Access and validation

Governance details

Documents or webpages that describe the overall governance of the data source and processes and procedures for data capture and management, data quality check and validation results (governing data access or utilisation for research purposes).

FinOMOP_data_governance

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Biospecimen access

Are biospecimens available in the data source (e.g., tissue samples)?

Yes

Biospecimen access conditions

Hospital biobank can collect all kinds of biospecimen in different phases of the treatment based on patients' concent. E.g. DNA, serum, and plasma samples, fresh frozen tumor samples, SCF-samples and FFPE samples.

Access to subject details

Can individual patients/practitioners/practices included in the data source be contacted?

Yes

Description of data collection

All patients who visit the hospital are recorded in our IT system (Oberon). All visits, all procedures and given treatments have been recorded systematically in the electronic format. We use more than hundred different operational IT systems. For secondary use, the individual level data is pooled into a data lake. Data relevant for research is then collected through an ETL-process into a single analytical SQL data base. On top the research data base, we have the OMOP mapping and ETL processes built in collaboration with the other Finnish University Hospitals and the Institute of Health and Welbeing (FinOMOP Consortium). Patient events are mainly of the following types: outpatient visit (with a specific start and end time), inpatient episodes (with a specific start and end time) or additional clinical events (lab, radiology, procedure) with specific timestamps. The observation period for a patient starts from the earliest event and end at the latest event.
Event triggering registration

Event triggering registration of a person in the data source

Birth
Disease diagnosis
Start of treatment

Event triggering de-registration of a person in the data source

Other

Event triggering de-registration of a person in the data source, other

In the event of relocation to another county person is registered at the destination county. Patient history still stays in the data source.

Event triggering creation of a record in the data source

Any contact with HDSF/VarHa, first event.
Data source linkage

Linkage

Is the data source described created by the linkage of other data sources (prelinked data source) and/or can the data source be linked to other data source on an ad-hoc basis?

Yes

Linkage description, pre-linked

Information about deaths is loaded into ACI DW as batch transfer a few times a year

Linkage description, possible linkage

defined patient group in the hospital data base

Linked data source 1

Pre linked

Is the data source described created by the linkage of other data sources?

No

Data source, other

Data from many nation-wide health registries such as drug purchase, visual impairment, cancer, retirement due to a disease registries and many others, can be combined to the Turku University Hospital patient registry. The combination needs a specific research plan and data permit.

Linkage strategy

Combination

Linkage variable

SSN

Linked data source 2

Pre linked

Is the data source described created by the linkage of other data sources?

Yes

Data source, other

Statistics Finland

Linkage strategy

Deterministic

Linkage variable

Social security number

Linkage completeness

High completeness, deaths abroad can be missed
Data management specifications that apply for the data source

Data source refresh

Every 6 months

Informed consent for use of data for research

Not Required

Possibility of data validation

Can validity of the data in the data source be verified (e.g., access to original medical charts)?

Yes

Data source preservation

Are records preserved in the data source indefinitely?

Yes

Approval for publication

Is an approval needed for publishing the results of a study using the data source?

Yes

Data source last refresh

Common Data Model (CDM) mapping

CDM mapping

Has the data source been converted (ETL-ed) to a common data model?

Yes

CDM Mappings

Data source ETL CDM version

5.3.1

Data source ETL frequency

3,00 months

Data source ETL status

Completed