Class: ObservationUnit (ObservationUnit)¶
URI: mife:ObservationUnit
classDiagram
class ObservationUnit
click ObservationUnit href "../ObservationUnit/"
ObservationUnit : acid_flow_rate
ObservationUnit : acid_type
ObservationUnit : acid_weight
ObservationUnit : aeration_rate
ObservationUnit : agitation_rate
ObservationUnit : amount_of_inoculum
ObservationUnit : antifoam_type
ObservationUnit : antifoam_weight
ObservationUnit : bacdive_id
ObservationUnit : base_flow_rate
ObservationUnit : base_type
ObservationUnit : base_weight
ObservationUnit : biosafety_level
ObservationUnit : compound_name
ObservationUnit : concentration
ObservationUnit : concentration_method
ObservationUnit : control_scheme
ObservationUnit : cultivation_type
ObservationUnit : culture_collection_id
ObservationUnit : description
ObservationUnit : designations
ObservationUnit : dilution_rate
ObservationUnit : end_date
ObservationUnit : fedbatch_rate
ObservationUnit : fedbatch_trigger
ObservationUnit : fedbatch_type
ObservationUnit : feed_flow_rate
ObservationUnit : feed_type
ObservationUnit : feed_weight
ObservationUnit : gas_flow_rate
ObservationUnit : gas_input_composition
ObservationUnit : gmo
ObservationUnit : harvest_flow_rate
ObservationUnit : harvest_weight
ObservationUnit : harvesting_conditions
ObservationUnit : induction_rate
ObservationUnit : induction_trigger
ObservationUnit : induction_trigger_duration
ObservationUnit : induction_type
ObservationUnit : initial_working_volume
ObservationUnit : inoculation_source
ObservationUnit : inoculum_composition
ObservationUnit : inoculum_duration
ObservationUnit : inoculum_type
ObservationUnit : input_localisation
ObservationUnit : internal_id
ObservationUnit : local_id
ObservationUnit : modifications
ObservationUnit : morphology
ObservationUnit : observation_unit_identifier
ObservationUnit : organism
ObservationUnit : oxygen_dependence
ObservationUnit : pathogenicity
ObservationUnit : pco2
ObservationUnit : ph
ObservationUnit : phase
ObservationUnit : phase_duration
ObservationUnit : phase_end_time
ObservationUnit : phase_purpose
ObservationUnit : phase_start_time
ObservationUnit : po2
ObservationUnit : preculture_description
ObservationUnit : preculture_medium
ObservationUnit : predox
ObservationUnit : pressure
ObservationUnit : protocol
ObservationUnit : purification_method
ObservationUnit : relative_pressure
ObservationUnit : replicate_id
ObservationUnit : replicate_type
ObservationUnit : resistance
ObservationUnit : resistance_mic
ObservationUnit : sample_id
ObservationUnit --> "*" Sample : sample_id
click Sample href "../Sample/"
ObservationUnit : sequence_accession_number
ObservationUnit : source
ObservationUnit : species
ObservationUnit : sporulation
ObservationUnit : start_date
ObservationUnit : substrate_flow_rate
ObservationUnit : target_metabolite
ObservationUnit : taxonomy_id
ObservationUnit : temperature
ObservationUnit : temperature_of_inoculum
ObservationUnit : title
ObservationUnit : vessel_id_
ObservationUnit --> "1" Vessel : vessel_id_
click Vessel href "../Vessel/"
ObservationUnit : volume
ObservationUnit : water_flow_rate
ObservationUnit : weight
Slots¶
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| observation_unit_identifier | 1 String |
unique observation unit identifier | direct |
| vessel_id_ | 1 Vessel |
unique identifier of the vessel that was used to perform the run (refers to M... | direct |
| title | 1 String |
title of the cultivation/fermentation (bioreactor, well) | direct |
| description | 1 String |
description of the purpose of the fermentation run | direct |
| start_date | 0..1 Date |
date that the fermentation run was initiated | direct |
| end_date | 0..1 Date |
date that the fermentation run ended | direct |
| internal_id | 0..1 String |
A laboratory specific internal ID from the labotatory that performed the anal... | direct |
| protocol | 0..1 String |
URL of a document that described the "protocol" of the fermentation run | direct |
| sample_id | * Sample |
unique identifier (does not need to be human readable) of the related sample ... | direct |
| culture_collection_id | * String |
culture collection numbers of the strain | direct |
| designations | 0..1 String |
designations of the strains | direct |
| source | 0..1 String |
where does the strain come from | direct |
| organism | 0..1 String |
type of organism | direct |
| species | 0..1 String |
name of the species | direct |
| taxonomy_id | 0..1 Integer |
NCBI taxonomy ID of the strain | direct |
| local_id | 0..1 String |
ID used by the laboratory that uses/developed the strain | direct |
| bacdive_id | 0..1 String |
ID used by the bacdive database | direct |
| sequence_accession_number | 0..1 String |
accession number of the sequence in public sequence databases | direct |
| biosafety_level | 0..1 String |
The levels of containment range from the lowest biosafety level 1 to the high... | direct |
| pathogenicity | 0..1 String |
pathogenic to a specific group (e | direct |
| gmo | 0..1 Boolean |
is the strain genetically modified? | direct |
| modifications | 0..1 String |
what was genetically modified? | direct |
| resistance | * String |
what substance is the strain resistant to? | direct |
| resistance_mic | 0..1 Float |
concentration for the resistance (MIC) | direct |
| oxygen_dependence | 0..1 String |
oxygen dependent metabolism of the strain | direct |
| morphology | 0..1 String |
morphology of the strain | direct |
| sporulation | 0..1 Boolean |
does the strain exhibits endospore formation? | direct |
| feed_type | 0..1 String |
The type of feed used during the fermentation process, such as liquid, solid,... | direct |
| feed_weight | 0..1 Float |
The total weight of feed material added during the fermentation process | direct |
| compound_name | 0..1 String |
Chemical compounds used in the fermentation process as feed | direct |
| concentration | 0..1 Float |
The amount of a compound present per unit volume or mass (expressed in mg/L o... | direct |
| feed_flow_rate | 0..1 Float |
The rate at which feed is added to the fermentation vessel, (mL/min or L/h) | direct |
| control_scheme | 0..1 String |
The system or methodology used to monitor, regulate, and optimize the various... | direct |
| input_localisation | 0..1 String |
The physical location or point where inputs like feed or gas are introduced i... | direct |
| phase | 0..1 String |
A distinct stage in the fermentation process, such as lag phase, log phase, o... | direct |
| phase_purpose | 0..1 String |
The intended outcome or goal of a specific phase in the process, e | direct |
| phase_start_time | 0..1 Date |
The time when a specific phase begins during the fermentation process | direct |
| phase_end_time | 0..1 Date |
The time when a specific phase ends during the fermentation process | direct |
| phase_duration | 0..1 Duration |
The total time duration of a specific phase in minutes during the fermentatio... | direct |
| temperature | 0..1 Float |
The inital set temperature | direct |
| ph | 0..1 Float |
The initial set pH value | direct |
| po2 | 0..1 Float |
partial O2 pressure | direct |
| pco2 | 0..1 Float |
partial CO2 pressure | direct |
| predox | 0..1 Float |
Oxidation-reduction potential (ORP) in the vessel | direct |
| volume | 0..1 Integer |
Liquid volume in the vessel | direct |
| pressure | 0..1 Float |
The set pressure level maintained during the fermentation process | direct |
| weight | 0..1 Float |
The total weight of the vessel contents, including medium and biomass | direct |
| substrate_flow_rate | 0..1 Float |
The rate at which the substrate is added to the fermentation vessel | direct |
| acid_type | 0..1 String |
The type of acid used for pH adjustment in the fermentation process | direct |
| base_type | 0..1 String |
The type of base used for pH adjustment in the fermentation process | direct |
| antifoam_type | 0..1 String |
The type of antifoam agent used to control foam formation in the vessel | direct |
| acid_weight | 0..1 Float |
The total weight of acid added during the fermentation process | direct |
| base_weight | 0..1 Float |
The total weight of base added during the fermentation process | direct |
| antifoam_weight | 0..1 Float |
The total weight of antifoam added during the fermentation process | direct |
| harvest_weight | 0..1 Float |
The total weight of material collected at the end of the fermentation process | direct |
| acid_flow_rate | 0..1 Float |
The rate at which acid is added to the system for pH control (mL/min) | direct |
| base_flow_rate | 0..1 Float |
The rate at which base is added to the system for pH control (mL/min) | direct |
| aeration_rate | 0..1 Float |
The rate at which the oxygen-containing gas is supplied to the vessel | direct |
| water_flow_rate | 0..1 Float |
The rate at which water is added to the system, (L/h or mL/min) | direct |
| harvest_flow_rate | 0..1 Float |
The rate at which the biomass or product is collected from the vessel | direct |
| agitation_rate | 0..1 Float |
The speed of agitation or stirring in the vessel (rpm) | direct |
| gas_flow_rate | 0..1 Float |
The rate of gas introduced into the vessel (mL/min or L/min) | direct |
| gas_input_composition | * String |
The initial composition of gases supplied to the vessel (e | direct |
| relative_pressure | 0..1 Float |
The pressure relative to atmospheric pressure maintained in the vessel | direct |
| fedbatch_type | 0..1 String |
The type of fed-batch fermentation (e | direct |
| fedbatch_rate | 0..1 Integer |
The rate at which feed is supplied during fed-batch fermentation | direct |
| fedbatch_trigger | 0..1 String |
The conditions that trigger feed addition in fed-batch processes, such as sub... | direct |
| induction_type | 0..1 String |
The method used to induce gene expression or metabolic activity, e | direct |
| induction_trigger | 0..1 String |
The specific condition or signal that initiates induction, such as temperatur... | direct |
| induction_trigger_duration | 0..1 Duration |
The time period for which induction conditions are maintained | direct |
| induction_rate | 0..1 Float |
The speed or extent of the induction (per volume of culture or per time unit) | direct |
| cultivation_type | 0..1 String |
The type of cultivation process used, e | direct |
| inoculum_type | 0..1 String |
The type of inoculum used, such as a single strain or a mixed culture | direct |
| preculture_medium | 0..1 String |
The medium used to grow the preculture before inoculation | direct |
| inoculum_composition | 0..1 String |
The composition of the inoculum, including strains and concentrations/proport... | direct |
| harvesting_conditions | 0..1 String |
The specific conditions under which the inoculum is harvested, such as temper... | direct |
| concentration_method | 0..1 String |
The method used to concentrate the inoculum, e | direct |
| purification_method | 0..1 String |
The method used to purify the product, e | direct |
| preculture_description | 0..1 String |
A detailed description of the preculture, including growth conditions | direct |
| inoculum_duration | 0..1 Duration |
The time for which the inoculum is cultured before use | direct |
| temperature_of_inoculum | 0..1 Float |
The temperature at which the inoculum is maintained | direct |
| amount_of_inoculum | 0..1 String |
The volume, OD or mass of inoculum added to the fermentation vessel | direct |
| initial_working_volume | 0..1 Float |
The starting volume of liquid in the fermentation vessel | direct |
| dilution_rate | 0..1 Float |
The inital rate at which fresh medium is added and spent medium is removed in... | direct |
| inoculation_source | 0..1 String |
The origin of the inoculum, such as a strain collection or preculture flask | direct |
| target_metabolite | 0..1 String |
The specific compound or metabolite that is the desired outcome of the fermen... | direct |
| replicate_id | 0..1 String |
A unique identifier for experimental replicates in the fermentation study | direct |
| replicate_type | 0..1 String |
The type of replicate, e | direct |
Usages¶
| used by | used in | type | used |
|---|---|---|---|
| Study | observation_unit_id | range | ObservationUnit |
Identifier and Mapping Information¶
Schema Source¶
- from schema: https://ontology.ibisba.eu/mife/
Mappings¶
| Mapping Type | Mapped Value |
|---|---|
| self | mife:ObservationUnit |
| native | mife:ObservationUnit |
LinkML Source¶
Direct¶
name: ObservationUnit
title: ObservationUnit
from_schema: https://ontology.ibisba.eu/mife/
slots:
- observation_unit_identifier
- vessel_id_
- title
- description
- start_date
- end_date
- internal_id
- protocol
- sample_id
- culture_collection_id
- designations
- source
- organism
- species
- taxonomy_id
- local_id
- bacdive_id
- sequence_accession_number
- biosafety_level
- pathogenicity
- gmo
- modifications
- resistance
- resistance_mic
- oxygen_dependence
- morphology
- sporulation
- feed_type
- feed_weight
- compound_name
- concentration
- feed_flow_rate
- control_scheme
- input_localisation
- phase
- phase_purpose
- phase_start_time
- phase_end_time
- phase_duration
- temperature
- ph
- po2
- pco2
- predox
- volume
- pressure
- weight
- substrate_flow_rate
- acid_type
- base_type
- antifoam_type
- acid_weight
- base_weight
- antifoam_weight
- harvest_weight
- acid_flow_rate
- base_flow_rate
- aeration_rate
- water_flow_rate
- harvest_flow_rate
- agitation_rate
- gas_flow_rate
- gas_input_composition
- relative_pressure
- fedbatch_type
- fedbatch_rate
- fedbatch_trigger
- induction_type
- induction_trigger
- induction_trigger_duration
- induction_rate
- cultivation_type
- inoculum_type
- preculture_medium
- inoculum_composition
- harvesting_conditions
- concentration_method
- purification_method
- preculture_description
- inoculum_duration
- temperature_of_inoculum
- amount_of_inoculum
- initial_working_volume
- dilution_rate
- inoculation_source
- target_metabolite
- replicate_id
- replicate_type
class_uri: mife:ObservationUnit
Induced¶
name: ObservationUnit
title: ObservationUnit
from_schema: https://ontology.ibisba.eu/mife/
attributes:
observation_unit_identifier:
name: observation_unit_identifier
description: unique observation unit identifier
examples:
- value: REAC_1_001
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:identifier
alias: observation_unit_identifier
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: true
multivalued: false
vessel_id_:
name: vessel_id_
description: unique identifier of the vessel that was used to perform the run
(refers to MIM for equipment)
examples:
- value: REAC_1_V3
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:performedIn
alias: vessel_id_
owner: ObservationUnit
domain_of:
- ObservationUnit
range: Vessel
required: true
multivalued: false
title:
name: title
description: title of the cultivation/fermentation (bioreactor, well)
examples:
- value: 12h Bioreactor run of PBAD in PET28A under 0.05% Arabinose
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:title
alias: title
owner: ObservationUnit
domain_of:
- Assay
- Investigation
- Study
- ObservationUnit
range: string
required: true
multivalued: false
description:
name: description
description: description of the purpose of the fermentation run
examples:
- value: A 12h Bioreactor run using PBAD in PET28A with a concentration of 0.05%
Arabinose
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:description
alias: description
owner: ObservationUnit
domain_of:
- Assay
- Investigation
- Study
- ObservationUnit
range: string
required: true
multivalued: false
start_date:
name: start_date
description: date that the fermentation run was initiated
examples:
- value: 12-01-2023
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:startDate
alias: start_date
owner: ObservationUnit
domain_of:
- Assay
- Investigation
- Study
- ObservationUnit
range: date
required: false
multivalued: false
end_date:
name: end_date
description: date that the fermentation run ended
examples:
- value: 13-01-2023
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:endDate
alias: end_date
owner: ObservationUnit
domain_of:
- Assay
- Investigation
- Study
- ObservationUnit
range: date
required: false
multivalued: false
internal_id:
name: internal_id
description: 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
examples:
- value: A04
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:identifier
alias: internal_id
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
protocol:
name: protocol
description: URL of a document that described the "protocol" of the fermentation
run
examples:
- value: https://ibisbahub.eu/sops/21
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:procedure
alias: protocol
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
sample_id:
name: sample_id
description: unique identifier (does not need to be human readable) of the related
sample (multiple samples can be taken from the same observationUnits)
examples:
- value: 245978vn475nv34575m597hcvn7vfnv57gvn57
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: jermontology:hasPart
alias: sample_id
owner: ObservationUnit
domain_of:
- ObservationUnit
range: Sample
required: false
multivalued: true
culture_collection_id:
name: culture_collection_id
description: culture collection numbers of the strain
examples:
- value: DSM 1234
- value: ATCC 2345
- value: CBS 9876
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasCultureCollectionID
alias: culture_collection_id
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: true
designations:
name: designations
description: designations of the strains
examples:
- value: R7
- value: J.Smith.11
- value: Dec-2023-42
- value: '#556'
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:alternateName
alias: designations
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
source:
name: source
description: where does the strain come from
examples:
- value: Institut Pasteur
- value: WI-KNAW
- value: John Doe
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:sourceOrganization
alias: source
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
organism:
name: organism
description: type of organism
examples:
- value: Bacteria
- value: Archeae
- value: Yeast
- value: Fungi
- value: Algae
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasOrganism
alias: organism
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
species:
name: species
description: name of the species
examples:
- value: E.coli
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasSpecies
alias: species
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
taxonomy_id:
name: taxonomy_id
description: NCBI taxonomy ID of the strain
examples:
- value: '7556'
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:identifier
alias: taxonomy_id
owner: ObservationUnit
domain_of:
- ObservationUnit
range: integer
required: false
multivalued: false
local_id:
name: local_id
description: ID used by the laboratory that uses/developed the strain
examples:
- value: IMB_500
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:identifier
alias: local_id
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
bacdive_id:
name: bacdive_id
description: ID used by the bacdive database
examples:
- value: bds_1
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:identifier
alias: bacdive_id
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
sequence_accession_number:
name: sequence_accession_number
description: accession number of the sequence in public sequence databases
examples:
- value: AB595134
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasSequenceAccessionNumber
alias: sequence_accession_number
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
biosafety_level:
name: biosafety_level
description: The levels of containment range from the lowest biosafety level 1
to the highest at level 4
examples:
- value: '2'
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasBiosafetyLevel
alias: biosafety_level
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
pathogenicity:
name: pathogenicity
description: pathogenic to a specific group (e.g. human, animal, plant)
examples:
- value: human
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasStrainPathogenicity
alias: pathogenicity
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
gmo:
name: gmo
description: is the strain genetically modified?
examples:
- value: yes/no
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:isGMO
alias: gmo
owner: ObservationUnit
domain_of:
- ObservationUnit
range: boolean
required: false
multivalued: false
modifications:
name: modifications
description: what was genetically modified?
examples:
- value: free text
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasStrainGeneticModifications
alias: modifications
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
resistance:
name: resistance
description: what substance is the strain resistant to?
examples:
- value: ampicillin
- value: kanamycin
- value: streptomycin
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: w3id6:associated_with_resistance_to
alias: resistance
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: true
resistance_mic:
name: resistance_mic
description: concentration for the resistance (MIC)
examples:
- value: 4 mg/L
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:mic
alias: resistance_mic
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
oxygen_dependence:
name: oxygen_dependence
description: oxygen dependent metabolism of the strain
examples:
- value: aerobic/anaerobic
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:relationshipToOxygen
alias: oxygen_dependence
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
morphology:
name: morphology
description: morphology of the strain
examples:
- value: rod-shaped
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasStrainMorphology
alias: morphology
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
sporulation:
name: sporulation
description: does the strain exhibits endospore formation?
examples:
- value: yes/no
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasStrainSporulation
alias: sporulation
owner: ObservationUnit
domain_of:
- ObservationUnit
range: boolean
required: false
multivalued: false
feed_type:
name: feed_type
description: The type of feed used during the fermentation process, such as liquid,
solid, or gas.
examples:
- value: liquid
- value: solid
- value: gas
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasFeedType
alias: feed_type
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
feed_weight:
name: feed_weight
description: The total weight of feed material added during the fermentation process.
examples:
- value: 100 g
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasFeedMass
alias: feed_weight
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
compound_name:
name: compound_name
description: Chemical compounds used in the fermentation process as feed.
examples:
- value: glucose
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: obolibrary:OBI_0000293
alias: compound_name
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
concentration:
name: concentration
description: The amount of a compound present per unit volume or mass (expressed
in mg/L or %)
examples:
- value: 2 g/L
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasConcentration
alias: concentration
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
feed_flow_rate:
name: feed_flow_rate
description: The rate at which feed is added to the fermentation vessel, (mL/min
or L/h).
examples:
- value: 0.5 L/h
- value: 40 mL/min
- value: exponential, mu=0.1h-1, starting from 1 mL/min
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:feedRate
alias: feed_flow_rate
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
control_scheme:
name: control_scheme
description: The system or methodology used to monitor, regulate, and optimize
the various operational parameters of the bioreactor
examples:
- value: pH control
- value: temperature control
- value: user control
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:usedProcedure
alias: control_scheme
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
input_localisation:
name: input_localisation
description: The physical location or point where inputs like feed or gas are
introduced into the system.
examples:
- value: top feed
- value: bottom feed
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:inputLocation
alias: input_localisation
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
phase:
name: phase
description: A distinct stage in the fermentation process, such as lag phase,
log phase, or stationary phase.
examples:
- value: lag phase
- value: log phase
- value: stationary phase
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasGrowthPhase
alias: phase
owner: ObservationUnit
domain_of:
- Sample
- ObservationUnit
range: string
required: false
multivalued: false
phase_purpose:
name: phase_purpose
description: The intended outcome or goal of a specific phase in the process,
e.g., growth or product synthesis.
examples:
- value: growth
- value: antibody synthesis
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasPhasePurpose
alias: phase_purpose
owner: ObservationUnit
domain_of:
- Sample
- ObservationUnit
range: string
required: false
multivalued: false
phase_start_time:
name: phase_start_time
description: The time when a specific phase begins during the fermentation process.
examples:
- value: 2024-01-05 09:55
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:startDate
alias: phase_start_time
owner: ObservationUnit
domain_of:
- ObservationUnit
range: date
required: false
multivalued: false
phase_end_time:
name: phase_end_time
description: The time when a specific phase ends during the fermentation process.
examples:
- value: 2024-01-05 13:55
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:endDate
alias: phase_end_time
owner: ObservationUnit
domain_of:
- ObservationUnit
range: date
required: false
multivalued: false
phase_duration:
name: phase_duration
description: The total time duration of a specific phase in minutes during the
fermentation process.
examples:
- value: 240 minutes
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasPhaseDuration
alias: phase_duration
owner: ObservationUnit
domain_of:
- Sample
- ObservationUnit
range: duration
required: false
multivalued: false
temperature:
name: temperature
description: The inital set temperature
examples:
- value: 25 degrees celsius
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasInitialSetTemperature
alias: temperature
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
ph:
name: ph
description: The initial set pH value
examples:
- value: '7.1'
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: w3id:0001001
alias: ph
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
po2:
name: po2
description: partial O2 pressure
examples:
- value: 20%
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasPartialO2Pressure
alias: po2
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
pco2:
name: pco2
description: partial CO2 pressure
examples:
- value: 5%
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasPartialCO2Pressure
alias: pco2
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
predox:
name: predox
description: Oxidation-reduction potential (ORP) in the vessel
examples:
- value: 250 mV
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasOxidationReductionPotential
alias: predox
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
volume:
name: volume
description: Liquid volume in the vessel
examples:
- value: 800 mL
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasVolume
alias: volume
owner: ObservationUnit
domain_of:
- Sample
- ObservationUnit
range: integer
required: false
multivalued: false
pressure:
name: pressure
description: The set pressure level maintained during the fermentation process
examples:
- value: 1.5 bar
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: w3id:0000412
alias: pressure
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
weight:
name: weight
description: The total weight of the vessel contents, including medium and biomass.
examples:
- value: 12 kg
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:netWeight
alias: weight
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
substrate_flow_rate:
name: substrate_flow_rate
description: The rate at which the substrate is added to the fermentation vessel
examples:
- value: 0.1 g/L/h
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasSubstrateFlowRate
alias: substrate_flow_rate
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
acid_type:
name: acid_type
description: The type of acid used for pH adjustment in the fermentation process.
examples:
- value: HCl
- value: H2SO4
- value: acetic acid
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasAcidType
alias: acid_type
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
base_type:
name: base_type
description: The type of base used for pH adjustment in the fermentation process.
examples:
- value: NaOH
- value: Sodium Carbonate
- value: Tris
- value: NH3
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasBaseType
alias: base_type
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
antifoam_type:
name: antifoam_type
description: The type of antifoam agent used to control foam formation in the
vessel.
examples:
- value: Antifoam A
- value: Antifoam B
- value: Tegostar
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasAntifoamType
alias: antifoam_type
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
acid_weight:
name: acid_weight
description: The total weight of acid added during the fermentation process.
examples:
- value: 10 g
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:netAcidWeight
alias: acid_weight
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
base_weight:
name: base_weight
description: The total weight of base added during the fermentation process.
examples:
- value: 10 g
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:netBaseWeight
alias: base_weight
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
antifoam_weight:
name: antifoam_weight
description: The total weight of antifoam added during the fermentation process.
examples:
- value: 2 g
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:netAntifoamWeight
alias: antifoam_weight
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
harvest_weight:
name: harvest_weight
description: The total weight of material collected at the end of the fermentation
process.
examples:
- value: 10 g
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:netMaterialWeight
alias: harvest_weight
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
acid_flow_rate:
name: acid_flow_rate
description: The rate at which acid is added to the system for pH control (mL/min)
examples:
- value: 1.5 mL/min
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:acidAdditionRate
alias: acid_flow_rate
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
base_flow_rate:
name: base_flow_rate
description: The rate at which base is added to the system for pH control (mL/min)
examples:
- value: 1.5 mL/min
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:baseAdditionRate
alias: base_flow_rate
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
aeration_rate:
name: aeration_rate
description: The rate at which the oxygen-containing gas is supplied to the vessel
examples:
- value: 2 vvm (volume of gas per volume of liquid per minute)
- value: 20 L/min
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:oxygenAdditionRate
alias: aeration_rate
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
water_flow_rate:
name: water_flow_rate
description: The rate at which water is added to the system, (L/h or mL/min).
examples:
- value: 13 mL/min
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:waterAdditionRate
alias: water_flow_rate
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
harvest_flow_rate:
name: harvest_flow_rate
description: The rate at which the biomass or product is collected from the vessel
examples:
- value: 100 mL/min
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:productCollectionRate
alias: harvest_flow_rate
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
agitation_rate:
name: agitation_rate
description: The speed of agitation or stirring in the vessel (rpm).
examples:
- value: 300 rpm
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasAgitationRate
alias: agitation_rate
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
gas_flow_rate:
name: gas_flow_rate
description: The rate of gas introduced into the vessel (mL/min or L/min).
examples:
- value: 20 L/min
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasGasFlowRate
alias: gas_flow_rate
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
gas_input_composition:
name: gas_input_composition
description: The initial composition of gases supplied to the vessel (e.g., oxygen,
nitrogen, or carbon dioxide)
examples:
- value: 40% O2, 59% N2, 1% CO2
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasGasInputComposition
alias: gas_input_composition
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: true
relative_pressure:
name: relative_pressure
description: The pressure relative to atmospheric pressure maintained in the vessel.
examples:
- value: 2 kPa
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasGaugePressure
alias: relative_pressure
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
fedbatch_type:
name: fedbatch_type
description: The type of fed-batch fermentation (e.g., constant, linear, or exponential
feeding).
examples:
- value: constant feeding
- value: linear feeding
- value: exponential feeding
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasFedBatchType
alias: fedbatch_type
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
fedbatch_rate:
name: fedbatch_rate
description: The rate at which feed is supplied during fed-batch fermentation.
examples:
- value: 0.8 g/L/h
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasFedBatchRate
alias: fedbatch_rate
owner: ObservationUnit
domain_of:
- ObservationUnit
range: integer
required: false
multivalued: false
fedbatch_trigger:
name: fedbatch_trigger
description: The conditions that trigger feed addition in fed-batch processes,
such as substrate depletion.
examples:
- value: glucose depletion
- value: pH values
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasFedBatchTrigger
alias: fedbatch_trigger
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
induction_type:
name: induction_type
description: The method used to induce gene expression or metabolic activity,
e.g., chemical or thermal.
examples:
- value: chemical
- value: thermal
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasInductionType
alias: induction_type
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
induction_trigger:
name: induction_trigger
description: The specific condition or signal that initiates induction, such as
temperature or nutrient level.
examples:
- value: lactose
- value: IPTG
- value: temperature shift from 30°C to 42°C
- value: glucose depletion
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasInductionTrigger
alias: induction_trigger
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
induction_trigger_duration:
name: induction_trigger_duration
description: The time period for which induction conditions are maintained.
examples:
- value: 240 minutes
- value: 12 minutes
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasInductionTriggerDuration
alias: induction_trigger_duration
owner: ObservationUnit
domain_of:
- ObservationUnit
range: duration
required: false
multivalued: false
induction_rate:
name: induction_rate
description: The speed or extent of the induction (per volume of culture or per
time unit).
examples:
- value: 0.1 mL/min
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasInducerAdditionRate
alias: induction_rate
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
cultivation_type:
name: cultivation_type
description: The type of cultivation process used, e.g., batch, fed-batch, or
continuous.
examples:
- value: batch
- value: fed-batch
- value: continuous
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasCultivationType
alias: cultivation_type
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
inoculum_type:
name: inoculum_type
description: The type of inoculum used, such as a single strain or a mixed culture.
examples:
- value: single strain
- value: mixed culture
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasInoculumType
alias: inoculum_type
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
preculture_medium:
name: preculture_medium
description: The medium used to grow the preculture before inoculation.
examples:
- value: LB
- value: TB
- value: MOPS
- value: 20 g/L tryptone, 5 g/L yeast extract, 2.4 g/L MgSO4, 0.5 g/L NaCl, 0.186
g/L KCl
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasPrecultureMedium
alias: preculture_medium
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
inoculum_composition:
name: inoculum_composition
description: The composition of the inoculum, including strains and concentrations/proportions
of the composition when more than one strain is involved.
examples:
- value: Escherichia coli BL21(DE3)
- value: Saccharomyces cerevisiae S288C, 2 mL/L - Escherichia coli BL21(DE3) 1
mL/L
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasInoculumComposition
alias: inoculum_composition
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
harvesting_conditions:
name: harvesting_conditions
description: The specific conditions under which the inoculum is harvested, such
as temperature or pH.
examples:
- value: 10°C
- value: pH 7.0
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasHarvestingConditions
alias: harvesting_conditions
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
concentration_method:
name: concentration_method
description: The method used to concentrate the inoculum, e.g., filtration or
centrifugation.
examples:
- value: filtration
- value: centrifugation
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasConcentrationMethod
alias: concentration_method
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
purification_method:
name: purification_method
description: The method used to purify the product, e.g., chromatography or precipitation.
examples:
- value: chromatography
- value: precipitation
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasPurificationMethod
alias: purification_method
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
preculture_description:
name: preculture_description
description: A detailed description of the preculture, including growth conditions.
examples:
- value: 16 h at 35°C in LB Broth
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: schema:description
alias: preculture_description
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
inoculum_duration:
name: inoculum_duration
description: The time for which the inoculum is cultured before use. (note, maybe
use OD?)
examples:
- value: 960 minutes
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasInoculumDuration
alias: inoculum_duration
owner: ObservationUnit
domain_of:
- ObservationUnit
range: duration
required: false
multivalued: false
temperature_of_inoculum:
name: temperature_of_inoculum
description: The temperature at which the inoculum is maintained.
examples:
- value: 37 degrees celsius
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:HasInoculumTemperature
alias: temperature_of_inoculum
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
amount_of_inoculum:
name: amount_of_inoculum
description: The volume, OD or mass of inoculum added to the fermentation vessel.
examples:
- value: 5% vol:vol
- value: 200 mL
- value: 10 g
- value: 1 mL at OD600nm 0.8
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasInoculumAmount
alias: amount_of_inoculum
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
initial_working_volume:
name: initial_working_volume
description: The starting volume of liquid in the fermentation vessel.
examples:
- value: 4 L
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasInitialWorkingVolume
alias: initial_working_volume
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
dilution_rate:
name: dilution_rate
description: The inital rate at which fresh medium is added and spent medium is
removed in continuous cultures.
examples:
- value: 0.05 h-1
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasDilutionRate
alias: dilution_rate
owner: ObservationUnit
domain_of:
- ObservationUnit
range: float
required: false
multivalued: false
inoculation_source:
name: inoculation_source
description: The origin of the inoculum, such as a strain collection or preculture
flask.
examples:
- value: preculture flask
- value: seed train
- value: ATCC
- value: DSMZ
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasInnoculationSource
alias: inoculation_source
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
target_metabolite:
name: target_metabolite
description: The specific compound or metabolite that is the desired outcome of
the fermentation process.
examples:
- value: recombinant insulin
- value: streptokinase
- value: EPO
- value: nanobody
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasTargetMetabolite
alias: target_metabolite
owner: ObservationUnit
domain_of:
- Study
- ObservationUnit
range: string
required: false
multivalued: false
replicate_id:
name: replicate_id
description: A unique identifier for experimental replicates in the fermentation
study.
examples:
- value: R1
- value: R2
- value: R3
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:hasReplicateIdentifier
alias: replicate_id
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
replicate_type:
name: replicate_type
description: The type of replicate, e.g., biological or technical.
examples:
- value: biological
- value: technical
from_schema: https://ontology.ibisba.eu/mife/
rank: 1000
slot_uri: mife:replicateType
alias: replicate_type
owner: ObservationUnit
domain_of:
- ObservationUnit
range: string
required: false
multivalued: false
class_uri: mife:ObservationUnit