| active_area_percentage |
Percentage of epithelial surface with actively beating cilia |
| adverse_outcome |
The adverse outcome that is the apical endpoint of this AOP |
| adverse_outcome_pathways |
Collection of Adverse Outcome Pathways |
| age |
Age of the subject |
| age_range |
Age range of the study population |
| airway_region |
Region of airway from which cells originated |
| akt_phosphorylation |
AKT phosphorylation level |
| alpha_diversity |
Alpha diversity (microbiome) |
| analysis_software |
Software used for analysis (e |
| anatomical_origin |
|
| antibodies_used |
Antibodies used in staining or detection |
| antioxidant_capacity |
Total antioxidant capacity or GSH/GSSG ratio |
| antioxidant_enzyme_activities |
Antioxidant enzyme activities (SOD, catalase, GPx) |
| aopwiki_id |
The AOP-Wiki identifier for this entity (e |
| asl_assays |
Collection of airway surface liquid assays |
| asl_height_um |
Airway surface liquid height in micrometers |
| asl_ph |
pH of airway surface liquid |
| assay_date |
Date when the assay was performed |
| authentication_method |
|
| bacterial_load |
Bacterial load (16S copies or CFU) |
| balf_sputum_assays |
Collection of BALF and sputum assays |
| base_medium |
|
| beat_frequency_hz |
Ciliary beat frequency measured in Hz |
| beta_diversity |
Beta diversity (microbiome) |
| biological_action |
The type of change (increased, decreased, altered, impaired) |
| biological_object |
The biological entity affected (protein, cell, tissue, organ) |
| biological_process |
The biological process affected by this key event |
| bronchodilator_agent |
Bronchodilator agent used (e |
| bronchodilator_dose |
Dose of bronchodilator administered |
| bronchodilator_response |
Response to bronchodilator (% change in FEV1) |
| catalase_activity |
Catalase activity |
| catalog_number |
|
| cell_culture_growth_mode |
|
| cell_free_dna |
Cell-free DNA concentration |
| cell_line |
|
| cell_type |
The cell type being studied |
| cell_type_ratios |
|
| cftr_assays |
Collection of CFTR function assays |
| cftr_chloride_secretion |
CFTR-mediated chloride secretion in uA/cm2 |
| cftr_forskolin_response |
Forskolin-stimulated CFTR response |
| cftr_specific_current |
CFTR-specific chloride secretory current |
| cilia_length |
Length of cilia measured in micrometers |
| cilia_per_cell |
Number of cilia per ciliated cell |
| ciliary_beat_amplitude |
Amplitude of ciliary beat |
| ciliary_function_assays |
Collection of ciliary function assays |
| ciliary_motion_patterns |
Patterns of ciliary motion (coordinated, dyskinetic, immotile) |
| clinical_context |
Clinical context for in vivo measurements (e |
| coating |
|
| cohort_size |
Number of subjects in the cohort or population |
| collection_date |
Date when the sample was collected |
| collection_site |
Anatomical site of sample collection |
| concentration |
|
| confluence_level |
|
| counterstain |
Counterstain used (e |
| culture_conditions |
|
| culture_media |
|
| days_at_air_liquid_interface |
|
| days_at_differentiation |
Days at air-liquid interface or differentiation stage |
| decline_rate |
Longitudinal decline rate in mL/year |
| description |
A detailed description of the entity |
| detection_method |
Detection method used (e |
| detection_method_details |
Detection method details |
| disease_state |
|
| dlco |
Diffusing capacity for carbon monoxide |
| dna_damage_markers |
DNA damage markers (8-OHdG) |
| donor_count |
|
| donor_info |
Information about cell donor (e |
| downstream_event |
The downstream key event in this relationship (effect) |
| downstream_key_events |
Key events that follow this key event (downstream in the pathway) |
| downstream_kinase_activation |
Activation levels of downstream kinases |
| egfr_ligand_expression |
Expression of EGFR ligands (EGF, TGF-alpha, amphiregulin) |
| egfr_membrane_localization |
EGFR membrane localization percentage |
| egfr_phosphorylation_y1068 |
EGFR phosphorylation at Y1068 residue (fold change) |
| egfr_phosphorylation_y1173 |
EGFR phosphorylation at Y1173 residue (fold change) |
| egfr_signaling_assays |
Collection of EGFR signaling assays |
| eight_isoprostane_level |
8-isoprostane level |
| eight_ohdg_level |
8-OHdG level (DNA oxidation marker) |
| eosinophil_percentage |
Eosinophil percentage in BALF/sputum |
| equipment_required |
Equipment required for this protocol |
| erk_phosphorylation |
ERK phosphorylation level |
| evaporation_prevention |
Method used to prevent evaporation (e |
| evidence_support |
Level of evidence supporting this key event relationship |
| exposure_agent |
The chemical, biological, or environmental agent used for exposure or treatme... |
| exposure_concentration |
Concentration of the exposure agent applied |
| exposure_duration |
Duration of exposure or treatment |
| fef25_75 |
Forced expiratory flow 25-75% |
| feno |
Fractional exhaled nitric oxide in ppb |
| fev1 |
Forced expiratory volume in 1 second |
| fev1_fvc_ratio |
Ratio of FEV1 to FVC (Tiffeneau-Pinelli index) |
| fixation_method |
Fixation method used for tissue/cell preparation |
| fluorescent_labeling |
Fluorescent label or tracer used |
| fluorescent_tracer |
Fluorescent tracer used for tracking (MCC assays) |
| follows_protocols |
The Protocol(s) that this assay follows |
| four_hydroxynonenal_level |
4-HNE level - lipid peroxidation marker |
| foxj1_mrna_expression |
FoxJ1 mRNA expression level |
| foxj1_nuclear_localization |
FoxJ1 nuclear localization |
| foxj1_positive_cell_percentage |
Percentage of FoxJ1-positive cells |
| foxj1_protein_expression |
FoxJ1 protein expression level |
| foxj_assays |
Collection of FoxJ1/ciliogenesis assays |
| functional_residual_capacity |
Functional residual capacity |
| fvc |
Forced vital capacity |
| gene_expression_assays |
Collection of gene expression assays |
| gene_expression_method |
Method used for gene expression (qRT-PCR, RNA-seq, etc |
| general_procedure |
High-level description of the procedure |
| glutathione_peroxidase_activity |
GPx activity |
| glutathione_ratio |
GSH/GSSG ratio indicating antioxidant status |
| goblet_cell_assays |
Collection of goblet cell and mucin assays |
| goblet_cell_count |
Number of goblet cells (raw count) |
| goblet_cell_percentage |
Percentage of goblet cells |
| goblet_to_ciliated_ratio |
Ratio of goblet cells to ciliated cells |
| has_exposure_condition |
The exposure condition(s) applied to the study subject |
| has_specified_output |
The measurement results produced by this assay — the specified output of a pl... |
| hemoglobin_level |
Hemoglobin level |
| humidity_control |
Humidity conditions during the procedure |
| id |
A unique identifier for the entity |
| il1_beta_concentration |
IL-1 beta concentration |
| il6_concentration |
IL-6 concentration |
| il8_concentration |
IL-8 concentration |
| imaging_duration |
Duration of imaging session |
| imaging_frame_rate |
Frame rate for video/imaging acquisition (e |
| imaging_protocol |
Reference to the imaging protocol used |
| inclusion_criteria |
Criteria for inclusion in the study population |
| informs_on_key_event |
The Key Event that this assay provides evidence for |
| inhibitor_sensitive_current |
Inhibitor-sensitive current measurement |
| inhibitor_used |
Inhibitor used (e |
| institution |
Institution where protocol was developed |
| ion_composition |
Ionic composition (Cl-, Na+, K+) |
| key_event_relationships |
The key event relationships connecting events in this AOP |
| key_events |
The key events in this AOP (intermediate events between MIE and AO) |
| key_reagents |
Key reagents needed for this protocol |
| last_updated |
Date protocol was last updated |
| level_of_biological_organization |
The level of biological organization at which this key event occurs |
| lipid_peroxidation |
Lipid peroxidation level |
| lot_number |
|
| lung_compliance |
Lung compliance |
| lung_elastance |
Lung elastance |
| lung_function_assays |
Collection of lung function assays |
| lung_resistance |
Lung resistance |
| lymphocyte_percentage |
Lymphocyte percentage in BALF/sputum |
| lysis_buffer |
Lysis buffer used for sample preparation |
| macrophage_percentage |
Macrophage percentage in BALF/sputum |
| malondialdehyde_level |
MDA level - lipid peroxidation marker |
| manufacturer |
|
| matrix_composition |
|
| max_value |
|
| mcc_assays |
Collection of mucociliary clearance assays |
| min_value |
|
| model_species |
The species of origin for the cells or organism being studied |
| molecular_initiating_event |
The molecular initiating event that starts this AOP |
| molecular_protocol |
Reference to the molecular assay protocol used |
| mrna_level |
mRNA expression level |
| muc5ac_mrna_expression |
MUC5AC mRNA expression level (fold change) |
| muc5ac_muc5b_ratio |
MUC5AC to MUC5B ratio |
| muc5ac_protein_expression |
MUC5AC protein expression level |
| muc5b_mrna_expression |
MUC5B mRNA expression level (fold change) |
| muc5b_protein_expression |
MUC5B protein expression level |
| mucin_protein_concentration |
Total mucin protein concentration |
| mucin_secretion_rate |
Mucin secretion rate |
| mucus_composition |
Composition of mucus |
| mucus_layer_thickness |
Thickness of the mucus gel layer in micrometers |
| mucus_viscosity |
Mucus viscosity in centipoise |
| mycoplasma_status |
|
| name |
A human-readable name for the entity |
| nasal_potential_difference |
Nasal potential difference in mV |
| neutrophil_percentage |
Neutrophil percentage in BALF/sputum |
| nitrotyrosine_level |
Nitrotyrosine level |
| normalization_method |
Method used for data normalization |
| normalization_reference |
Normalization reference (beta-actin, GAPDH, total EGFR) |
| nrf2_activation |
Nrf2 activation level |
| obi_mapping |
OBI ontology term for this method |
| occurs_in_anatomy |
The anatomical location where this key event occurs |
| occurs_in_cell_type |
The cell type in which this key event occurs |
| organoid_type |
|
| osmolality |
|
| outcome_level |
The level at which the adverse outcome manifests (individual, population) |
| oxidative_stress_assays |
Collection of oxidative stress assays |
| particle_clearance_time |
Time for particle clearance |
| particle_size |
Size of tracking particles |
| particle_tracking_method |
Method used for tracking particles or mucus |
| passage_number |
|
| pathway_biomarkers |
Pathway-specific biomarker signatures |
| peak_expiratory_flow |
Peak expiratory flow |
| percent_solids |
Percent solids in apical secretion (overall secretion) |
| percentage_active_transport |
Percentage of area showing active transport |
| percentage_ciliated_cells |
Percentage of cells that are ciliated |
| percentage_positive_cells |
Percentage of positive cells (IHC, flow cytometry) |
| periciliary_layer_depth |
Depth of the periciliary layer in micrometers |
| phosphorylation_site |
Specific phosphorylation site being measured |
| platform |
Assay platform or instrument used (e |
| plethysmography_method |
Method for plethysmography measurement |
| preparation_date |
|
| primary_cell |
|
| primer_sequences |
Primer sequences used for PCR-based methods |
| protein_carbonyl_content |
Protein carbonyl content |
| protein_level |
Protein expression level |
| protein_oxidation_markers |
Protein oxidation markers (carbonyls, nitrotyrosine) |
| protocol_author |
Author of the protocol |
| protocol_type |
The specific type of protocol |
| protocol_version |
Version of the protocol |
| protocols |
Collection of protocols |
| publication_reference |
Reference to protocol publication |
| quality_control_criteria |
Quality control acceptance criteria |
| quantitative_understanding |
Level of quantitative understanding of the relationship |
| reactive_oxygen_species |
ROS level as fold change or fluorescence intensity |
| recent_respiratory_illness |
Recent respiratory illness (affects spirometry) |
| reference_dataset |
Reference dataset for interpretation (GLI-2012 for humans) |
| reference_gene |
Reference/housekeeping gene used for normalization |
| relationship_type |
The type of causal relationship (directly leads to, indirectly leads to) |
| replicate_requirements |
Number of replicates required |
| replicates_per_donor |
Number of biological replicates per donor |
| residual_volume |
Residual volume |
| ros_probe_type |
Type of ROS probe used (DCFDA, DHE, MitoSOX, etc |
| sample_collection_method |
Method used for sample collection in vivo (e |
| sample_type |
Type of biological sample (e |
| seeding_density |
|
| serum_concentration |
|
| serum_type |
|
| sex |
Biological sex of the subject |
| size_range |
|
| sop_reference |
Reference to standard operating procedure document |
| spatial_resolution |
Spatial resolution of imaging (e |
| spirometry_protocol |
Reference to the spirometry protocol used |
| spirometry_standard |
Spirometry standard followed (e |
| staining_protocol |
Reference to staining protocol (AB-PAS, immunochem) |
| staining_type |
Type of staining used (e |
| stimulation_agent |
Stimulation agent used (e |
| stressors |
Chemical or physical stressors that can trigger this AOP |
| study_subject |
The subject of the study — what the assay is performed on |
| sub_protocols |
Other protocols that are part of this protocol's workflow |
| subject_characteristics |
Relevant subject characteristics (disease state, medications, etc |
| subject_type |
The specific type of study subject |
| subjects |
Individual subjects in the population or cohort |
| substrate_type |
|
| superoxide_dismutase_activity |
SOD activity |
| supplement_type |
|
| supplements |
|
| supplier |
|
| sweat_chloride_concentration |
Sweat chloride concentration in mEq/L (CF diagnostic) |
| target_cell_type |
The specific cell type that is the primary focus of this assay's analysis, wh... |
| target_gene |
Target gene being measured |
| target_molecule |
The molecular target of the stressor in the MIE (e |
| temperature_control |
Temperature conditions during the procedure (e |
| timing_post_exposure |
Time after exposure when the measurement was taken |
| tissue_origin |
|
| tnf_alpha_concentration |
TNF-alpha concentration |
| total_antioxidant_capacity |
Total antioxidant capacity |
| total_cell_count |
Total cell count in BALF/sputum |
| total_egfr_protein |
Total EGFR protein level (loading control) |
| total_lung_capacity |
Total lung capacity |
| total_protein_concentration |
Total protein concentration |
| transport_directionality |
Directionality of mucociliary transport |
| transport_rate |
Mucociliary transport rate |
| unit |
The unit of measurement |
| upstream_event |
The upstream key event in this relationship (cause) |
| upstream_key_events |
Key events that lead to this key event (upstream in the pathway) |
| validation_status |
Validation status of the protocol |
| value |
The numeric value of the quantity |