Specimen
Epic equivalent: Specimen collection records / Surgical pathology / LIMS / Biobank systems
The specimen table captures biological samples collected from a patient — blood, tissue, urine, swabs, and other materials sent for lab analysis, pathology review, or biobanking. At Emory, Winship populates cancer biospecimen data through OpenSpecimen integration.
Each row is a single specimen. Note: the actual lab results go in measurement — this table captures sample metadata.
Epic-to-OMOP Field Mapping
Field reference (click to expand)
| OMOP Field | Epic Equivalent | What It Captures |
|---|---|---|
specimen_id |
Specimen accession ID | Unique identifier |
person_id |
Patient ID / MRN | Links to the patient |
specimen_concept_id |
Sample type | Standardized type (blood, urine, tissue, etc.) |
specimen_type_concept_id |
Data provenance | How captured (EHR, biobank, etc.) |
specimen_date |
Collection date | When the sample was collected; specimen_datetime has time |
quantity |
Amount collected | Volume or size (if available) |
unit_concept_id |
Unit | mL, grams, etc. |
anatomic_site_concept_id |
Collection site | Body part (e.g., "left breast", "bone marrow") |
disease_status_concept_id |
Disease context | Whether collected in disease state (e.g., tumor tissue) |
specimen_source_id |
Local specimen ID | Original ID from the lab system |
specimen_source_value |
Local name/code | Original description from EHR/LIMS |
What to Watch For
Common pitfalls
- Specimens are not measurements
- The lab values go in
measurement. This table captures what was collected, not what the result was. - Often underused
- Many OMOP implementations don't fully populate this table unless biospecimen workflows are in place.
- Critical for omics
- This table becomes essential when linking to sequencing, proteomics, or precision medicine data.
Research Patterns
| Question | Tables Involved |
|---|---|
| Tumor tissue samples from breast cancer patients | specimen (tissue + anatomic site) + condition_occurrence (breast cancer) |
| Blood collection timing relative to drug start | specimen.specimen_date + drug_exposure.drug_exposure_start_date |
| CSF samples for diagnostic testing | specimen_concept_id (CSF) |
| Archived FFPE samples for lung cancer cases | specimen_type_concept_id + anatomic_site_concept_id + condition_occurrence |
| Biopsy-to-pathology report turnaround time | specimen.specimen_date + note.note_date (pathology notes) |