Mapping of MIABIS 3.1 to the bbmri.de FHIR profile
To support migration from the bbmri.de FHIR profile to the new FHIRised MIABIS we propose the following mapping from MIABIS to bbmri.de
- Sample (Specimen Resource)
- Sample Type (Specimen Resource)
- Storage Temperature (Specimen Resource)
- Anatomical Site (Specimen Resource)
- Sample Donor (Patient Resource)
- Sex/Gender (Patient Resource)
- Disease (Condition or Observation Resource)
Sample/Specimen
| MIABIS Attribute Code | MIABIS Attribute Name | MIABIS Description | Data Type | bbmri.de Code | Lens Display |
|---|---|---|---|---|---|
| MIABIS-SAMPLE-01 | Sample ID | Unique ID of the sample within a sample collection, often represented by the sample barcode; text identifier. The Sample ID is meant for sharing. | String | identifier | not displayed |
| MIABIS-SAMPLE-02 | Detailed sample type | The type of biological specimen intended for testing diagnostics, disease propagation, treatment, or for research purposes. | Enumerated Value | MaterialType | Sample Type |
| MIABIS-SAMPLE-03 | Sample storage temperature | The long-term temperature at which the sample is stored after preparation, based on SPREC v4 | Enumerated Value | storageTemperature | Storage Temperature |
| MIABIS-SAMPLE-04 | Sample creation date and time | The date and time the sample was created in the form previously described in MIABIS-SAMPLE-02. Date/time format must be ISO8601-compliant or partial, for example, YYYY | Datetime, yyyy-mm-ddThh:mm:ss | collectedDateTime | Sampling Date |
| MIABIS-SAMPLE-10 | Sample content diagnosis | The ICD-10 code describing the diagnosis of the sample content, such as whether the sample contains carcinogenic material. | Enumerated Value: Use the value code from ICD-10 or ORPHA classifications | DiagnosisReport (ressource) | Sample Diagnosis |
| MIABIS-SAMPLE-11 | Use & Access conditions | The conditions that may change the availability of the samples donated by the sample donor. | Enumerated Value: Commercial use, Collaboration, Specific research use, Genetic data use, Outside EU access, Xenograft, Other animal work, Other | not given | Use Restrictions |
| MIABIS-SAMPLE-12 | Sample source | The source from which the samples were collected or isolated. | Enumerated Value: Human, Animal, Environment | not given | Sample Source |
Sample Type
| MIABIS Attribute Code | MIABIS Attribute Name | SPREC Code | SPREC V4 Sample Type | SCT Code | SCT Sample Type | bbmri.de Code | Lens Display |
|---|---|---|---|---|---|---|---|
| MIABIS-SAMPLE-02 | Amniotic fluid | AMN | Amniotic fluid | 119373006 | Amniotic fluid specimen (specimen) | Amniotic fluid | |
| MIABIS-SAMPLE-02 | Ascites fluid | ASC | Ascites fluid | 309201001 | Ascitic fluid sample (specimen) | ascites | Ascites |
| MIABIS-SAMPLE-02 | Bile | no equivalent | no equivalent | 119341000 | Bile specimen (specimen) | Bile | |
| MIABIS-SAMPLE-02 | Body cavity fluid | no equivalent | no equivalent | no equivalent | no equivalent | Body cavity fluid | |
| MIABIS-SAMPLE-02 | Bone | BON | Bone | 430268003 | Specimen from bone (specimen) | Bone | |
| MIABIS-SAMPLE-02 | Bone marrow aspirate | BMA | Bone marrow aspirate | 396997002 | Specimen from bone marrow obtained by aspiration (specimen) | bone-marrow | Bone marrow |
| MIABIS-SAMPLE-02 | Bone marrow plasma | no equivalent | no equivalent | no equivalent | no equivalent | bone-marrow | Bone marrow |
| MIABIS-SAMPLE-02 | Bone marrow, whole | no equivalent | no equivalent | no equivalent | no equivalent | bone-marrow | Bone marrow |
| MIABIS-SAMPLE-02 | Breast milk | BMK | Breast milk | 446676001 | Expressed breast milk specimen (specimen) | Breast milk | |
| MIABIS-SAMPLE-02 | Bronchoalveolar lavage | BAL | Bronchoalveolar lavage | 258607008 | Bronchoalveolar lavage fluid sample (specimen) | Bronchoalveolar lavage | |
| MIABIS-SAMPLE-02 | Buffy Coat | no equivalent | no equivalent | 258587000 | Buffy coat (specimen) | buffy-coat | Buffy-Coat |
| MIABIS-SAMPLE-02 | Cancer cell lines | no equivalent | no equivalent | no equivalent | no equivalent | Cancer cell lines | |
| MIABIS-SAMPLE-02 | Cerebrospinal fluid | CSF | Cerebrospinal fluid | 258450006 | Cerebrospinal fluid sample (specimen) | csf-liquor | CSF/Liquor |
| MIABIS-SAMPLE-02 | Cord blood | CRD | Cord blood | 122556008 | Cord blood specimen (specimen) | Cord blood | |
| MIABIS-SAMPLE-02 | Dental pulp | no equivalent | no equivalent | no equivalent | no equivalent | Dental pulp | |
| MIABIS-SAMPLE-02 | DNA | no equivalent | no equivalent | 258566005 | Deoxyribonucleic acid sample (specimen) | dna | DNA |
| MIABIS-SAMPLE-02 | Embryo | no equivalent | no equivalent | no equivalent | no equivalent | Embryo | |
| MIABIS-SAMPLE-02 | Entire body organ | no equivalent | no equivalent | no equivalent | no equivalent | Entire body organ | |
| MIABIS-SAMPLE-02 | Faeces | STL | Stool | 119339001 | Stool specimen (specimen) | stool-faeces | Stool/Faeces |
| MIABIS-SAMPLE-02 | Fetal tissue | no equivalent | no equivalent | no equivalent | no equivalent | Fetal tissue | |
| MIABIS-SAMPLE-02 | Fibroblasts | no equivalent | no equivalent | 119333000 | Fibroblast specimen (specimen) | Fibroblasts | |
| MIABIS-SAMPLE-02 | Food specimen | no equivalent | no equivalent | 119320006 | Food specimen | Food specimen | |
| MIABIS-SAMPLE-02 | Gas, exhaled (=breath) | no equivalent | no equivalent | no equivalent | no equivalent | Gas, exhaled (=breath) | |
| MIABIS-SAMPLE-02 | Gastric fluid | no equivalent | no equivalent | 258459007 | Gastric fluid specimen (specimen) | Gastric fluid | |
| MIABIS-SAMPLE-02 | Hair | HAR | Hair | 119326000 | Hair specimen (specimen) | Hair | |
| MIABIS-SAMPLE-02 | Immortalised cell lines | no equivalent | no equivalent | 702451000 | Cultured cells (substance) | Immortalised cell lines | |
| MIABIS-SAMPLE-02 | Isolated microbes | no equivalent | no equivalent | 119303007 | Microbial isolate specimen (specimen) | Isolated microbes | |
| MIABIS-SAMPLE-02 | Isolated or enriched exosomes | EXO | Isolated or enriched exosomes | no equivalent | no equivalent | Isolated or enriched exosomes | |
| MIABIS-SAMPLE-02 | Isolated Tumour Cell (neoplastic cell) | no equivalent | no equivalent | 252987004 | tumour cell (cell! not specimen) | Isolated Tumour Cell (neoplastic cell) | |
| MIABIS-SAMPLE-02 | Menstrual blood | no equivalent | no equivalent | 119345009 | Menstrual blood specimen (specimen) | Menstrual blood | |
| MIABIS-SAMPLE-02 | Nail | NAL | Nails | 119327009 | Nail specimen (specimen) | Nail | |
| MIABIS-SAMPLE-02 | Nasal washing | NAS | Nasal washing | 258467004 | Nasopharyngeal washings (specimen) | Nasal washing | |
| MIABIS-SAMPLE-02 | Organoids | no equivalent | no equivalent | no equivalent | no equivalent | Organoids | |
| MIABIS-SAMPLE-02 | Other | ZZZ | Other | no equivalent | no equivalent | Other | |
| MIABIS-SAMPLE-02 | Pericardial fluid | no equivalent | no equivalent | 122571007 | Pericardial fluid specimen (specimen) | Pericardial fluid | |
| MIABIS-SAMPLE-02 | Peripheral blood mononuclear cells (PBMC) | CEL | Density-gradient-centrifugation-separated mononuclear cells, viable | 404798000 | Peripheral blood mononuclear cell (cell) | peripheral-blood-cells-vital | Peripheral blood mononuclear cells (PBMCs, viable) |
| MIABIS-SAMPLE-02 | Placenta | PLC | Placenta | 119403008 | Specimen from placenta (specimen) | Placenta | |
| MIABIS-SAMPLE-02 | Plasma | no equivalent | no equivalent | 119361006 | Plasma specimen (specimen) | blood-plasma | Plasma |
| MIABIS-SAMPLE-02 | Pleural fluid | PFL | Pleural fluid | 418564007 | Pleural fluid specimen (specimen) | Pleural fluid | |
| MIABIS-SAMPLE-02 | Post-mortem tissue | no equivalent | no equivalent | 258484005 | Postmortem tissue specimen (specimen) | Post-mortem tissue | |
| MIABIS-SAMPLE-02 | Primary cells | no equivalent | no equivalent | no equivalent | no equivalent | Primary cells | |
| MIABIS-SAMPLE-02 | Protein | no equivalent | no equivalent | 88878007 | Protein (substance) | Protein | |
| MIABIS-SAMPLE-02 | Red blood cells | RBC | Red blood cells | 119351004 | Erythrocyte specimen (specimen) | Red blood cells | |
| MIABIS-SAMPLE-02 | RNA | no equivalent | no equivalent | 441673008 | Ribonucleic acid specimen (specimen) | rna | RNA |
| MIABIS-SAMPLE-02 | Saliva | SAL | Saliva | 119342007 | Saliva specimen (specimen) | saliva | Saliva |
| MIABIS-SAMPLE-02 | Semen | SEM | Semen | 119347001 | Seminal fluid specimen (specimen) | Semen | |
| MIABIS-SAMPLE-02 | Serum | SER | Serum | 119364003 | Serum specimen (specimen) | blood-serum | Serum |
| MIABIS-SAMPLE-02 | Specimen from environment | no equivalent | no equivalent | 440229008 | Specimen from environment | Specimen from environment | |
| MIABIS-SAMPLE-02 | Sputum | SPT | Sputum | 119334006 | Sputum specimen (specimen) | Sputum | |
| MIABIS-SAMPLE-02 | Stem cells (and iPS cells) | no equivalent | no equivalent | 57731000052104 | Stem cell specimen (Specimen) | Stem cells (and iPS cells) | |
| MIABIS-SAMPLE-02 | Swab | no equivalent | no equivalent | 257261003 | Swab (specimen) | swab | Swab |
| MIABIS-SAMPLE-02 | Sweat | no equivalent | Sweat | 122569007 | Sweat specimen (specimen) | Sweat | |
| MIABIS-SAMPLE-02 | Synovial fluid | SYN | Synovial fluid | 119332005 | Synovial fluid specimen (specimen) | Synovial fluid | |
| MIABIS-SAMPLE-02 | Tears | TER | Tears | 122594008 | Tears specimen (specimen) | Tears | |
| MIABIS-SAMPLE-02 | Teeth | TTH | Teeth | 430319000 | Specimen from tooth (specimen) | Teeth | |
| MIABIS-SAMPLE-02 | Tissue (fixed) | no equivalent | no equivalent | no equivalent | no equivalent | tissue-ffpe | Tissue FFPE |
| MIABIS-SAMPLE-02 | Tissue (fresh frozen) | no equivalent | no equivalent | no equivalent | no equivalent | tissue-frozen | Tissue frozen |
| MIABIS-SAMPLE-02 | Umbilical cord | no equivalent | no equivalent | 258436001 | Umbilical cord tissue specimen (specimen) | Umbilical cord | |
| MIABIS-SAMPLE-02 | Urine | no equivalent | no equivalent | 122575003 | Urine specimen (specimen) | urine | Urine |
| MIABIS-SAMPLE-02 | Urine Sediment | no equivalent | no equivalent | 122567009 | Urine sediment specimen (specimen) | urine | Urine |
| MIABIS-SAMPLE-02 | Vitreous fluid | no equivalent | no equivalent | 258438000 | Vitreous humour specimen (specimen) | Vitreous fluid | |
| MIABIS-SAMPLE-02 | Whole blood | BLD | Blood (whole) | 258580003 | Whole blood specimen (specimen) | whole-blood | Whole blood |
| MIABIS-SAMPLE-02 | Whole blood, dried (e.g. Guthrie cards) | DWB | Dried whole blood (e.g., Guthrie cards) | 119294007 | Dried blood specimen (specimen) | dried-whole-blood | Dried whole blood |
Storage Temperature
| MIABIS Attribute Code | MIABIS Attribute Name | MIABIS Description | Source [SPREC 4.0] | bbmri.de Code | Lens Display |
|---|---|---|---|---|---|
| MIABIS-SAMPLE-03 | RT | Room temperature | SPREC V4.0 | temperatureRoom | Room Temperature |
| MIABIS-SAMPLE-03 | 2 °C to 10°C | between 2 °C and 10 °C | SPREC V4.0 | temperature2to10 | 2 °C to 10°C |
| MIABIS-SAMPLE-03 | -18 °C to -35 °C | between -18 °C and -35 °C | SPREC V4.0 | temperature-18to-35 | -18 °C to -35 °C |
| MIABIS-SAMPLE-03 | -60 °C to -85 °C | between -60 °C and -85 °C | SPREC V4.0 | temperature-60to-85 | -60 °C to -85 °C |
| MIABIS-SAMPLE-03 | LN | liquid nitrogen vapour-phase | no equivalent | temperatureGN | Liquid Nitrogen (liquid-phase) |
| MIABIS-SAMPLE-03 | LN | liquid nitrogen liquid-phase | no equivalent | temperatureLN | Liquid Nitrogen (vapour-phase) |
| MIABIS-SAMPLE-03 | Other | any other temperature or long time storage information | SPREC V4.0 | temperatureOther | Other |
Anatomical Site/Body Site
| Attribute Codes | Attribute Name | MIABIS Description | Data Type | bbmri.de Code | Lens Display |
|---|---|---|---|---|---|
| MIABIS-SAMPLE-05-01 | Anatomical site ontology | Name of ontology used for describing the anatomical source of the sample material, for example, ICD-O-3 topography code | String | bodySite | not displayed |
| MIABIS-SAMPLE-05-02 | Anatomical site ontology version | Version of selected ontology for anatomical site | String | coding version | not displayed |
| MIABIS-SAMPLE-05-03 | Anatomical site ontology code | Anatomical site code from the selected anatomical site ontology version | String | bodySite coding | not displayed |
| MIABIS-SAMPLE-05-04 | Anatomical site ontology description | Description from the selected anatomical site ontology code | String | bodySite coding display | Body Site Coding Display |
| MIABIS-SAMPLE-05-05 | Anatomical site free text | Explanation about Anatomical site in case of unknown Anatomical site or insufficient information | String | bodySite coding display | not displayed |
Sample Donor/Patient
| MIABIS Attribute Code | MIABIS Attribute Name | MIAIBS Description | Data Type | bbmri.de Code | Lens Display |
|---|---|---|---|---|---|
| MIABIS-SAMPLEDONOR-01 | Sample donor ID | Sample donor ID. Unique ID code of the sample donor within the sample collection/biobank | String | Patient ID | not displayed |
| MIABIS-SAMPLEDONOR-02 | Sex | Biological sex of the sample donor. MIABIS-2.0-9 | Enumerated Value | gender | Administrative Gender |
| MIABIS-SAMPLEDONOR-03 | Data categories | The data categories from which data are available or can be linked to the sample donor. Can be several values (list modified after MIABIS-2.0-13). | Enumerated Value: Lifestyle dataset, Environmental dataset, Physiological dataset, Biochemical dataset, Clinical dataset, Psychological dataset, Genomic dataset, Proteomic dataset, Metabolomic dataset, Body (Radiological) image, Whole slide image, Photo image, Genealogical records, Other. | no equivalent | ? |
| MIABIS-SAMPLEDONOR-04 | Birth date | Birth date of the sample donor. Coding ISO8601. Can also be partial, for example, YYYY. | yyyy-mm-ddThh:mm:ss | birthdate | Birth Date (Year) |
Sex/Gender
| MIABIS Attribute Code | MIABIS Attribute Name | MIABIS Description | bbmri.de Code | Lens Display |
|---|---|---|---|---|
| MIABIS-COLLECTION-08, MIABIS-RESEARCHRESOURCE-08, MIABIS-SAMPLEDONOR-02 | Male | male | male | Male |
| MIABIS-COLLECTION-08, MIABIS-RESEARCHRESOURCE-08, MIABIS-SAMPLEDONOR-03 | Female | female | female | Female |
| MIABIS-COLLECTION-08, MIABIS-RESEARCHRESOURCE-08, MIABIS-SAMPLEDONOR-04 | Unknown | a proper value is applicable but not known | unknown | Unknown |
| MIABIS-COLLECTION-08, MIABIS-RESEARCHRESOURCE-08, MIABIS-SAMPLEDONOR-05 | Undifferentiated | undifferentiated, the gender could not be uniquely identified such as hermaphrodite | other | Undifferentiated |
| MIABIS-COLLECTION-08, MIABIS-RESEARCHRESOURCE-08, MIABIS-SAMPLEDONOR-06 | Not applicable | The samples have no applicable sex (to enable description of non-human samples) | other | Not applicable |
Disease/Diagnosis
| MIABIS Attribute Code | MIABIS Attribute Name | MIABIS Description | bbmri.de Code | Lens Display |
|---|---|---|---|---|
| MIABIS-COLLECTION-17-01, MIABIS-RESEARCHRESOURCE-15-01 | Disease Ontology | Name of ontology used for disease. Can be several values e.g. ICD, SNOMED | ||
| MIABIS-COLLECTION-17-01, MIABIS-RESEARCHRESOURCE-15-02 | Disease Ontology Version | Version of selected ontology for disease e.g. ICD-9, ICD-10, SNOMED-CT | ||
| MIABIS-COLLECTION-17-01, MIABIS-RESEARCHRESOURCE-15-03 | Disease Ontology Code | Disease code or main category from the selected Disease Ontology Version e.g. C61 | Disease Ontology Code | |
| MIABIS-COLLECTION-17-01, MIABIS-RESEARCHRESOURCE-15-04 | Disease Ontology Description | Description from the selected Disease Ontology Code e.g : Malignant neoplasm of prostate | ||
| MIABIS-COLLECTION-17-01, MIABIS-RESEARCHRESOURCE-15-05 | Disease Free Text | Explanation about disease or symptom in case of unknown disease or insufficient information | not displayed |