3.4 MG/ML / pyridoxine hydrochloride 0.2 MG/ML / riboflavin 0.28 MG/ML / thiamine hydrochloride 0.24 MG/ML / vitamin A palmitate 460 UNT/ML / vitamin B12 0.0002 MG/ML / vitamin K1 0.04 MG/ML Injectable Solution [Infuvite Pediatric]"

    

    





## General Use Functions

These functions are derived from the API, but are specialized and have been modified

for ease of use. For example, the functions may take either a drug name or an RxCUI

identifier as argument.





####    rcui(name)

Take a name of a drug as String argument, return its RxCUI as String.





####    drugs(name)

Given a drug name, return a list of all available dosing forms of the drug.





####    interact(list::Vector)

####    interact(s1::String, severeonly::Bool=true)

####    interact(s1::String, s2::String, args...)

Get a list of interactions for a single drug (or rxcui drug id) or pairwise interactions for more than one drug (or rxcuid).





####    interaction(id; ONCHigh = true)

    

Given a drug name or rxcui id string, return known drug interations for that drug.

If ONCHigh is true only return the ONCHigh database entries, which returns fewer

entries, tending to list only the more significant interactions. Set ONCHigh

to false to get all known interactions, which can be multiple and sometimes redundant.

Returns a `Vector` of `NamedTuple`s as in (drug1, drug2, severity, description).





####    interaction_within_list(idlist::Vector{String})

Given a list of drug names or rxcui id strings, return known drug interations for 

that combination of drugs. Results are organized pairwise, so if A, B, and C have

mutual interactions this will be reported for example as A with B, A with C, B with C.

Returns a `Vector` of `NamedTuple`s as in (drug1, drug2, severity, description)








## API functions

Note: There are two different RxNorm databases.  The more complete one, RxNorm, contains

medications including veterinary-use-only medications and medications no longer in use or

which are not available in United States pharmacies. The Julia functions default to this

database. In order to confine search results to generally available human medications,

the RxNorm database also supports the "Prescribable" RxNorm API, which gives results only

within medications currently available for medical prescription in the US. If you want the

"Prescribable" database used for your RxNorm API calls, you should first call the function 





    prescribable(true)





after which all calls to the RxNorm API will use the somewhat smaller Prescribable database.

To set this back to using the more general database, call `prescribable(false)`.





Some of the API functions take optional arguments. For details of the values for such arguments 

you should consult the NLM documentation (links are below). If the function takes an optional argument

called `extra`, this means that the function's optional argument `extra` should be provided as a `Dict`

or as a `Vector` of `Pairs`, with the keys to the Dict being the label for the optional term and the

values for that key as either a string or a vector of strings to be assigned to that value in the

final URL request. For example, `extra = Dict("sources" => ["ACTIVE", "OBSOLETE"], "toReturn" => 25)`

would be translated to `"&sources=ACTIVE+OBSOLETE&toReturn=25"` in the REST call request string sent by HTTP.

The list of API functions is extensive. The API function names are not exported from RxNav, so to call,

for example, `getSpellingSuggestions("asprin")` you must call this as `RxNav.getSpellingSuggestions("asprin")`.








### RxClass API




See https://rxnav.nlm.nih.gov/RxClassAPIs.html, as copied below:




| Function | REST Resource | Description |

| ---      |     ---       |   ---      |

findClassByName | /class/byName | Drug classes with a specified class name

findClassesById | /class/byId | Drug classes with a specified class identifier

findSimilarClassesByClass | /class/similar | Classes with similar clinically-significant RxNorm ingredients

findSimilarClassesByDrugList | /class/similarByRxcuis | Classes with clinically-significant RxNorm ingredients similar to a specified list

getAllClasses | /allClasses | All classes (may limit by class type)

getClassByRxNormDrugId | /class/byRxcui | Classes containing a specified drug RXCUI

getClassByRxNormDrugName | /class/byDrugName | Classes containing a drug of the specified name

getClassContexts | /classContext | Paths from the specified class to the root of its class hierarchies

getClassGraphBySource | /classGraph | Classes along the path from a specified class to the root of a class hierarchy

getClassMembers | /classMembers | Drug members of a specified class

getClassTree | /classTree | Subclasses or descendants of the specified class

getClassTypes | /classTypes | Class types

getRelas | /relas | Relationships expressed by a source of drug relations

getSimilarityInformation | /class/similarInfo | Similarity of the clinically-significant membership of two classes

getSourcesOfDrugClassRelations | /relaSources | Sources of drug-class relations

getSpellingSuggestions | /spellingsuggestions | Drug or class names similar to a given string





####    findClassByName(classname::String, types::Vector{String} = String[])

Get drug classes with a specified class name





####    findClassesById(classid::String)

Get drug classes with a specified class identifier





####    findSimilarClassesByClass(classid::String, relasource::String, extra=[])

    

Get classes with similar clinically-significant RxNorm ingredients





####    findSimilarClassesByDrugList(rxcuis::Vector{String}, extra=[])

Get classes with clinically-significant RxNorm ingredients similar to a specified list





####    getAllClasses(classtypes::Vector{String}=String[])

Get all classes (may limit by class type with optional argument)





####    getClassByRxNormDrugId(rxcui::String, extras = [])

Get classes containing a specified drug RXCUI





####    getClassByRxNormDrugName(drugname::String, extras = [])

Get classes containing a drug of the specified name





####    getClassContexts(classid::String)

    

Get name and type context for paths from the specified class to the root of its class hierarchies





####    getClassGraphBySource(classId, source="")

    

Get classes along the path from a specified class to the root of a class hierarchy





####    getClassMembers(classid::String, source::String="")

    

Get drug members of a specified class





####    getClassTree(classid::String, type="")

    

Get subclasses or descendants of the specified class





####    getClassTypes()

Get class types





####    getRelas()

    

Get relationships expressed by a source of drug relations





####    getSimilarityInformation(id1, source1, id2, source2, extras=[])

Get similarity of the clinically-significant membership of two classes by id and source





####    getSourcesOfDrugClassRelations()

    

Get sources of drug-class relations





####    getSpellingSuggestions(term::String, type="")

Get drug or class names similar to a given string








### RxNorm API




See https://rxnav.nlm.nih.gov/RxNormAPIs.html, as copied below:




| Function | REST Resource | Description |

| ---      |     ---       |   ---      |

filterByProperty | /rxcui/rxcui/filter | Concept RXCUI if the predicate is true | Active

findRxcuiById | /rxcui?idtype=...&id=... | Concepts associated with a specified identifier | Active or Current

findRxcuiByString | /rxcui?name=... | Concepts with a specified name | Active or Current

getAllConceptsByStatus | /allstatus | Concepts having a specified status | Current and Historical

getAllConceptsByTTY | /allconcepts | Concepts having a specified term type | Active

getAllHistoricalNDCs | /rxcui/rxcui/allhistoricalndcs | National Drug Codes (NDC) ever associated with a concept | Current and Historical

getAllNDCs (Deprecated) | /rxcui/rxcui/allndcs | National Drug Codes (NDC) associated with a concept | Current

getAllNDCsByStatus | /allNDCstatus | NDCs having a specified NDC status | Current and Historical

getAllProperties | /rxcui/rxcui/allProperties | Concept details | Active

getAllRelatedInfo | /rxcui/rxcui/allrelated | Concepts related directly or indirectly to a specified concept | Active

getApproximateMatch | /approximateTerm | Concept and atom IDs approximately matching a query | Active or Current

getDisplayTerms | /displaynames | Strings to support auto-completion in a user interface | Active

getDrugs | /drugs | Drugs related to a specified name | Active

getIdTypes | /idtypes | Identifier types | Current

getMultiIngredBrand | /brands | Brands containing specified ingredients | Active

getNDCProperties | /ndcproperties | National Drug Code (NDC) details | Active

getNDCStatus | /ndcstatus | Status of a National Drug Code (NDC) | Current and Historical

getNDCs | /rxcui/rxcui/ndcs | National Drug Codes (NDC) associated with a concept | Active

getPropCategories | /propCategories | RxNav property categories | Active

getPropNames | /propnames | Property names | Active

getProprietaryInformation | /rxcui/rxcui/proprietary | Strings from sources that require a UMLS license | Current

getRelaTypes | /relatypes | RxNorm Relationship types | Active

getRelatedByRelationship | /rxcui/rxcui/related?rela=... | Concepts directly related to a specified concept by a specified relationship | Active

getRelatedByType | /rxcui/rxcui/related?tty=... | Concepts of specified types that are directly or indirectly related to a specified concept | Active

getRxConceptProperties | /rxcui/rxcui/properties | Concept name, TTY, and a synonym | Active

getRxNormName | /rxcui/rxcui | Name of a concept | Active

getRxNormVersion | /version | RxNorm data set and API versions | Current

getRxProperty | /rxcui/rxcui/property | A property of a concept | Active

getRxcuiHistoryStatus | /rxcui/rxcui/historystatus | Status, history, and other attributes of a concept | Current and Historical

getSourceTypes | /sourcetypes | Vocabulary sources | Current

getSpellingSuggestions | /spellingsuggestions | Strings similar to a specified string | Active

getTermTypes | /termtypes | Term types | Active





####    filterByProperty(rxcui::String, propName::String, propValues::Vector{String} = [])

   

Returns true if rxcui has the propName property (and fits optional propValues criteria if given)





####    findRxcuiById(idtype::String, id::String, allsrc = 0)

    

Get concepts associated with a specified identifier





####    findRxcuiByString(name::String, extras=[])

Get concepts with a specified name	Active or Current





####    getAllConceptsByStatus(status = "ALL")

Get concepts having a specified status





####    getAllConceptsByTTY(tty::Vector{String})

Get concepts having a specified term type (tty)





####    getAllHistoricalNDCs()

Get National Drug Codes (NDC) ever associated with a concept





####    getAllNDCsByStatus(status = "ALL")

NDCs having a specified NDC status





####    getAllProperties(rxcui, properties = ["ALL"])

Get concept details





####    getAllRelatedInfo(rxcui::String)

Get concepts related directly or indirectly to a specified concept (rxcui)





####    getApproximateMatch(term::String, extras = [])

Get concept and atom IDs approximately matching a query





####    getDisplayTerms()

Get strings to support auto-completion, as used in a user interface





####    getDrugs(name::String)

Get drugs related to a specified name





####    getIdTypes()

Get identifier types





####    getMultiIngredBrand(ingredientids::Vector{String})

Get brands containing specified ingredients





####    getNDCProperties(value::String)

Get National Drug Code (NDC) details





####    getNDCStatus(ndc::String, extras = [])

Get status of a National Drug Code (NDC)





####    getNDCs(rxcui::String)

Get National Drug Codes (NDC) associated with a concept





####    getPropCategories()

Get RxNav property categories





####    getPropNames()

Get property names





####    getProprietaryInformation(rxcui::String, ticket::String, extras = [])

Get strings from sources that require a UMLS license





####    getRelaTypes()

Get RxNorm Relationship types





####    getRelatedByRelationship(rxcui::String, relata::Vector{String})

Get concepts directly related to a specified concept by a specified relationship





####    getRelatedByType(rxcui::String, ttys::Vector{String})

Get concepts of specified types that are directly or indirectly related to a specified concept





####    getRxConceptProperties(rxcui::String)

Get concept name, TTY, and a synonym





####    getRxNormName(rxcui::String)

Get name of a concept





####    getRxNormVersion()

Get	RxNorm data set and API versions





####    getRxProperty(rxcui::String, propname::String)

Get a property of a concept





####    getRxcuiHistoryStatus(rxcui::String)

Get XML for status, history, and other attributes of a concept.


Note: as the XML content labels vary, this function returns the metadata in XML form.





####    getSourceTypes()

Get vocabulary sources





####    getSpellingSuggestions(phrase::String)

Get strings similar to a specified string





####    getTermTypes()

Get term types








### RxTerms API




See https://rxnav.nlm.nih.gov/RxTermsAPIs.html, as copied below:




| Function | REST Resource | Description |

| ---      |     ---       |   ---      |

getAllConcepts | /allconcepts | All RxTerms concepts

getAllRxTermInfo | /rxcui/rxcui/allinfo | RxTerms information for a specified RxNorm concept

getRxTermDisplayName | /rxcui/rxcui/name | RxTerms display name for a specified RxNorm concept

getRxTermsVersion | /version | RxTerms version





####    getAllConcepts()

Get all RxTerms concepts





####    getAllRxTermInfo(rxcui::String)

Get RxTerms information for a specified RxNorm concept.


Returns the (quite variable) properties data in XML form.





####    getRxTermDisplayName(rxcui::String)

Get	RxTerms display name for a specified RxNorm concept





####    getRxTermsVersion()

Get RxTerms version








### Drug Interaction API




See https://rxnav.nlm.nih.gov/RxTermsAPIs.html, as copied below:




| Function | REST Resource | Description |

| ---      |     ---       |   ---      |

findDrugInteractions | /interaction | Interactions of an RxNorm drug

findInteractionsFromList | /list | Interactions between a list of drugs

getInteractionSources | /sources | Sources of the interactions

getVersion | /version | Version of the data set(s)





####    findDrugInteractions(rxcui::String, extras = [])

Get interactions of an RxNorm drug with other items in the RxNorm database.

Returns a `Vector` of `NamedTuple`s as in (drug1, drug2, severity, description)





####    findInteractionsFromList(rxcuis::Vector{String}, extras = [])

    

Get pairwise interactions between items in a list of drugs.

Returns a `Vector` of `NamedTuple`s as in (drug1, drug2, severity, description)





####    getInteractionSources()

    

Get sources of the interactions





####    getVersion()

    

Get version of the data set(s)








## Installation




You may install the package from Github in the usual way, or to install the current master copy:

    

    using Pkg

    Pkg.add("http://github.com/wherrera10/RxNav.jl")