WARNING
This is a draft under the review by the BBMRI-ERIC Management Committee.
Definition
Assay attributes (container, preparation steps, …) covers various aspects related to container (glass slide) and laboratory preparation steps.
| Attribute Code | Attribute Name | Description | Data type | Allowed values | Constraints | Cardinality |
|---|---|---|---|---|---|---|
| MIABIS-DIGITALPATHOLOGYASSAY-01 | Container Configuration | Classifies a container based on the organization of its specimens | Enumerated Values | TMA, Multiple patients, Multiple blocks, Single block, Single section, Cytology sample, Other (the value is known but cannot be classified into any of the predefined categories), NULL (the value is unknown) | none | 1:n |
| MIABIS-DIGITALPATHOLOGYASSAY-02 | Container Identifier | A unique identifier for a container (as defined in DICOM) | String | An ID as a free-text string | none | 0:1 |
| MIABIS-DIGITALPATHOLOGYASSAY-03 | Specimens | Unique identifiers of one or more specimens placed in or on a container | String | Specimens IDs as a free-text string | none | 1:n |
| MIABIS-DIGITALPATHOLOGYASSAY-04 | Container Type | The type of a non-biological object used during the handling, preparation, and storage of a biospecimen | Enumerated Values | Tissue Cassette, Tissue Microarray Cassette, Microscope Slide, Specimen Container, Specimen Vial, Specimen Well, Electron Microscopy Grid | none | 0:1 |
| MIABIS-DIGITALPATHOLOGYASSAY-05 | Tissue Type | Types of tissue that are labeled and examined | Enumerated Values | Values are to be taken from CID 7166 Common Tissue Segmentation Type and be encoded as SNOMED-RD ID | none | 0:n |
| MIABIS-DIGITALPATHOLOGYASSAY-06 | Cell Type | A subset or a selected group of cells labeled and examined by a laboratory assay | Enumerated Values | Values are to be taken from the Cell Annotation Platform, and the Data Coordination Platform | none | 0:n |
| MIABIS-DIGITALPATHOLOGYASSAY-07 | Pathogen Type | The type of pathogenic microorganism tested through a laboratory assay | Enumerated Values | viruses, bacteria, fungi, parasites, prions | none | 0:n |
| MIABIS-DIGITALPATHOLOGYASSAY-08 | Pathogen Identifier | A name or an identifier of a microorganism for which a test has been performed | Enumerated Values | Values are to be taken from the National Healthcare Safety Network | none | 0:1 |
| MIABIS-DIGITALPATHOLOGYASSAY-09 | Biomarker Type | The basic cellular component of a biospecimen that has been tested or labeled | Enumerated Values | Protein, DNA, RNA, Carbohydrate, Lipid, Inorganic Ions, other (the value is known but cannot be classified into any of the predefined categories), NULL (the value is unknown) | none | 0:n |
| MIABIS-DIGITALPATHOLOGYASSAY-10 | Biomarker Spatial Localization | The subcellular location of a biomarker or biomarkers | Enumerated Values | extracellularMatrix, cellMembrane, cytoplasm, nucleus, microorganism | none | 0:n |
| MIABIS-DIGITALPATHOLOGYASSAY-11 | Assay Type | The laboratory test performed on a bio-specimen mounted on a glass slide | Enumerated Values | Hematoxylin And Eosin Stain, Special Stains, Immunohistochemistry, Immunocytochemistry, Immunofluorescence, Insitu Hybridization, Fluorescence Insitu Hybridization, Fluorescent Multiplex Immunohistochemistry, Multiplex Immunohistochemistry, other (the value is known but cannot be classified into any of the predefined categories), NULL (the value is unknown) | none | 1:1 |
| MIABIS-DIGITALPATHOLOGYASSAY-12 | Special Stain Technique | The method of a special staining technique performed to visualize a selected tissue type or tissue element, a cell type, or a pathogen, except for the H&E method | Enumerated Values | Values are to be taken from CID 8112 Specimen Stain and be encoded as SNOMED-RD ID | none | 0:n |
| MIABIS-DIGITALPATHOLOGYASSAY-13 | Dye Name | The neutral or synthetic colored substance used for staining specific tissues or cellular components | Enumerated Values | Values are to be taken from CID 8112 Specimen Stain and be encoded as SNOMED-RD ID | none | 0:n |
| MIABIS-DIGITALPATHOLOGYASSAY-14 | Antibody Name | The vendor-stated name of an antibody used to detect and visualize the presence of an antigen | String | Controlled Value Set encoded as text string | none | 0:n |
| MIABIS-DIGITALPATHOLOGYASSAY-15 | Antibody Identifier | The distinct ID for an antibody used in an assay | Enumerated Values | Values are to be taken from the Antibody Registry | none | 0:n |
| MIABIS-DIGITALPATHOLOGYASSAY-16 | Chromogenic Substrate Name | The name of a chromogenic compound used in an assay | Enumerated Values | 3,3′-Diaminobenzidine, 3-Amino-9-Ethylcarbazole, 3,3´,5,5´ tetramethylbenzidine, fastRed, permanentRed, emerald, BCIP/NBT | none | 0:n |
| MIABIS-DIGITALPATHOLOGYASSAY-17 | Fluorophore Substance Name | The name of a fluorescent material used in an assay | Enumerated Values | Values to be taken from the https://fluorophores.tugraz.at/ | none | 0:n |
| MIABIS-DIGITALPATHOLOGYASSAY-18 | FISH Signal Pattern | Describes a spatial location of fluorescent probes or signals | Enumerated Values | Deletion Probes, Amplification Probes, Dual-Colour Breakapart Probes, Deletion-Fusion Probes, Tri-Colour Breakapart Probes, Translocation, Dual Fusion Probes | none | 0:n |
| MIABIS-DIGITALPATHOLOGYASSAY-19 | FISH Probe Identifier | The vendor-stated name of a probe used in a FISH assay | String | The vendor-stated name of a probe used in a FISH assay | none | 0:n |
| MIABIS-DIGITALPATHOLOGYASSAY-20 | Counter Labeling | The counter-labeling technique used to highlight specific cellular or tissue structures, serving as a complementary method to the primary labeling for analysis | Enumerated Values | Hematoxylin, Eosin, Nuclear Fast Red, Methyl Green, 4',6-diamidino-2-phenylindole, Hoechst 33342, PropidiumIodide, Phalloidin, other (the value is known but cannot be classified into any of the predefined categories), NULL (the value is unknown) | none | 1:n |
| MIABIS-DIGITALPATHOLOGYASSAY-20 | Counter Labeling | The counter-labeling technique used to highlight specific cellular or tissue structures, serving as a complementary method to the primary labeling for analysis | String | Controlled Value Set: hematoxylin, eosin, nuclearFastRed, methylGreen, 4',6-diamidino-2-phenylindole, hoechst 33342, propidiumIodide, phalloidin, other, NULL | 0:n |