corneliu malciu, cofounder - devdays.com...corneliu malciu, cofounder. in a few words. 1 hospital =...
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November 20-22, Amsterdam | @HL7 @FirelyTeam | #fhirdevdays | www.devdays.com
Pyrog: an open-source mapping tool and ETL for FHIR
Corneliu MALCIU, cofounder
In a few words
1 Hospital = 100 independent softwares whose proprietary databases need to be synchronized
Remember when you were trying to install a new game
on you old cell phone?
An obsolete architecture...
✗ Difficult access to Data
✗ High costs
✗ No data governance
30 000 deaths1
Each year in France due to a lack of communication in healthcare
… and its consequences
80% time3
Lost in data processing for each research project.
¹ French Ministry of Social Affairs and Health, B. Bégaud et D. Costagliola, Rapport sur la surveillance et la promotion du bon usage du médicament en France (2013)² French Ministry of Social Affairs and Health, Atlas des systèmes d’information hospitaliers (2018)³ Figure Eight, 2016 Data science report (2016)
30k€ per software2
Spent for each deployment to access clinical data. Half projects do not make it to production.
Now you just download it from your app store!
ARKHN : Data integration and standardization from proprietary formats to FHIR
Our solution: a common platform
✔ Clean and accessible Data
✔ Low deployment costs
✔ Full Data sovereignty
. for everyone
Data integration for Healthcare facilities
1
FHIR API & server for software developers
2
3 Network access for data users & hospitals
Products & Tools
Mapping DB to FHIR: PYROG1
github.com/arkhn
Products & Tools
Mapping DB to FHIR: PYROG1
ETL to FHIR: FHIR PIPE2
github.com/arkhn
Products & Tools
Mapping DB to FHIR: PYROG1
ETL to FHIR: FHIR PIPE2
Native FHIR storage: PY FHIR STORE3
github.com/arkhn
Products & Tools
Mapping DB to FHIR: PYROG1
ETL to FHIR: FHIR PIPE2
Native FHIR storage: PY FHIR STORE3
Flask API: WAREHOUSE API4
github.com/arkhn
Products & Tools
Mapping DB to FHIR: PYROG1
ETL to FHIR: FHIR PIPE2
Native FHIR storage: PY FHIR STORE3
Some demo apps: TIMELINE, DASHBOARD...5
Flask API: WAREHOUSE API4
github.com/arkhn
Products & Tools
Mapping DB to FHIR: PYROG1
ETL to FHIR: FHIR PIPE2
Native FHIR storage: PY FHIR STORE3
Some demo apps: TIMELINE, DASHBOARD...5
Network access & Federated Learning6
Flask API: WAREHOUSE API4
github.com/arkhn
An open source mapping
tool for .
PYROG
github.com/arkhn/pyrog
~ 10K tables~ 100k columns
~ 10K tables~ 100k columns
~ 10K tables~ 100k columns
- FHIR friendly- Documentation
Required features:
- FHIR friendly- Documentation- Cleaning scripts
Required features:
M → male
F → female
* → unknown
PAT_ID GENDER
... ...
106 F
107 M
108 F
... ...
- FHIR friendly- Documentation- Cleaning scripts
Required features:
- Joins
SELECT COUNTRY_LBL FROM COUNTRY LEFT JOIN ...
PAT_ID COUNTRY_ID
... ...
106 1
107 1
108 3
... ...
COUNTRY_ID COUNTRY_LBL
1 Neetherlands
2 France
... ...
PAT_ADR COUNTRY
- FHIR friendly- Documentation- Cleaning scripts
Required features:
- Joins- Instantiation
BLOOD_PRESSURE → Observation (Blood Pressure)
GLYCEMIA → Observation (Glycemia)
- FHIR friendly- Documentation- Cleaning scripts
Required features:
- Joins- Instantiation- DB Exploration
~ 10K tables~ 100k columns
Storing mapping rules with .
SOURCE
[RESSOURCE] FHIR_TYPE [ATTRIBUTE] input_column [join] script [attributes]
Mimic
Patient Gender
datamodel.prisma
type Source { resources: [Resource!]!}
type Resource { fhirType: FhirType! attributes: [Attribute!]!}
type Attribute { inputColumn: InputColumn join: Join attributes: [Attribute!]}
(Simplified) Data Model
Storing mapping rules with .
(Simplified) Data Model Query
SOURCE
[RESSOURCE] FHIR_TYPE [ATTRIBUTE] input_column [join] script [attributes]
Mimic
Patient Gender
Storing mapping rules with .
(Simplified) Data Model Query
Json response
SOURCE
[RESSOURCE] FHIR_TYPE [ATTRIBUTE] input_column [join] script [attributes]
Mimic
Patient Gender
What next?
● SQL Parser SELECT … FROM … LEFT JOIN … LEFT JOIN … LEFT JOIN … LEFT JOIN ...
What next?
● SQL Parser
● FHIR Profiling
What next?
● SQL Parser
● FHIR Profiling
● Mapping suggestion
github.com/arkhn/pagai
What next?
● SQL Parser
● FHIR Profiling
● Mapping suggestion
● Use StructureMap?
7 people (hiring!)20+ contributors (join us!)
Don’t miss:● Corneliu Malciu
Startup Track
● Florian BriandBuilding a Multi-Purpose Stack Using FHIR as a Persistence Layer
● Thomas Walter, Lumio MedicalData Privacy in AI using Federated Learning on FHIR
github.com/arkhn
www.devdays.com
Corneliu MALCIU, [email protected]