CINECA WP3 - Text Mining Integrated Pipeline - High Level Schematic Diagram

Coming ......

Models

LexMapr TM-Pipeline

for CINECA

SORTA

(by Chao Pang)

Dictionary*

UMLS

Lookup table

MetaMap

Match to exactly

one concept

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CINECA cohort

free text

Spelling corrector

Free text

normalized

Normalization pipeline

Exact match module

Learning to rank module

Getting more than two

candidates from MetaMap

Learning to rank

(new candidates order)

CUI

CUI

CUI

CUI

CUI

CUI

CUI

Simplified diagram of HES-SO/SIB text mining workflow

* N2C2, MedMentions data

still not normalized?

API concept

-disease

-drug

-gender

-procedure

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-HES-SO/SIB

-LexMapr

-SORTA

-Zooma/EBI

Input free text

API sketch: https://wireframe.cc/Vqu0ij

Load free text/semi-structured text from local file

API concept

Output: Normalized free text

Web API

Free text:

HEADACHE, BACK PAINS

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Concept type:

Disease

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Model:

HES-SO/SIB

Normalization pipeline

API input/output example

Input:

• Free text
• Concept
• Model

API input/output example (LexMapr)

ZOOMA

API input/output example: ZOOMA