| accuracy |
Overall accuracy of the model (0 |
| active_pathways |
List of biological pathways that are active in both systems |
| activity_endpoint |
Biological activity or property being predicted |
| activity_score |
Quantitative measure of pathway activity |
| adjusted_p_value |
Multiple testing corrected p-value |
| age |
The age of the animal used in the model system |
| architecture_type |
The overall architecture type of the microfluidic device |
| assay_result |
Quantitative result of the assay |
| assay_type |
Type of functional assay (e |
| auc |
Area under the ROC curve |
| authentication_method |
Method used for cell line authentication (e |
| authors |
Authors of the publication |
| barrier_functions |
Tissue barrier functions modeled (epithelial, endothelial, etc |
| batch_to_batch_variation |
Measure of variation between different experimental batches |
| biological_context |
tissue/region (anatomy), cell types, sex/age equivalents, mechanics (e |
| biological_organization_level |
The level of biological organization represented by the model |
| biological_proportion |
Proportion of this cell type in the biological system |
| biological_specific_phenotypes |
List of phenotypes present only in the biological system |
| biological_system_modeled |
|
| blood_flow |
Blood flow to the compartment (L/h) |
| cell_ratios |
Ratios of different cell types in the co-culture |
| cell_source |
Source of cells (e |
| cell_type |
The cell type for which the ratio is specified |
| cell_type_coverage |
|
| cell_type_proportions |
Quantitative comparison of cell type proportions |
| cell_types |
Cell types present in the cellular system |
| channel_configuration |
Configuration of channels (e |
| channel_dimensions |
Dimensions of the channels in the device |
| channel_name |
Name or identifier of the channel (e |
| clearance |
Total body clearance (L/h) |
| coculture_configuration |
Configuration of co-culture (direct contact, transwell, conditioned media) |
| coefficient_of_variation |
Coefficient of variation across experimental replicates |
| compartment_type |
Type of physiological compartment |
| compartments |
Physiological compartments included in the model |
| complexity_level |
Level of biological complexity represented (subcellular, cellular, tissue, or... |
| compound_tested |
Name of compound used in dose-response testing |
| computational_method |
Primary computational method or algorithm used |
| concordance |
Metrics used to assess the concordance between the model system and the biolo... |
| confidence_interval_lower |
Lower bound of confidence interval |
| confidence_interval_upper |
Upper bound of confidence interval |
| confluence_level |
Typical confluence level maintained (0 |
| conserved_functions |
List of biological functions conserved between model and biological system |
| conserved_genes |
List of genes with conserved expression patterns between model and target |
| context_of_use |
What decision will this inform? Care? Policy? Drug approval? |
| correlation_coefficient |
Pearson correlation coefficient for expression profiles |
| coverage_percentage |
Percentage of target cell types represented in the model system |
| cross_validation |
Cross-validation strategy and results |
| culture_conditions |
Standard culture conditions and media used |
| culture_system |
Culture system used (e |
| cv_method |
Type of cross-validation used |
| cv_score |
Average cross-validation score |
| cv_std |
Standard deviation of cross-validation scores |
| cyclic_stretch_percent |
Percentage of cyclic stretch applied (if applicable) |
| data_source |
Source of molecular data (e |
| description |
A human-readable description for a thing |
| differentially_expressed_genes |
List of genes that are differentially expressed in the model system |
| differentiation_method |
Method used to differentiate cells into organoid (e |
| divergent_pathways |
List of pathways that show different activity patterns |
| dose_response_similarity |
Comparison of dose-response relationships for therapeutic compounds |
| drug_properties |
Physicochemical and pharmacological properties modeled |
| duration_minutes |
Duration of mechanical stimulation in minutes |
| ec50_ratio |
Ratio of EC50 values between model and biological system |
| elimination_pathways |
Drug elimination and metabolism pathways included |
| endpoints |
phenotypes, function (TEER/leak, beating rate), and multi-omics |
| enrichment_score |
Statistical enrichment score for the pathway |
| enrichment_statistics |
Statistical measures of pathway enrichment |
| ensembl_id |
Ensembl gene identifier |
| entrez_id |
NCBI Entrez gene identifier |
| environment |
The environmental conditions under which the animal model is maintained |
| feature_types |
Types of features used (molecular, phenotypic, imaging, etc |
| flow_control_method |
Methods used to control fluid flow in the device |
| fold_change |
Fold change in expression compared to control or reference |
| frequency_hz |
Frequency of mechanical stimulation in Hertz |
| functional_assays |
List of functional assays used to assess parity |
| functional_parity |
|
| functional_similarity_score |
Quantitative score (0 |
| gene_symbol |
Standard gene symbol (e |
| genes_in_dataset |
Number of genes from dataset found in pathway |
| genes_in_pathway |
Number of genes in the pathway |
| height |
Height of the channel in micrometers |
| id |
A unique identifier for a thing |
| impaired_functions |
List of functions that are impaired or absent in the model system |
| inter_laboratory_consistency |
Measure of consistency across different laboratories |
| interaction_mechanisms |
Mechanisms of cell-cell interaction (paracrine, direct contact, mechanical) |
| interface_type |
Type of interface(s) present in the device |
| is_computed |
Indicates whether the model is computed or derived from experimental data |
| journal |
Journal or publication venue |
| length |
Length of the channel in millimeters |
| logp |
Lipophilicity (log P) |
| material |
Materials used to construct the device |
| matrix_composition |
Composition of extracellular matrix or scaffold material |
| max_response_ratio |
Ratio of maximum responses between systems |
| mechanical_forces |
Mechanical forces applied to the model system |
| membrane_pore_size |
Pore size of the membrane in micrometers |
| membrane_thickness |
Thickness of the membrane in micrometers |
| membrane_type |
Type of membrane used in the device if applicable |
| methodology |
Description of experimental methods used for molecular comparison |
| metric_name |
Name of the quality control metric |
| metric_value |
Value of the quality control metric |
| microfluidic_design |
Detailed design specifications of the microfluidic device |
| missing_cell_types |
List of cell types present in biological system but missing in model |
| ml_algorithm |
Type of machine learning algorithm used |
| model_interpretability |
Level of model interpretability (black box, interpretable, explainable) |
| model_performance |
Statistical performance metrics of the model |
| model_proportion |
Proportion of this cell type in the model system |
| model_specific_phenotypes |
List of phenotypes present only in the model system |
| model_systems |
|
| models |
|
| molecular_descriptors |
Types of molecular descriptors used (topological, electronic, etc |
| molecular_similarity |
|
| molecular_weight |
Molecular weight (g/mol) |
| n_folds |
Number of folds in cross-validation |
| name |
A human-readable name for a thing |
| number_of_channels |
Total number of channels in the device |
| organ_modeled |
The organ or tissue being modeled |
| p_value |
Statistical p-value for differential expression |
| partition_coefficient |
Tissue-to-plasma partition coefficient |
| pass_fail_status |
Whether this metric passes quality control criteria |
| passage_protocol |
Standard passaging protocol and frequency |
| passage_range |
Recommended passage number range for experimental use |
| pathway_analysis_method |
Method used for pathway analysis (e |
| pathway_concordance |
|
| pathway_database |
Source database (e |
| pathway_id |
Database-specific pathway identifier |
| pathway_overlap_score |
Quantitative score (0 |
| perfusion_system |
Description of perfusion and flow systems |
| personalization_parameters |
Parameters used for personalization (genetic, phenotypic, etc |
| perturbations |
exposure/dose/time; diet/drugs/toxicants |
| phenotype_ontology |
Ontology used for phenotype classification (e |
| phenotype_overlap |
|
| phenotype_similarity_score |
Quantitative score (0 |
| pka |
Acid dissociation constant |
| plan_comparators |
human data, gold-standard assays, or high-quality animal references |
| prediction_scope |
Scope and limitations of model predictions |
| pressure_pascal |
Pressure applied in Pascals |
| proportion_ratio |
Ratio of model to biological proportions |
| protein_binding |
Fraction bound to plasma proteins (0 |
| q_value |
False discovery rate corrected p-value |
| quality_control_metrics |
List of quality control measures and their values |
| r_squared |
R-squared value for regression models |
| ratio |
Proportion or ratio of this cell type (0 |
| ratio_type |
Type of ratio specification (percentage, absolute, fold) |
| real_time_data_sources |
Sources of real-time data for model updating |
| reference_value |
Reference or control value for comparison |
| references |
Literature references that describe, validate, or support this model |
| replicate_count |
Number of experimental replicates used in assessment |
| represented_cell_types |
List of cell types present in both model and biological system |
| reproducibility |
|
| reproducibility_score |
Quantitative score (0 |
| rmse |
Root mean square error |
| sensitivity |
Sensitivity/recall of the model (0 |
| sensor_integration |
Sensors integrated for real-time monitoring |
| sensors_integrated |
Sensors integrated into the device for monitoring |
| shared_phenotypes |
List of phenotypes present in both model and biological system |
| shear_stress |
Shear stress applied in dyn/cm² |
| similarity_score |
Quantitative similarity score (0 |
| single_cell_method |
Method used for single-cell analysis (e |
| size_range |
Typical size range of 3D structures |
| software_platform |
Software platform or programming language used |
| spatial_context |
Description of spatial organization and context captured by the model |
| special_features |
Additional special features of the device (e |
| species |
The species of the animal used in the model system |
| species_modeled |
Species for which the model is designed |
| specificity |
Specificity of the model (0 |
| statistical_significance |
Statistical measures of significance for the molecular similarity |
| statistical_test |
Name of statistical test used |
| stimulation_type |
Type of mechanical stimulation applied |
| strain |
The specific strain of the animal used in the model system |
| structured_concordance |
Detailed structured assessment of concordance between the model system and th... |
| studies |
|
| substrate_type |
Type of culture substrate (e |
| surface_treatment |
Surface treatments or coatings applied to the device |
| three_d_architecture |
Type of 3D architecture (spheroid, organoid, scaffold-based, etc |
| threshold |
Acceptable threshold for this metric |
| tissue_architecture |
Description of tissue-level architecture and organization |
| tissue_modeled |
The specific tissue being modeled |
| title |
Title of the referenced publication or dataset |
| training_data_size |
Size of training dataset |
| training_dataset_size |
Number of compounds in training dataset |
| twin_scope |
Scope of digital twin (organ, patient, population) |
| type |
|
| units |
Units of measurement for the assay result |
| update_frequency |
Frequency of model updates based on new data |
| url |
URL to access the publication |
| validation_datasets |
Datasets used for model training and validation |
| volume |
Volume of the compartment (L) |
| width |
Width of the channel in micrometers |
| year |
Publication year |