[PDF] - Ci4SeR Curation Interface for Semantic Resources Evaluation with PDF Document

SLIDE 1

Ci4SeR

SOUVIGNET Julien SOUVIGNET Julien, , ASFARI Hadyl, DECLERCK Gunnar, LARDON Jérémy, ASFARI Hadyl, DECLERCK Gunnar, LARDON Jérémy, TROMBERT-PAVIOT Béatrice, JAULENT Marie-Christine, BOUSQUET Cédric TROMBERT-PAVIOT Béatrice, JAULENT Marie-Christine, BOUSQUET Cédric

INSERM 1142 – LIMICS, Paris, France CHU University of Saint-Etienne, France

Curation Interface for Semantic Resources Evaluation with Adverse Drug Reactions

SLIDE 2

Long-term Objective

Create and maintain an Ontology of Adverse Drug Reactions (OntoADR)
Formally define MedDRA terms using SNOMED-CT
Example:

Curatio Interfac fo Semant Resource SOUVIGNE Julien - INSERM U1142 – LIMIC MIE 2014 – Istanbul – Septembe 201

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“G GASTRIC

ASTRIC

BLEEDING

BLEEDING” (MEDDRA)

AXIOM 1 : HASFINDINGSITE SOME “S

STOMACH

TOMACH” (SNOMED-CT)

AXIOM 2 : HASASSOCIATEDMORPHOLOGY SOME “H

HEMORRHAGE

EMORRHAGE” (SNOMED-CT)

SLIDE 3

Context

Why MedDRA ?
Standard for Adverse Event reporting
First generation terminology
20k Preferred Terms
Why SNOMED-CT ?
Large medical coverage
400k concepts
Previous studies have already tried to map MedDRA with SNOMED-CT

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SLIDE 4

Research Status

One semantic resource: OntoADR
35k concepts
150k definitional axioms
Generated using multiple sources and through automatics methods
UMLS
NLP Methods
Syntactic methods
70% of MedDRA terms have at least one axiom

Curatio Interfac fo Semant Resource SOUVIGNE Julien - INSERM U1142 – LIMIC MIE 2014 – Istanbul – Septembe 201

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1) 1) Need Need for for other

ther

mappings mappings and/or and/or definitions definitions 2) 2) Need Need for expert for expert review review and/or and/or curation curation

SLIDE 5

Objectives

Manual review of MedDRA term definitions
Limited to 800 concepts
Expert validation of the existing definition
Completion of partial definitions
Creation of definition for currently undefined terms
Previous attempts showed that:
Protégé is not suitable
Spreadsheets are impractical
Others softwares too annotation oriented

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Need Need for a for a dedicated dedicated Graphical Graphical User User Interface Interface

SLIDE 6

Software Specifications

Target users
domain experts for the curation part
any user for the consultation part
Desired features
Search for a given term using id or string match;
Display of a list of concepts to define with optional user-defined list;
Display of a given term definition (list of axioms);
Validation/Invalidation of an axiom
Insertion of a new axiom, by selecting a property and a concept.
…

Curatio Interfac fo Semant Resource SOUVIGNE Julien - INSERM U1142 – LIMIC MIE 2014 – Istanbul – Septembe 201

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SLIDE 7

Ci4SeR

Curation Interface for Se SOUVIGNET Julien - INSERM MIE 2014 – Istanbul – 1

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1. Search 2. List 3. Definition 4. Validation buttons 5. Axioms insertion 6. Expert icon 7. Automatic proposals 8. Comments

1 2 3 4 5 6 7 8

SLIDE 8

Expert work

Manual expert validation
Medical dictionnaries & multiple sources
120 hours over 5 months
Work on first importance topics in Pharmacovigilance
Bullous eruptions, acute renal failure, anaphylactic shock, rhabdomyolysis, aplastic anemia /

pancytopenia, cardiac valve fibrosis, etc.

Expert role
Valid/Invalid
Improve (narrower or broader)
Enrich (new definitions)

Curatio Interfac fo Semant Resource SOUVIGNE Julien - INSERM U1142 – LIMIC MIE 2014 – Istanbul – Septembe 201

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SLIDE 9

Result example

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“G GASTRIC

ASTRIC

BLEEDING

BLEEDING”

HASFINDINGSITE SOME “S STOMACH

TOMACH”

+ HASFINDINGSITE SOME “U UPPER

PPER

GASTROINTESTINAL

TRACT

STRUCTURE

STRUCTURE”

HASASSOCIATEDMORPHOLOGY SOME “H HEMORRHAGE

EMORRHAGE”

+ OCCURSAFTER SOME “G GASTROINTESTINAL

ASTROINTESTINAL

ULCER

ULCER”

+ DUETO SOME “H HELICOBACTER

ELICOBACTER

PYLORI

GASTROINTESTINAL

TRACT

INFECTION

INFECTION”

+ HASDEFINITIONALMANIFESTATION SOME “A ABDOMINAL

BDOMINAL

PAIN

PAIN”

+ HASDEFINITIONALMANIFESTATION SOME “M MELENA

ELENA”

+ HASDEFINITIONALMANIFESTATION SOME “V VOMIT

OMIT :

: BLOOD

BLOOD

PRESENT

”

SLIDE 10

Preliminary Results

783 terms defined
1369 properties validated
488 invalidated properties
5333 new properties
80 narrower & 12 broader

Curatio Interfac fo Semant Resource SOUVIGNE Julien - INSERM U1142 – LIMIC MIE 2014 – Istanbul – Septembe 201

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Before After

Approx. 2.63 relations

per definition in average

Approx. 8.45 relations

per definition in average

SLIDE 11

Preliminary Results

Before Ci4SeR, our team

already tried to define MedDRA terms manually

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Before After +68% +486%

SLIDE 12

Discussion & Perspectives

OntoADR is based on partial definitions
Lots of new axioms
Some invalid definitions
Interface is time-saving
Time spent : 783 terms defined in 5 month (not full time)
Interface encourages completeness and accuracy
Need for collaboration with other experts

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SLIDE 13

Thank you for your attention !

Ci4SeR

SOUVIGNET Julien SOUVIGNET Julien, , ASFARI Hadyl, DECLERCK Gunnar, LARDON Jérémy, ASFARI Hadyl, DECLERCK Gunnar, LARDON Jérémy, TROMBERT-PAVIOT Béatrice, JAULENT Marie-Christine, BOUSQUET Cédric TROMBERT-PAVIOT Béatrice, JAULENT Marie-Christine, BOUSQUET Cédric

INSERM 1142 – LIMICS, Paris, France CHU University of Saint-Etienne, France

Curation Interface for Semantic Resources Evaluation with Adverse Drug Reactions