Webinar Series May 21, 2014 · 2014. 5. 21. · RxMix – Enabling complex queries to drug...
Transcript of Webinar Series May 21, 2014 · 2014. 5. 21. · RxMix – Enabling complex queries to drug...
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RxMix – Enabling complex queries to drug information sources
through functional composition Olivier Bodenreider
Lister Hill National Center for Biomedical Communications
Bethesda, Maryland - USA
Webinar Series May 21, 2014
Jonathan Mortensen
Stanford University
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Acknowledgments
Lee Peters Thang Nguyen Kelly Zeng Ramez Ghazzaoui
Stuart Nelson, John
Kilbourne (RxNorm) Kin Wah Fung (RxTerms) Mike Lincoln (NDF-RT)
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References
RxNav , RxMix and drug information sources APIs http://rxnav.nlm.nih.gov/
Drug information sources RxNorm
http://www.nlm.nih.gov/research/umls/rxnorm/index.html RxTerms
http://wwwcf.nlm.nih.gov/umlslicense/rxtermApp/rxTerm.cfm NDF-RT
http://evs.nci.nih.gov/ftp1/NDF-RT/ C3PI RxImageAccess
http://rximage.nlm.nih.gov/
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http://rxnav.nlm.nih.gov/
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References
Peters LB, Mortensen J, Nguyen T, Bodenreider O. Enabling complex queries to drug information sources through functional composition. Stud Health Technol Inform (Proc Medinfo) 2013;192:692-696.
http://mor.nlm.nih.gov/pubs/pdf/2013-medinfo-lp.pdf
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Outline
Introduction APIs to drug information sources Complex queries Functional composition
Interoperability among API functions Definition Implementation
RxMix demo
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Introduction
Olivier Bodenreider
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Motivation
Biomedical vocabularies are used as reference knowledge sources
They can be used programmatically through Application Programming Interfaces (APIs) Unified Medical Language Server (UMLS) BioPortal RxNorm
Difficult to compose complex queries across multiple APIs
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Drug information sources
Publicly available RxNorm NDF-RT RxTerms RxImageAccess
Created/distributed by NLM Datasets Application Programming Interfaces (APIs)
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Drug information sources
RxNorm Developed by NLM Normalized names and codes for drug entities Relations among drug entities form a graph
NDF-RT National Drug File-Reference Terminology Developed by the Veterans Health Administration Generic drugs described in terms of their active
ingredients, mechanisms of action, physiologic effects, and therapeutic intent (indications and contraindications)
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Drug information sources
RxTerms Developed at NLM Drug interface terminology derived from RxNorm for
prescription writing or medication history recording RxImageAccess
Developed at NLM High-definition images for oral solid
dose forms (“pills”), with additional metadata, for pill identification purposes
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Example use case
Find all the brand name products available for a given generic drug, whose identity is known by the FDA unique ingredient identifier code (UNII)
Workflow
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RxNorm ID (ingredient)
RxNorm ID (branded drug)
FDA UNII (ingredient)
findRxcuiById getRelatedByType
RxNorm API
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Interoperability among API functions
Jonathan Mortensen
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Objectives
To enable an end-user to create complex queries to drug information sources through functional composition
Complex query = workflow Sequence of web service functions Function interoperability driven by an ontology
Running example: Application to two different web services to drug information sources RxNorm API NDF-RT API – National Drug File-Reference
Terminology
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Web service annotation
Several web service annotation and composition frameworks SAWSDL (Semantic Annotations for WSDL and XML
Schema) – W3C SSWAP (Simple Semantic Web Architecture and Protocol)
– U. Arizona SADI (Semantic Automated Discovery and Integration) – U.
British Columbia Taverna – U. Manchester
Our approach Difficult to retrofit our services to these frameworks Use of an ontology in the background, not in the payload
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Methods
Problem: Determine and represent interoperability among RxNorm and NDF-RT API functions based on their input and output
Semantic representation of input and output Captured in an OWL ontology
Definition of interoperability between two functions Modeled through rules
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Ontology of functions
Developed in OWL using Protégé Main classes
Service (e.g., RxNorm, NDF-RT) Function: input and output parameters Function parameter: semantics of identifiers
Examples RxNorm API has_function findRxcuiByID findRxcuiById has_input id_type findRxcuiById has_input id findRxcuiById has_output RxCUI RxNorm API has_function getRelatedByType getRelatedByType has_input RxCUI
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Main class hierarchy
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Class “Service”
The 4 APIs are instances of the class Service 19
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Class “Function”
All API functions are instances of the class Function 20
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Function “findRxcuiById”
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source
input 1
input 2
input 3 output
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Function “findRxcuiById”
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source
input 1
input 2
input 3
output
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Function “getRelatedByType”
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input 1
output
input 2
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Function “getRelatedByType”
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input 1 output
input 2 …
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Rules of interoperability
Main rule – If the input of B matches the output of A, then A is potentially interoperable with B
Additional rules Interoperability between generic IDs and specific IDs in
the input or output of functions Example
A: rxnorm:findRxcuiById has_output RxCUI B: rxnorm:getRelatedByType has_input RxCUI input of B matches the output of A
=> rxnorm:getRelatedByType interoperable_with rxnorm:findRxcuiById
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findRxcuiById → getRelatedByType
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Implementation
The OWL ontology supports the interoperability rules
Interoperability relations inferred from the rules support the determination of interoperability for a given pair of functions
The ontology and the interoperability relations drive The validation of workflows The graphical interface for creating workflows
Only allowable functions are proposed in the menu
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Production rules (SWRL)
If the input of c matches the output of a Then c interoperable with a (i.e., c can follow a)
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Implementation
Rules applied through a reasoner in Protégé HermIT
Inferred properties added to the knowledge base Interoperable_with properties
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Properties before/after applying rules
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RxMix demo
Olivier Bodenreider
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“Real-life” use case
Find all the NDC codes for a given allergy class (e.g., barbiturates) Input: [NDF-RT] Barbiturates (N0000008016) Output: [RxNorm] list of NDC codes
Complex workflow RxNorm ID
(SCD/SBD)
201628 Amytal Sodium 100 MG/ML Injectable Solution […]
42998030301 […]
NDC code NDF-RT ID (chem. ingr.)
N0000008016 Barbiturates
name
Barbiturates
NDF-RT ID (drug/ingr.)
N0000005827 Amobarbital […]
RxNorm ID (ingredient)
719 Amobarbital […]
findConceptsByName getRel.ConceptsByRev.Role findRxcuiById getRelatedByType getNDCs
http://mor.nlm.nih.gov/RxMix/
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http://mor.nlm.nih.gov/RxMix/
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RxNorm ID (SCD/SBD) NDC code NDF-RT ID
(chem. ingr.) name NDF-RT ID (drug/ingr.)
RxNorm ID (ingredient)
findConceptsByName getRel.ConceptsByRev.Role findRxcuiById getRelatedByType getNDCs
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RxNorm ID (SCD/SBD) NDC code NDF-RT ID
(chem. ingr.) name NDF-RT ID (drug/ingr.)
RxNorm ID (ingredient)
findConceptsByName getRel.ConceptsByRev.Role findRxcuiById getRelatedByType getNDCs
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RxNorm ID (SCD/SBD) NDC code NDF-RT ID
(chem. ingr.) name NDF-RT ID (drug/ingr.)
RxNorm ID (ingredient)
findConceptsByName getRel.ConceptsByRev.Role findRxcuiById getRelatedByType getNDCs
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RxNorm ID (SCD/SBD) NDC code NDF-RT ID
(chem. ingr.) name NDF-RT ID (drug/ingr.)
RxNorm ID (ingredient)
findConceptsByName getRel.ConceptsByRev.Role findRxcuiById getRelatedByType getNDCs
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RxNorm ID (SCD/SBD) NDC code NDF-RT ID
(chem. ingr.) name NDF-RT ID (drug/ingr.)
RxNorm ID (ingredient)
findConceptsByName getRel.ConceptsByRev.Role findRxcuiById getRelatedByType getNDCs
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RxNorm ID (SCD/SBD) NDC code NDF-RT ID
(chem. ingr.) name NDF-RT ID (drug/ingr.)
RxNorm ID (ingredient)
findConceptsByName getRel.ConceptsByRev.Role findRxcuiById getRelatedByType getNDCs
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Complete workflow
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Add input and run (interactively)
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Output
Over 1000 NDCs retrieved
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Script of the demo RxMix overview
documentation is integrated Objective: Build a workflow
Find all the NDC codes for a given allergy class (e.g., barbiturates) Steps
[at first, all functions are available] 1) NDF-RT:findConceptsByName
select INGREDIENT_KIND [show output in mouse over] [show that only the functions compatible with the output are listed] 2) NDF-RT:getRelatedConceptsByReverseRole
role_type = has_ingredient transitive = 1 [show access to the documentation]
[show that the parameter passed between functions is listed] [cross over to RxNorm] 3) RxNorm:findRxcuiById
[NUI is already preselected -- only element from the output to match the input] 4) RxNorm:getRelatedByType
click SCD ctrl-click SBD
5) RxNorm:getNDCs [look at the complete workflow] Input value: barbiturates Execute workflow: Run
takes about 10 seconds Output
over 1000 NDCs Can save the workflow for reuse Can run any workflow on a list of input values (batch mode) Library of workflows
Find the National Drug Codes (NDCs) for clinical drugs of an ingredient fairly close to what we did
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Batch mode
Find all the NDC codes for generic packs in RxNorm
Simple workflow
Batch mode Iterate over all the generic packs in RxNorm (GPCK)
00378727253 […]
RxNorm ID (GPCK)
748961 {28 (Norethindrone 0.35 MG Oral Tablet) } Pack
[…]
NDC code
getNDCs
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Create workflow
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Select input and output
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JSON output
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Examples of use cases
Finding clinical drugs which may cause allergic reactions
Finding interactions to RxNorm clinical drugs Finding NDF-RT ingredients from RxNorm
clinical drugs Finding VA classes for RxNorm clinical dose
forms Finding brand names from clinical drug strings
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Library of common use cases integrated in RxMix
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Summary
Web service composition model for the RxNorm and NDF-RT APIs
Enables an end-user to create complex queries to drug information sources (“workflows”)
Our model supports common use cases, including checking interactions for RxNorm drugs and deploying allergy lists defined in reference to drug properties in NDF-RT
RxMix: http://mor.nlm.nih.gov/RxMix/
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Medical Ontology Research
Olivier Bodenreider
Lister Hill National Center for Biomedical Communications Bethesda, Maryland - USA
Contact: Web:
[email protected] mor.nlm.nih.gov