Sample Type mappings
This file contains mappings of codes from SPREC V3.0 and 4.0, SNOMED CT, OMOP and HL7 FHIR for sample type to MIABIS sample type V1.1 and the detailed and aggregated sample type V1.0.
Mapping Format
The mapping is provided as markdown where each row maps a sample type code to the code in one of the other specifications. The columns are:
MAIBIS Sample Type V1.1: The detailed list of sample types in the V1.1.MAIBIS Aggregate Sample Type V1.0: The corresponding aggregate sample type in the V1.0.
How to Use
You can convert the markdown to a CSV file and load it into your application or use it in a database to convert between the different specifications.
Limitations
This mapping covers all MIABIS sample types, but only a subset of the mapped other specifications. For full coverage, refer to the official:
- SPREC V3.0 and V4.0 https://doi.org/10.1089/bio.2024.0010
- SNOMED CT https://browser.ihtsdotools.org/?perspective=full&conceptId1=123038009&edition=MAIN/2023-09-01&release=&languages=en
- OMOP https://athena.ohdsi.org/search-terms/terms
- HL7 FHIR https://terminology.hl7.org/3.1.0/CodeSystem-v2-0487.html
Contributions
Feel free to contribute to this mapping by opening an issue or submitting a pull request.
| MIABIS Sample Type V1.1 | MIABIS Aggregated Sample Type V1.0 | MIABIS Detailed Sample Type V1.0 | SPREC_Code | SPREC V3_SampleType | SPREC V4_SampleType | SCT_Code | SCT_SampleType | OMOP concept_id | OMOP concept_name | HL7 FHIR Code | HL7 FHIR Display |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Amniotic fluid | Other body fluid | Amniotic fluid | AMN | Amniotic fluid | Amniotic fluid | 119373006 | Amniotic fluid specimen (specimen) | 4002223 | Amniotic fluid specimen | AMN | Amniotic fluid |
| Ascites fluid | Other body fluid | Ascites fluid | ASC | Ascites fluid | Ascites fluid | 309201001 | Ascitic fluid sample (specimen) | 4206413 | Ascitic fluid sample | no equivalent | no equivalent |
| Bile | Other body fluid | Bile | no equivalent | no equivalent | no equivalent | 119341000 | Bile specimen (specimen) | 4001061 | Bile specimen | BIFL | Bile Fluid |
| Body cavity fluid | Other body fluid | Body cavity fluid | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | ? | ? | no equivalent | no equivalent |
| Bone | Tissue (fresh frozen or fixed) | Bone | BON | Bone | Bone | 430268003 | Specimen from bone (specimen) | 4123176 | Bone tissue sample | BON / BONE | Bone / Bone |
| Bone marrow aspirate | Other body fluid | Bone marrow aspirate | BMA | Bone marrow aspirate | Bone marrow aspirate | 396997002 | Specimen from bone marrow obtained by aspiration (specimen) | 4264108 | Specimen from bone marrow obtained by aspiration | no equivalent | no equivalent |
| Bone marrow plasma | Other body fluid | Bone marrow plasma | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent |
| Bone marrow, whole | Other body fluid | Bone marrow, whole | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | 4000623 | Bone marrow specimen | MAR | Marrow |
| Breast milk | Other body fluid | Breast milk | BMK | Breast milk | Breast milk | 446676001 | Expressed breast milk specimen (specimen) | 765496 | Human breast milk specimen | MILK | Breast milk |
| Bronchoalveolar lavage | Other body fluid | Bronchoalveolar lavage | BAL | Bronchoalveolar lavage | Bronchoalveolar lavage | 258607008 | Bronchoalveolar lavage fluid sample (specimen) | 4121345 | Bronchoalveolar lavage fluid sample | LAVG | Lavage, Bronhial |
| Buffy Coat | Buffy coat | Buffy Coat | no equivalent | no equivalent | no equivalent | 258587000 | Buffy coat (specimen) | 4122286 | Buffy coat | no equivalent | no equivalent |
| Cancer cell lines | Cancer cell lines | Cancer cell lines | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent |
| Cerebrospinal fluid | Other body fluid | Cerebrospinal fluid | CSF | Cerebrospinal fluid | Cerebrospinal fluid | 258450006 | Cerebrospinal fluid sample (specimen) | 4124259 | Cerebrospinal fluid sample | CSF | Cerebral spinal fluid |
| Cord blood | Other body fluid | Cord blood | CRD | Cord blood | Cord blood | 122556008 | Cord blood specimen (specimen) | 4046835 | Cord blood specimen | BLCD | Cord blood |
| Dental pulp | Other body fluid | Dental pulp | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | ? | ? | no equivalent | no equivalent |
| no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | ? | ? | no equivalent | no equivalent | |||
| DNA | DNA | DNA | no equivalent | no equivalent | no equivalent | 258566005 | Deoxyribonucleic acid sample (specimen) | 4120355 | Deoxyribonucleic acid sample | no equivalent | no equivalent |
| Embryo | Embryo or fetal tissue | Embryo | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent |
| Entire body organ | Entire body organ | Entire body organ | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | ? | ? | no equivalent | no equivalent |
| Faeces | Faeces | Faeces | STL | Stool | Stool | 119339001 | Stool specimen (specimen) | 4002879 | Tears specimen | STL | Stool = Fecal |
| Fetal tissue | Embryo or fetal tissue | Fetal tissue | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | 4202977 | Fetus specimen | no equivalent | no equivalent |
| Fibroblasts | Primary cells | Fibroblasts | no equivalent | no equivalent | no equivalent | 119333000 | Fibroblast specimen (specimen) | 4001356 | Fibroblast specimen | FIB | Fibroblasts |
| Food specimen | Specimen from environment or food | Food specimen | no equivalent | no equivalent | no equivalent | 119320006 | Food specimen | ? | ? | EFOD | Environmental, food |
| Gas, exhaled (=breath) | Other | Gas, exhaled (=breath) | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | 4001357 | Exhaled air specimen | EXG / BRTH | Gas, exhailed (= breath) / Breath (use EXHLD) |
| Gastric fluid | Other body fluid | Gastric fluid | no equivalent | no equivalent | no equivalent | 258459007 | Gastric fluid specimen (specimen) | 4120336 | Gastric fluid sample | GAST | Fluid/ contents, gastric |
| Hair | Other | Hair | HAR | Hair | Hair | 119326000 | Hair specimen (specimen) | 4001355 | Hair specimen | HAR | Hair |
| Immortalized cell lines | Immortalised cell lines | Immortalized cell lines | no equivalent | no equivalent | no equivalent | 702451000 | Cultured cells (substance) | 42574511 | Cell culture specimen | no equivalent | no equivalent |
| Isolated microbes | Isolated microbes | Isolated microbes | no equivalent | no equivalent | no equivalent | 119303007 | Microbial isolate specimen (specimen) | 4002737 | Microbial isolate | no equivalent | no equivalent |
| Isolated or enriched exosomes | Other | no equivalent | EXO | no equivalent | Isolated or enriched exosomes | no equivalent | no equivalent | ? | ? | no equivalent | no equivalent |
| Isolated Tumor Cell (neoplastic cell) | Primary cells | no equivalent | no equivalent | no equivalent | no equivalent | 252987004 | tumor cell (cell! not specimen) | ? | ? | no equivalent | no equivalent |
| Liquid Biopsy | Blood | no equivalent | no equivalent | no equivalent | no equivalent | 1285453009 | Detection of neoplasm in body fluid (observable entity! Not specimen) | ? | ? | ? | ? |
| Menstrual blood | Other body fluid | Menstrual blood | no equivalent | no equivalent | no equivalent | 119345009 | Menstrual blood specimen (specimen) | 4002219 | Menstrual blood specimen | MBLD | Blood, Menstrual |
| Nail | Other | Nail | NAL | Nails | Nails | 119327009 | Nail specimen (specimen) | 4000618 | Nail specimen | NAIL | Nail |
| Nasal washing | Other body fluid | Nasal washing | NAS | Nasal washing | Nasal washing | 258467004 | Nasopharyngeal washings (specimen) | 762931 | Nasal washings | NASDR | Drainage, Nasal |
| Organoids | Other | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | ? | ? | no equivalent | no equivalent |
| Other | Other | no equivalent | ZZZ | Other | Other | no equivalent | no equivalent | ? | ? | no equivalent | no equivalent |
| Pericardial fluid | Other body fluid | Pericardial fluid | no equivalent | no equivalent | no equivalent | 122571007 | Pericardial fluid specimen (specimen) | 4048848 | Pericardial fluid specimen | PCFL | Fluid, pericardial |
| Peripheral blood mononuclear cells (PBMC) | Primary cells | Peripheral blood mononuclear cells (PBMC) | CEL | Density-gradient-centrifugation-separatedmononuclear cells, viable | Density-gradient-centrifugation-separatedmononuclear cells, viable | 404798000 | Peripheral blood mononuclear cell (cell) | 4229415 | Peripheral blood mononuclear cell | no equivalent | no equivalent |
| Placenta | Entire body organ | Placenta | PLC | Placenta | Placenta | 119403008 | Specimen from placenta (specimen) | 4001192 | Specimen from placenta | PLC | Placenta |
| Plasma | Plasma | Plasma | no equivalent | no equivalent | no equivalent | 119361006 | Plasma specimen (specimen) | 4000626 | Plasma specimen | PLAS | Plasma |
| Pleural fluid | Other body fluid | Pleural fluid | PFL | Pleural fluid | Pleural fluid | 418564007 | Pleural fluid specimen (specimen) | 4302933 | Pleural fluid specimen | PLR | Pleural fluid |
| Post-mortem tissue | Post-mortem tissue | Post-mortem tissue | no equivalent | no equivalent | no equivalent | 258484005 | Postmortem tissue specimen (specimen) | 4124267 | Postmortem tissue | AUTP | Autopsy |
| Primary cells | Primary cells | Primary cells | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | 4167682 | Cytologic material | no equivalent | no equivalent |
| Protein | Other | Proteins | no equivalent | no equivalent | no equivalent | 88878007 | Protein (substance) | no equivalent | no equivalent | no equivalent | no equivalent |
| Red blood cells | Primary cells | Red blood cells | RBC | Red blood cells | Red blood cells | 119351004 | Erythrocyte specimen (specimen) | 4000622 | Erythrocyte specimen | RBC | Erythrocytes |
| RNA | RNA | RNA | no equivalent | no equivalent | no equivalent | 441673008 | Ribonucleic acid specimen (specimen) | 40480050 | Ribonucleic acid specimen | no equivalent | no equivalent |
| Saliva | Saliva | Saliva | SAL | Saliva | Saliva | 119342007 | Saliva specimen (specimen) | 4001062 | Saliva specimen | SAL | Saliva |
| Semen | Other body fluid | Semen | SEM | Semen | Semen | 119347001 | Seminal fluid specimen (specimen) | 44808818 | Semen specimen | SMN / SPRM | Seminal fluid / Spermatozoa |
| Serum | Serum | Serum | SER | Serum | Serum | 119364003 | Serum specimen (specimen) | 4001181 | Serum specimen | SER | Serum |
| Specimen from environment | Specimen from environment or food | Specimen from environment | no equivalent | no equivalent | no equivalent | 440229008 | Specimen from environment | ? | ? | EOTH | Environmental, other substance |
| Sputum | Other body fluid | Sputum | SPT | Sputum | Sputum | 119334006 | Sputum specimen (specimen) | 4002876 | Sputum specimen | SPT | Sputum |
| Stem cells (and iPS cells) | Immortalised cell lines | Stem cells (and iPS cells) | no equivalent | no equivalent | no equivalent | 57731000052104 | Stem cell specimen (Specimen) | no equivalent | no equivalent | no equivalent | no equivalent |
| Swab | Swab | Swab | no equivalent | no equivalent | no equivalent | 257261003 | Swab (specimen) | 4120698 | Swab | no equivalent | no equivalent |
| Sweat | Other body fluid | Sweat | no equivalent | no equivalent | Sweat | 122569007 | Sweat specimen (specimen) | 4046838 | Sweat specimen | SWT | Sweat |
| Synovial fluid | Other body fluid | Synovial fluid | SYN | Synovial fluid | Synovial fluid | 119332005 | Synovial fluid specimen (specimen) | 4002875 | Synovial fluid specimen | SNV | Fluid, synovial |
| Tears | Other body fluid | Tears | TER | Tears | Tears | 122594008 | Tears specimen (specimen) | 4046369 | Tears specimen | TEAR | Tears |
| Teeth | Entire body organ | Teeth | TTH | Teeth | Teeth | 430319000 | Specimen from tooth (specimen) | 4332635 | Specimen from tooth | no equivalent | no equivalent |
| Tissue (fixed) | Tissue (fresh frozen or fixed) | Tissue (FFPE) | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent |
| Tissue (FFPE) | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | 40480027 | Formalin-fixed paraffin-embedded tissue specimen | no equivalent | no equivalent | ||
| Tissue (fresh frozen) | Tissue (fresh frozen or fixed) | Tissue (frozen) | no equivalent | no equivalent | no equivalent | no equivalent | no equivalent | 46270236 | Frozen tissue section specimen | no equivalent | no equivalent |
| Umbilical cord | Tissue (fresh frozen or fixed) | Umbilical cord | no equivalent | no equivalent | no equivalent | 258436001 | Umbilical cord tissue specimen (specimen) | 4122249 | Umbilical cord tissue sample | no equivalent | no equivalent |
| Urine | Urine | Urine | no equivalent | no equivalent | no equivalent | 122575003 | Urine specimen (specimen) | 4046280 | Urine specimen | UR | Urine |
| Urine Sediment | Urine | Urine Sediment | no equivalent | no equivalent | no equivalent | 122567009 | Urine sediment specimen (specimen) | 4045758 | Urine sediment specimen | URNS | Urin sediment |
| Vitreous fluid | Other body fluid | Vitreous fluid | no equivalent | no equivalent | no equivalent | 258438000 | Vitreous humor specimen (specimen) | 4120333 | Vitreous humor sample | VITF | Vitreous |
| Whole blood | Blood | Whole blood | BLD | Blood (whole) | Blood (whole) | 258580003 | Whole blood specimen (specimen) | 4122283 | Whole blood sample | WB | Blood, whole |
| Whole blood, dried (e.g. Guthrie cards) | Blood | Whole blood, dried (e.g. Guthrie cards) | DWB | Dried whole blood (e.g., Guthrie cards) | Dried whole blood (e.g., Guthrie cards) | 119294007 | Dried blood specimen (specimen) | 4000611 | Dried blood specimen | no equivalent | no equivalent |