Patoloji Bilgi Yönetim Sistemi (LIS)

Notes, integration guides, and operational documentation for the pathology laboratory information system — the upstream source of nearly all structured research data.

Purpose

Document the LIS as a research data source: what the data model is, which interfaces exist, how to request a de-identified cohort, and which fields can actually be trusted.

Data used

The LIS itself. Case / specimen / block / slide data model with accession numbering.

Methods

Topics documented: structure (the data model and accession numbering); interfaces (HL7 messaging, Kris report exports, scanner integration endpoints); research data pulls (how to request a de-identified cohort, which fields are available, which are unreliable); quality signals (turnaround, amendment rates, missing-field rates); interoperability bridges to QuPath, Sectra, and the analytics stack.

Current state / open questions

Active, registered as ongoing project “patoloji bilgi yönetim sistemi”. Governance rule: all research pulls go through the de-identification pipeline before touching a repo, and research repos consume cleaned tables only. Documented pitfalls, all of which are data-quality traps worth taking seriously: field reliability varies by subspecialty practice and presence of a field does not imply trustworthiness; the LIS records several distinct timestamps (received, grossed, signed-out, amended) each with a specific documented meaning; accession numbers are identifying even without names because their patterns are, so research exports use hashed accession IDs exclusively.

Downstream consumers: Extract Report Text for narrative content, Scanning Time in Real Life for timing data, Konsultasyon for consultation tracking.

Derived from: lis/lis.qmd, patoloji-ve-bilisim/patolojivebilisim.qmd.