Medizininformatik Initiative - Implementation Guide - Bioprobendaten v2026
Terminologien
Soweit möglich sollen Terminologien und eindeutige Codes verwendet werden, die internationalen Standards entsprechen.
Zur eindeutigen Identifizierung von Additiven, Containertypen, Probenart und Verarbeitungstyp wird die Verwendung von SNOMED CT empfohlen. Die ValueSets sind im Specimen-Profil hinterlegt.
Für Body Site kann neben SNOMED CT auch die International Classification of Diseases for Oncology, v.3, Topography (ICD-O-3) verwendet werden.
Die entsprechenden Value Sets wurden erstellt.
Standard PREanalytical Code (SPREC)
Der SPREC 4.0 (Standard PREanalytical Code) wurde entwickelt, um ein umfassendes und einfach zu implementierendes Werkzeug zur Dokumentation der präanalytischen Sammlung, Verarbeitung und Lagerung von Bioproben bereitzustellen. Viele Elemente der SPREC, wie z. B. Probentypen, sind bereits in SNOMED CT INTERNATIONAL enthalten, viele aber auch nicht. Insbesondere der Modus der Zentrifugation lässt sich mit den aktuellen SNOMED International Codes nicht darstellen.
Die SNOMED CT Codes für SPREC-Begriffe wurden von der SNOMED CT Spanish Extension als Ergebnis der Arbeit des Spanish Network of Biobanks zu Definition des Biobank-Refsets in SNOMED CT veröffentlicht.
Die gleichen Codes werden für die SNOMED International Edition eingereicht werden. Das Spanish Network of Biobanks und das Spanish National Release Center haben sich freundlicherweise bereit erklärt, die SNOMED CT Codes für SPREC noch vor der Veröffentlichung in der SNOMED International Edition mit der Medizininformatik-Initiative zu teilen. Insbesondere die Codes für den Modus der Zentrifugation können zusätzlich zu 73373003 |Specimen centrifugation (procedure)| in Specimen.processing.procedure verwendet werden.
| Code | Display EN |
|---|---|
| 1001000257109 | Centrifugation at less than 1000g (relative centrifugal force) for 30 minutes without braking ramp at room temperature between 18 and 28 degrees Celsius |
| 911000257109 | Centrifugation at less than 3000g (relative centrifugal force) between 10 and 15 minutes with braking ramp at room temperature between 18 and 28 degrees Celsius |
| 931000257100 | Centrifugation at less than 3000g (relative centrifugal force) between 10 and 15 minutes with braking ramp at temperature between 2 and 10 degrees Celsius |
| 901000257107 | Centrifugation at less than 3000g (relative centrifugal force) between 10 and 15 minutes without braking ramp at room temperature between 18 and 28 degrees Celsius |
| 921000257102 | Centrifugation at less than 3000g (relative centrifugal force) between 10 and 15 minutes without braking ramp at temperature between 2 and 10 degrees Celsius |
| 2094511000122105 | Centrifugation at less than 3000g (relative centrifugal force) more than 15 minutes with braking ramp at temperature between 2 and 10 degrees Celsius |
| 2094501000122107 | Centrifugation at less than 3000g (relative centrifugal force) more than 15 minutes without braking ramp at temperature between 2 and 10 degrees Celsius |
| 981000257101 | Centrifugation at more than 10000g (relative centrifugal force) between 10 and 15 minutes with braking ramp at room temperature between 18 and 28 degrees Celsius |
| 991000257104 | Centrifugation at more than 10000g (relative centrifugal force) between 10 and 15 minutes with braking ramp at temperature between 2 and 10 degrees Celsius |
| 2094521000122104 | Centrifugation between 10000 y 80000g (relative centrifugal force) between 30 and 120 minutes with braking ramp at temperature between 2 and 10 degrees Celsius |
| 2094491000122101 | Centrifugation between 3000 - 6000 g (relative centrifugal force) in less than 10 minutes without brake ramp at room temperature between 18 and 28 degrees Celsius |
| 941000257105 | Centrifugation between 3000 and 6000g (relative centrifugal force) between 10 and 15 minutes with braking ramp at room temperature between 18 and 28 degrees Celsius |
| 951000257108 | Centrifugation between 3000 and 6000g (relative centrifugal force) between 10 and 15 minutes with braking ramp at room temperature between 2 and 10 degrees Celsius |
| 2094541000122109 | Centrifugation between 3000 and 6000g (relative centrifugal force) 15 to 30 minutes with brake ramp at room temperature between 18 and 28 degrees Celsius |
| 2094551000122106 | Centrifugation between 3000 and 6000g (relative centrifugal force) 15 to 30 minutes without brake ramp at room temperature between 18 and 28 degrees Celsius |
| 2094561000122108 | Centrifugation between 3000 and 6000g (relative centrifugal force) 30 to 60 minutes without brake ramp at room temperature between 18 and 28 degrees Celsius |
| 961000257106 | Centrifugation between 6000 and 10000g (relative centrifugal force) between 10 and 15 minutes with braking ramp at room temperature between 18 and 28 degrees Celsius |
| 971000257103 | Centrifugation between 6000 and 10000g (relative centrifugal force) between 10 and 15 minutes with braking ramp at room temperature between 2 and 10 degrees Celsius |
| 2094531000122101 | Ultracentrifugation at more than 80000g (relative centrifugal force) at temperature between 2 and 10 degrees Celsius |
Für die Achsen des SPREC, die sich bereits auf existierende SNOMED Codes mappen lassen, wurden ConceptMaps entwickelt. Diese umfassen nicht immer alle möglichen Ausprägungen, da aufgrund der SPREC Werte nicht immer ein eindeutiges Mapping möglich ist. Hier sollte ein Mapping aufgrund der im Quellsystem verfügbaren Daten erfolgen, alternativ kann auf die oben beschriebenen spanischen Codes ausgewichen werden.
Mappings
Die im Folgenden aufgeführten Mappings sind als ConceptsMaps maschinenlesbar als Teil des zu diesem IG gehörenden Packages verfügbar und können z.B. als Teil eines ETL-Prozesses oder mit einem Terminologieserver genutzt werden.
Probentypen
Die Codes werden typischerweise im Specimen.type verwendet werden.
| Source | Equivalence | Target |
|---|---|---|
| ASC (Ascites fluid) | equivalent | 309201001 (Ascitic fluid sample (specimen)) |
| AMN (Amniotic fluid) | equivalent | 119373006 (Amniotic fluid specimen (specimen)) |
| BAL (Bronchoalveolar lavage) | equivalent | 258607008 (Bronchoalveolar lavage fluid sample (specimen)) |
| BLD (Blood (whole)) | equivalent | 258580003 (Whole blood specimen (specimen)) |
| BMA (Bone marrow aspirate) | equivalent | 396997002 (Specimen from bone marrow obtained by aspiration (specimen)) |
| BMK (Breast milk) | equivalent | 446676001 (Expressed breast milk specimen (specimen)) |
| BUF (Nondensity-gradient-centrifugation-separated buffy coat, viable) | wider | 258587000 (Buffy coat (specimen)) |
| BFF (Nondensity-gradient-centrifugation-separated buffy coat, nonviable) | wider | 258587000 (Buffy coat (specimen)) |
| CEL (Density-gradient-centrifugation-separated mononuclear cells, viable) | wider | 404798000 (Peripheral blood mononuclear cell (cell)) |
| BON (Bone) | equivalent | 430268003 (Specimen from bone (specimen)) |
| CRD (Cord blood) | equivalent | 122556008 (Cord blood specimen (specimen)) |
| CSF (Cerebrospinal fluid) | equivalent | 258450006 (Cerebrospinal fluid sample (specimen)) |
| EBC (Exhaled breath condensate) | equivalent | 418468008 (Exhaled breath condensate (substance)) |
| FNA (Cells from fine needle aspirate) | wider | 122550002 (Specimen obtained by fine needle aspiration procedure (specimen)) |
| HAR (Hair) | equivalent | 119326000 (Hair specimen (specimen)) |
| NAL (Nails) | equivalent | 119327009 (Nail specimen (specimen)) |
| NAS (Nasal washing) | equivalent | 16224371000119105 (Nasal lavage fluid sample (specimen)) |
| PLC (Placenta) | equivalent | 119403008 (Specimen from placenta (specimen)) |
| PFL (Pleural fluid) | equivalent | 418564007 (Pleural fluid specimen (specimen)) |
| PTF (Peritoneal fluid) | equivalent | 168139001 (Peritoneal fluid specimen (specimen)) |
| RBC (Red blood cells) | equivalent | 119351004 (Erythrocyte specimen (specimen)) |
| SEM (Semen) | equivalent | 119347001 (Seminal fluid specimen (specimen)) |
| SPT (Sputum) | equivalent | 119334006 (Sputum specimen (specimen)) |
| SYN (Synovial fluid) | equivalent | 119332005 (Synovial fluid specimen (specimen)) |
| TER (Tears) | equivalent | 122594008 (Tears specimen (specimen)) |
| TTH (Teeth) | equivalent | 430319000 (Specimen from tooth (specimen)) |
| SER (Serum) | equivalent | 119364003 (Serum specimen (specimen)) |
| SAL (Saliva) | equivalent | 119342007 (Saliva specimen (specimen)) |
| STL (Stool) | equivalent | 119339001 (Stool specimen (specimen)) |
| SWT (Sweat) | equivalent | 122569007 (Sweat specimen (specimen)) |
| U24 (24 h urine) | equivalent | 276833005 (24 hour urine sample (specimen)) |
| URN (Urine, random (‘‘spot’’)) | equivalent | 278020009 (Spot urine sample (specimen)) |
| URM (Urine, first morning) | wider | 258575007 (Early morning urine sample (specimen)) |
| URT (Urine, timed) | equivalent | 409821005 ( Timed urine specimen (specimen)) |
| DWB (Dried whole blood (e.g., Guthrie cards)) | equivalent | 119294007 (Dried blood specimen (specimen)) |
| PL1 (Plasma, single spun) | wider | 119361006 (Plasma specimen (specimen)) |
| PL2 (Plasma, double spun) | wider | 119361006 (Plasma specimen (specimen)) |
Fixierungsart
Die Codes werden typischerweise in einer Substance verwendet werden, die als Additiv referenziert wird.
| Source | Equivalence | Target |
|---|---|---|
| ACA (Nonaldehyde with acetic acid) | wider | 2869004 (Acetic acid (substance)) |
| ALD (Aldehyde based) | wider | 768750002 (Product containing aldehyde (product)) |
| ETH (Alcohol based) | wider | 333164008 (Product containing alcohol (product)) |
| FOR (Nonbuffered formalin) | wider | 431510009 (Formalin (substance)) |
| NBF (Neutral buffered formalin) | equivalent | 434162003 (Neutral buffered formalin (substance)) |
| OCT (Optimum cutting temperature medium) | wider | 433469005 (Frozen section embedding medium (substance)) |
Primärcontainer
Diese ConceptMap kann nur als Tabelle dargestellt werden, da die aus dem SPREC-Code abgeleiteten Informationen zum einen den Specimen.container.type, zum anderen den Code der im Specimen.container.additive verlinkten Substance betreffen. Die Informationen zum Container sind im target selbst, die zur Substance im target.product enthalten. Die Kapazität des Containers, die teilweise mit im SPREC codiert ist, soll gesondert über Specimen.container.capacity abgebildet werden (als Quantity). Die Temperaturbedingungen der Lagerung sollen ebenfalls gesondert über die Extension Temperaturbedingungen erfasst werden.
| Source Concept | Equivalence | Target Concept | Comment | |
|---|---|---|---|---|
| Code [http://www.isber.org/sprec/type-of-primary-container] | Code [http://snomed.info/sct] | http://hl7.org/fhir/StructureDefinition/Specimen#Specimen.container.additive[x] [] | ||
| ACD (Acid citrate dextrose) | Unmatched | 75399008 (Citric acid (substance)) | ||
| CAT (Serum separator tube without clot activator) | Narrower | 702256007 (Non-evacuated blood collection tube, no additive (physical objec)) | Use only for non-evacuated blood collection tubes. | |
| Narrower | 702278000 (Evacuated blood collection tube, no additive and metal-free (physical object)) | Use only for metal-free evacuated blood collection tubes. | ||
| CPD (Citrate phosphate dextrose) | Unmatched | 412546005 (Sodium citrate (substance)) | ||
| CIF (Citrate fluoride) | Unmatched | 412546005 (Sodium citrate (substance)) | ||
| CPT (Cell Preparation Tube citrate) | Wider | 706052002 (Evacuated blood collection tube (physical object)) | 59351004 (Citrate (substance)) | |
| CPH (Cell Preparation Tube heparin) | Wider | 706052002 (Evacuated blood collection tube (physical object)) | 372877000 (Heparin (substance)) | |
| CSV (Aldehyde-based stabilizer for CTCs) | Unmatched | 768750002 (Product containing aldehyde (product)) | ||
| EDG (EDTA and gel) | Unmatched | 69519002 (Ethylenediamine tetra-acetate (substance)) | ||
| GLS (Glass) | Equivalent | 76123001 (Glass tube, device (physical object)) | ||
| HEP (Lithium heparin) | Narrower | 702284002 (Non-evacuated blood collection tube, lithium heparin (physical object)) | 85899009 (Lithium (substance)) | Use only for non-evacuated blood collection tubes. |
| HIR (Hirudin) | Unmatched | 414407009 (Hirudin (substance)) | ||
| LHB (Lithium heparin and rubber plug) | Wider | 702284002 (Non-evacuated blood collection tube, lithium heparin (physical object)) | 85899009 (Lithium (substance)) | |
| LHG (Lithium heparin and gel) | Narrower | 767390000 (Evacuated blood collection tube with heparin lithium and gel separator (physical object)) | Use only for evacuated blood collection tubes. | |
| Narrower | 702285001 (Sterile lithium heparin non-evacuated blood collection tube with gel separator (physical object)) | Use only for sterile non-evacuated blood collection tubes. | ||
| Narrower | 702300005 (Non-evacuated blood collection tube, lithium heparin/gel separator, non-sterile (physical object)) | 85899009 (Lithium (substance)) | Use only for non-sterile non-evacuated blood collection tubes. | |
| ORG (Oragene collection container or equivalent) | Equivalent | 706058003 (Secretory specimen container (physical object)) | ||
| OMN (Stool collection container with DNA stabilizer) | Wider | 706047007 (Fecal specimen container (physical object)) | ||
| PAX (PAXgene blood RNA) | Wider | 702280006 (Evacuated blood collection tube, ribonucleic acid stabilizer (physical object)) | ||
| PED (Potassium EDTA) | Unmatched | 69519002 (Ethylenediamine tetra-acetate (substance)) | ||
| PET (Polyethylene tube sterile) | Equivalent | 702269006:840560000=71463006 (|General specimen container, no additive, sterile (physical object)|:|Has compositional material| = |Polyethylene (substance)|) | ||
| PI1 (S8820 protease inhibitor tablets or equivalent) | Unmatched | 372528003 (Substance with protease inhibitor mechanism of action (substance)) | ||
| PIX (Protease inhibitors) | Unmatched | 372528003 (Substance with protease inhibitor mechanism of action (substance)) | ||
| PPS (Polypropylene tube sterile) | Equivalent | 702269006:840560000=256633009 (General specimen container, no additive, sterile (physical object)|:|Has compositional material| = |Polypropylene (substance)|) | ||
| SCI (Sodium citrate) | Narrower | 702296009 (Non-evacuated blood collection tube, sodium citrate (physical object)) | 412546005 (Sodium citrate (substance)) | Use only for non-evacuated blood collection tubes. |
| SED (Sodium EDTA) | Unmatched | 39972003 (Sodium (substance)) | ||
| SHP (Sodium heparin) | Narrower | 767382000 (Evacuated blood collection tube with heparin sodium (physical object) ) | 50045009 (Heparin sodium (substance)) | Use only for evacuated blood collection tubes. |
| SPO (Sodium fluoride/potassium oxalate) | Narrower | 702287009 (Non-evacuated blood collection tube, potassium oxalate/sodium fluoride (physical object) ) | 6910009 (Sodium fluoride (substance)) | Use only for non-evacuated blood collection tubes. |
| SST (Serum separator tube with clot activator) | Narrower | 702297000 (Non-evacuated blood collection tube, clot activator (physical object) ) | Use only for non-evacuated blood collection tubes. | |
| Narrower | 767384004 (Evacuated blood collection tube with clot activator (physical object) ) | Use only for evacuated blood collection tubes. | ||
| TEM (Tempus tube) | Wider | 702280006 (Evacuated blood collection tube, ribonucleic acid stabilizer (physical object)) | ||
Langzeitlagerung
Diese ConceptMap kann nur als Tabelle dargestellt werden, da die aus dem SPREC-Code abgeleiteten Informationen zum einen den Specimen.container.type, zum anderen den Code der im Specimen.container.additive verlinkten Substance betreffen. Die Informationen zum Container sind im target selbst, die zur Substance im target.product enthalten. Die Kapazität des Containers, die teilweise mit im SPREC codiert ist, soll gesondert über Specimen.container.capacity abgebildet werden (als Quantity). Die Temperaturbedingungen der Lagerung sollen ebenfalls gesondert über die Extension Temperaturbedingungen erfasst werden.
| Source Concept | Equivalence | Target Concept | Comment | |
|---|---|---|---|---|
| Code [http://www.isber.org/sprec/long-term-storage] | Code [http://snomed.info/sct] | http://hl7.org/fhir/StructureDefinition/Specimen#Specimen.container.additive[x] [] | ||
| A (PP tube) | Wider | 702269006:840560000=256633009 (General specimen container, no additive, sterile (physical object): Has compositional material=Polypropylene (substance)) | ||
| B (PP tube) | Wider | 702269006:840560000=256633009 (General specimen container, no additive, sterile (physical object): Has compositional material=Polypropylene (substance)) | ||
| V (PP tube) | Wider | 702269006:840560000=256633009 (General specimen container, no additive, sterile (physical object): Has compositional material=Polypropylene (substance)) | ||
| J (PP tube) | Wider | 702269006:840560000=256633009 (General specimen container, no additive, sterile (physical object): Has compositional material=Polypropylene (substance)) | ||
| K (PP tube) | Wider | 702269006:840560000=256633009 (General specimen container, no additive, sterile (physical object): Has compositional material=Polypropylene (substance)) | ||
| S (PP tube) | Wider | 702269006:840560000=256633009 (General specimen container, no additive, sterile (physical object): Has compositional material=Polypropylene (substance)) | ||
| T (PP tube) | Wider | 702269006:840560000=256633009 (General specimen container, no additive, sterile (physical object): Has compositional material=Polypropylene (substance)) | ||
| W (PP tube) | Wider | 702269006:840560000=256633009 (General specimen container, no additive, sterile (physical object): Has compositional material=Polypropylene (substance)) | ||
| C (Cryotube) | Wider | 702269006 (General specimen container, no additive, sterile (physical object)) | ||
| D (Cryotube) | Wider | 702269006 (General specimen container, no additive, sterile (physical object)) | ||
| E (Cryotube) | Wider | 702269006 (General specimen container, no additive, sterile (physical object)) | ||
| N (Cryotube) | Wider | 702269006 (General specimen container, no additive, sterile (physical object)) | ||
| F (Straw) | Narrower | 464601003 (Tissue storage straw (physical object)) | Der SNOMED Code gilt nur für Tissue straws. | |
| G (Straw) | Narrower | 464601003 (Tissue storage straw (physical object)) | Der SNOMED Code gilt nur für Tissue straws. | |
| H (Straw) | Narrower | 464601003 (Tissue storage straw (physical object)) | Der SNOMED Code gilt nur für Tissue straws. | |
| I (Straw) | Narrower | 464601003 (Tissue storage straw (physical object)) | Der SNOMED Code gilt nur für Tissue straws. | |
| O (Straw) | Narrower | 464601003 (Tissue storage straw (physical object)) | Der SNOMED Code gilt nur für Tissue straws. | |
| L (Microplate well) | Wider | 434822004 (Specimen well (physical object)) | ||
| M (Microplate well) | Wider | 434822004 (Specimen well (physical object)) | ||
| P (Paraffin block) | Unmatched | 311731000 (Paraffin wax (substance)) | ||
| U (Paraffin block) | Unmatched | 311731000 (Paraffin wax (substance)) | ||
| Q (Bag) | Equivalent | 463490008 (Medical bag (physical object)) | ||
| Z (Other) | Wider | 706437002 (Container (physical object)) | ||
Cell Line Ontology
Für Angaben im Zusammenhang mit Zellinien und Organoiden sollen Codes aus der Cell Line Ontology verwendet werden. Dabei wurde sich für die Darstellungsweise mit Prefix "CLO:" entschieden. Da es hier noch keine Vorgabe durch HL/ International gibt, kann es zu Fehlern mit Terminologieservern kommen, die die Darstellung mit "CLO_" gewählt haben. Sollte es dazu zu Problemem mit technischer Infrastruktur kommen, bitten wir um Meldung im MII-Zulip-Chat, um das Thema gemeinsam mit der SU-TermServ weiter bearbeiten zu können.