ExperimentSchema Unified ontology for MiM for experiments, including Investigation, Study, ObservationUnit, Sample, and Assay. value owl:Thing 1 0 1 0 0 0 0 1 1 1 1 1 1 1 1 1 0 1 0 0 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 0 1 1 1 1 1 1 1 1 linkml:Boolean linkml:ClassDefinition linkml:Date linkml:Integer linkml:SlotDefinition linkml:String linkml:TypeDefinition ExperimentSchema Unified ontology for MiM for experiments, including Investigation, Study, ObservationUnit, Sample, and Assay. mife:AcidFlowRate AcidFlowRate AcidFlowRate mife:AcidType AcidType AcidType mife:AcidWeight AcidWeight AcidWeight mife:AerationRate AerationRate AerationRate mife:AgitationRate AgitationRate AgitationRate mife:AmountOfInoculum AmountOfInoculum AmountOfInoculum mife:AntifoamType AntifoamType AntifoamType mife:AntifoamWeight AntifoamWeight AntifoamWeight mife:Assay Assay Assay Specific individual experiments or measurements applied on samples. (An assay is a combination of a process (experiment) and a protocol., http://jermontology.org/ontology/JERMOntology#Assay) mife:AssayType AssayType AssayType mife:BaseFlowRate BaseFlowRate BaseFlowRate mife:BaseType BaseType BaseType mife:BaseWeight BaseWeight BaseWeight mife:BiosafetyLevel BiosafetyLevel BiosafetyLevel mife:CompoundName CompoundName CompoundName mife:Concentration Concentration Concentration mife:ConcentrationMethod ConcentrationMethod ConcentrationMethod mife:ControlScheme ControlScheme ControlScheme mife:CultivationType CultivationType CultivationType mife:Designations Designations Designations mife:DilutionRate DilutionRate DilutionRate mife:FeedFlowRate FeedFlowRate FeedFlowRate mife:FeedWeight FeedWeight FeedWeight mife:GasFlowRate GasFlowRate GasFlowRate mife:Gmo Gmo Gmo mife:HarvestFlowRate HarvestFlowRate HarvestFlowRate mife:HarvestWeight HarvestWeight HarvestWeight mife:InductionRate InductionRate InductionRate mife:InitialWorkingVolume InitialWorkingVolume InitialWorkingVolume mife:InoculationSource InoculationSource InoculationSource mife:InoculumComposition InoculumComposition InoculumComposition mife:Investigation Investigation Investigation A high level description of the overall area of research. This may be the overall aims of the project, as stated on your grant. If your project has several subprojects that do not share any data, you should define an investigation for each. mife:LocalId LocalId LocalId mife:Modifications Modifications Modifications mife:Morphology Morphology Morphology mife:ObservationUnit ObservationUnit ObservationUnit mife:Observationunit Observationunit Observationunit A single bioreactor/microwell/flask cultivation fermentation run. mife:Organism Organism Organism mife:OxygenDependence OxygenDependence OxygenDependence mife:Pathogenicity Pathogenicity Pathogenicity mife:Pco2 Pco2 Pco2 mife:Ph Ph Ph mife:Phase Phase Phase mife:Po2 Po2 Po2 mife:PrecultureDescription PrecultureDescription PrecultureDescription mife:PrecultureMedium PrecultureMedium PrecultureMedium mife:Predox Predox Predox mife:Pressure Pressure Pressure mife:Protocol Protocol Protocol mife:ProtocolUrl ProtocolUrl ProtocolUrl mife:PurificationMethod PurificationMethod PurificationMethod mife:RecipeUrl RecipeUrl RecipeUrl mife:RelativePressure RelativePressure RelativePressure mife:Replicate Replicate Replicate mife:ReplicateId ReplicateId ReplicateId mife:ReplicateType ReplicateType ReplicateType mife:Resistance Resistance Resistance mife:ResistanceMic ResistanceMic ResistanceMic mife:Sample Sample Sample Entity (material from a fermentation run) that is converted into a new item (material or data) via a process (physical or computational). mife:SampleCollectionDevice SampleCollectionDevice SampleCollectionDevice mife:SampleCollectionMethod SampleCollectionMethod SampleCollectionMethod mife:SampleDescription SampleDescription SampleDescription mife:SampleDryMass SampleDryMass SampleDryMass mife:SampleMaterial SampleMaterial SampleMaterial mife:SampleMaterialProcessing SampleMaterialProcessing SampleMaterialProcessing mife:SampleName SampleName SampleName mife:SampleStorageBuffer SampleStorageBuffer SampleStorageBuffer mife:SampleStorageConditions SampleStorageConditions SampleStorageConditions mife:SampleStorageContainer SampleStorageContainer SampleStorageContainer mife:SampleStorageDuration SampleStorageDuration SampleStorageDuration mife:SampleStorageLocation SampleStorageLocation SampleStorageLocation mife:SampleStorageTemperature SampleStorageTemperature SampleStorageTemperature mife:SampleTreatment SampleTreatment SampleTreatment mife:SampleWetMass SampleWetMass SampleWetMass mife:SamplingTimePoint SamplingTimePoint SamplingTimePoint mife:SequenceAccessionNumber SequenceAccessionNumber SequenceAccessionNumber mife:Source Source Source mife:Species Species Species mife:Study Study Study A particular biological hypothesis, which you are planning to test in various ways, using various techniques, which could be experimental. mife:SubstrateFlowRate SubstrateFlowRate SubstrateFlowRate mife:TargetMetabolite TargetMetabolite TargetMetabolite mife:TaxonomyId TaxonomyId TaxonomyId mife:TechnologyType TechnologyType TechnologyType mife:Temperature Temperature Temperature mife:TemperatureOfInoculum TemperatureOfInoculum TemperatureOfInoculum mife:Vessel Vessel Vessel mife:Volume Volume Volume mife:WaterFlowRate WaterFlowRate WaterFlowRate mife:Weight Weight Weight acid_flow_rate The rate at which acid is added to the system for pH control (mL/min) acid_type The type of acid used for pH adjustment in the fermentation process. acid_weight The total weight of acid added during the fermentation process. aeration_rate The rate at which the oxygen-containing gas is supplied to the vessel agitation_rate The speed of agitation or stirring in the vessel (rpm). amount_of_inoculum The volume, OD or mass of inoculum added to the fermentation vessel. antifoam_type The type of antifoam agent used to control foam formation in the vessel. antifoam_weight The total weight of antifoam added during the fermentation process. assay_identifier unique assay identifier assay_type type of the assay bacdive_id ID used by the bacdive database base_flow_rate The rate at which base is added to the system for pH control (mL/min) base_type The type of base used for pH adjustment in the fermentation process. base_weight The total weight of base added during the fermentation process. biosafety_level The levels of containment range from the lowest biosafety level 1 to the highest at level 4 compound_name Chemical compounds used in the fermentation process as feed. concentration The amount of a compound present per unit volume or mass (expressed in mg/L or %) concentration_method The method used to concentrate the inoculum, e.g., filtration or centrifugation. control_scheme The system or methodology used to monitor, regulate, and optimize the various operational parameters of the bioreactor cultivation_type The type of cultivation process used, e.g., batch, fed-batch, or continuous. culture_collection_id culture collection numbers of the strain description description of the purpose of the fermentation run designations designations of the strains dilution_rate The inital rate at which fresh medium is added and spent medium is removed in continuous cultures. mife:duration end_date date that the fermentation run ended fedbatch_rate The rate at which feed is supplied during fed-batch fermentation. fedbatch_trigger The conditions that trigger feed addition in fed-batch processes, such as substrate depletion. fedbatch_type The type of fed-batch fermentation (e.g., constant, linear, or exponential feeding). feed_flow_rate The rate at which feed is added to the fermentation vessel, (mL/min or L/h). feed_type The type of feed used during the fermentation process, such as liquid, solid, or gas. feed_weight The total weight of feed material added during the fermentation process. gas_flow_rate The rate of gas introduced into the vessel (mL/min or L/min). gas_input_composition The initial composition of gases supplied to the vessel (e.g., oxygen, nitrogen, or carbon dioxide) gmo is the strain genetically modified? harvest_flow_rate The rate at which the biomass or product is collected from the vessel harvest_weight The total weight of material collected at the end of the fermentation process. harvesting_conditions The specific conditions under which the inoculum is harvested, such as temperature or pH. id unique investigation identifier induction_rate The speed or extent of the induction (per volume of culture or per time unit). induction_trigger The specific condition or signal that initiates induction, such as temperature or nutrient level. induction_trigger_duration The time period for which induction conditions are maintained. induction_type The method used to induce gene expression or metabolic activity, e.g., chemical or thermal. initial_working_volume The starting volume of liquid in the fermentation vessel. inoculation_source The origin of the inoculum, such as a strain collection or preculture flask. inoculum_composition The composition of the inoculum, including strains and concentrations/proportions of the composition when more than one strain is involved. inoculum_duration The time for which the inoculum is cultured before use. (note, maybe use OD?) inoculum_type The type of inoculum used, such as a single strain or a mixed culture. input_localisation The physical location or point where inputs like feed or gas are introduced into the system. internal_id A laboratory specific internal ID from the labotatory that performed the analysis for example the bioreactor name or the biolector plate ID and corresponding well local_id ID used by the laboratory that uses/developed the strain modifications what was genetically modified? morphology morphology of the strain observation_unit_id unique identifier of the related study (multiple observationUnits can be part of the same study) observation_unit_identifier unique observation unit identifier organism type of organism oxygen_dependence oxygen dependent metabolism of the strain pathogenicity pathogenic to a specific group (e.g. human, animal, plant) pco2 partial CO2 pressure ph The initial set pH value phase A distinct stage in the fermentation process, such as lag phase, log phase, or stationary phase. phase_duration The total time duration of a specific phase in minutes during the fermentation process. phase_end_time The time when a specific phase ends during the fermentation process. phase_purpose The intended outcome or goal of a specific phase in the process, e.g., growth or product synthesis. phase_start_time The time when a specific phase begins during the fermentation process. po2 partial O2 pressure preculture_description A detailed description of the preculture, including growth conditions. preculture_medium The medium used to grow the preculture before inoculation. predox Oxidation-reduction potential (ORP) in the vessel pressure The set pressure level maintained during the fermentation process protocol URL of a document that described the "protocol" of the fermentation run protocol_url standard operating procedure (or protocol) purification_method The method used to purify the product, e.g., chromatography or precipitation. recipe_url standard operating procedure (or protocol) for sampling references useful articles used as basis/starting point for the present study relative_pressure The pressure relative to atmospheric pressure maintained in the vessel. replicate A role played by a a biological sample in the context of an experiment where the intent is that biological or technical variation is measured. replicate_id A unique identifier for experimental replicates in the fermentation study. replicate_type The type of replicate, e.g., biological or technical. resistance what substance is the strain resistant to? resistance_mic concentration for the resistance (MIC) sample_collection_device The device used for collecting the sample sample_collection_method The method employed for collecting the sample sample_description description of the sample sample_dry_mass measurement of dry mass at the time of sample collection sample_id unique identifier (does not need to be human readable) of the related sample (multiple samples can be taken from the same observationUnits) sample_identifier unique sample identifier sample_material Sample material from which data deposited was generated sample_material_processing Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2013-10-25) terms please see http://purl.bioontology.org/ontology/OBI sample_name name of the sample sample_storage_buffer buffer used for sample storage sample_storage_conditions Additional information about the conditions at which sample was stored sample_storage_container Container that sample was stored in e.g. tube type sample_storage_duration duration for which sample was stored sample_storage_location location at which sample was stored, usually name of a specific freezer/room sample_storage_temperature temperature at which sample was stored sample_treatment Treatment applied to the sample sample_wet_mass measurement of wet mass at the time of sample collection sampling_time_point date that the sample was collected sequence_accession_number accession number of the sequence in public sequence databases source where does the strain come from species name of the species sporulation does the strain exhibits endospore formation? start_date date that the fermentation run was initiated study_id unique identifier of the related study (multiple studies can be part of the same investigation) substrate_flow_rate The rate at which the substrate is added to the fermentation vessel target_metabolite The specific compound or metabolite that is the desired outcome of the fermentation process. taxonomy_id NCBI taxonomy ID of the strain technology_type technology used to perform the assay temperature The inital set temperature temperature_of_inoculum The temperature at which the inoculum is maintained. title title of the cultivation/fermentation (bioreactor, well) vessel_id_ unique identifier of the vessel that was used to perform the run (refers to MIM for equipment) volume Liquid volume in the vessel water_flow_rate The rate at which water is added to the system, (L/h or mL/min). weight The total weight of the vessel contents, including medium and biomass.