OnSIR: Ontology for Seed Irradiation and Plant Radiobiology

An OWL 2 DL ontology of seed-irradiation treatments and their dose-dependent biological effects, with dose-to-effect axioms and taxon dose windows, conditioned on endpoint and stage, for description-logic reasoning. Its classes are aligned, with IRIs checked against the EBI Ontology Lookup Service, to BFO, IAO, OBI, PO, NCBITaxon, ChEBI, GO, PATO, PECO and TO, taxa are stated with the RO relation in taxon, and its units are QUDT terms.

Namespace	https://w3id.org/onsir/
Prefix	onsir
Version	1.7.0
Version IRI	https://w3id.org/onsir/1.7.0
License	https://creativecommons.org/licenses/by/4.0/
Created	2025-09-21
Issued	2026-10-05
Modified	2026-10-05
Publisher	https://orcid.org/0009-0005-4227-5568
Citation	Alves LFM, de Franco Rosa F, Arthur V. OnSIR: Ontology for Seed Irradiation and Plant Radiobiology, version 1.7.0. https://w3id.org/onsir/1.7.0
Authors	https://orcid.org/0000-0001-9504-496X; https://orcid.org/0000-0003-3521-9136; https://orcid.org/0009-0005-4227-5568
Provenance	https://doi.org/10.22456/2175-2745.146658 https://doi.org/10.56238/sevened2025.039-003 https://doi.org/10.69547/TSFJB.030203
Size	2496 triples · 118 named classes · 24 object properties · 11 datatype properties · 10 obsolete classes and properties

Taxon-specific dose windows

Each taxon carries numeric dose windows for the endpoint and the stage its source scored, and a reasoner places a dose assessment in a window from its dose, the taxon of its subject, its endpoint and its stage. Each window records its source, the passage of the source its bound rests on, the strength of the bound and the doses the source tested.

Window class	Definition	Source	Strength of the bound	Doses tested
Lablab_purpureus_Germination_AtOrAboveLD50Dose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_35936 and forEndpoint some GerminationPercentage and atStage some GerminationStage and doseGy some [minInclusive 304.1 (xsd:decimal, xsd:double)])	Mahesha et al. 2023, Environ. Ecol. 41(4C):2838-2844, doi:10.60151/envec/EFHD5757	The source reports probit estimates of 34.67 kR in Petri plates and 33.11 kR in polybags and adopts 30 kR as the LD50 in its abstract and methods; at 8.77 mGy per roentgen (air kerma) these are 304.1, 290.4 and 263.1 Gy. The window below the LD50 ends below 263.1 Gy and the window at or above it starts at 304.1 Gy; doses between them fall in no window.	The source irradiated doses from 87.7 to 526.2 Gy and scored germination seven days after sowing, in Petri plates and in polybags; where the window extends past the tested doses, the position is arithmetic only.
Lablab_purpureus_Germination_BelowLD50Dose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_35936 and forEndpoint some GerminationPercentage and atStage some GerminationStage and doseGy some [minExclusive 0.0 and maxExclusive 263.1 (xsd:decimal, xsd:double)])	Mahesha et al. 2023, Environ. Ecol. 41(4C):2838-2844, doi:10.60151/envec/EFHD5757	The source reports probit estimates of 34.67 kR in Petri plates and 33.11 kR in polybags and adopts 30 kR as the LD50 in its abstract and methods; at 8.77 mGy per roentgen (air kerma) these are 304.1, 290.4 and 263.1 Gy. The window below the LD50 ends below 263.1 Gy and the window at or above it starts at 304.1 Gy; doses between them fall in no window.	The source irradiated doses from 87.7 to 526.2 Gy and scored germination seven days after sowing, in Petri plates and in polybags; where the window extends past the tested doses, the position is arithmetic only.
Magnolia_champaca_Germination_AtOrAboveLD50Dose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_86757 and forEndpoint some GerminationPercentage and atStage some GerminationStage and doseGy some [minInclusive 40.0 (xsd:decimal, xsd:double)])	Zanzibar and Sudrajat 2016, Indones. J. For. Res. 3(2):95-106, doi:10.20886/ijfr.2016.3.2.95-106	The source estimates the LD50 by regression of germination lethality relative to the control and places it above 30 Gy and below 40 Gy. Its observations agree: germination at 20 Gy was 65 % of the control and at 40 Gy 24 %.	The source irradiated doses from 5 to 100 Gy and scored germination percentage of fresh seeds in a germination test, as lethality relative to the control; where the window extends past the tested doses, the position is arithmetic only.
Magnolia_champaca_Germination_BelowLD50Dose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_86757 and forEndpoint some GerminationPercentage and atStage some GerminationStage and doseGy some [minExclusive 0.0 and maxExclusive 30.0 (xsd:decimal, xsd:double)])	Zanzibar and Sudrajat 2016, Indones. J. For. Res. 3(2):95-106, doi:10.20886/ijfr.2016.3.2.95-106	The source estimates the LD50 by regression of germination lethality relative to the control and places it above 30 Gy and below 40 Gy. Its observations agree: germination at 20 Gy was 65 % of the control and at 40 Gy 24 %.	The source irradiated doses from 5 to 100 Gy and scored germination percentage of fresh seeds in a germination test, as lethality relative to the control; where the window extends past the tested doses, the position is arithmetic only.
Nicotiana_tabacum_SeedlingPerformance_AboveFavourableBandDose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some [CotyledonFreeing, FreshMass, GerminationPercentage, GerminationRate, HypocotylEmergence] and atStage some [EarlySeedlingStage, GerminationStage] and doseGy some [minExclusive 15.0 (xsd:decimal, xsd:double)])	Alves et al. 2027, Radiat. Phys. Chem. 250:114279, doi:10.1016/j.radphyschem.2026.114279	Both band ends are approximate: the source places the most favourable responses broadly between approximately 5 and 15 Gy across its endpoints, with the apparent maximum depending on variety, endpoint and sampling time.	The source irradiated doses from 2.5 to 20 Gy and scored germination, hypocotyl emergence and cotyledon liberation from 3 to 9 days after sowing, and seedling fresh weight at two and four weeks, in three varieties; where the window extends past the tested doses, the position is arithmetic only.
Nicotiana_tabacum_SeedlingPerformance_BelowFavourableBandDose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some [CotyledonFreeing, FreshMass, GerminationPercentage, GerminationRate, HypocotylEmergence] and atStage some [EarlySeedlingStage, GerminationStage] and doseGy some [minExclusive 0.0 and maxExclusive 5.0 (xsd:decimal, xsd:double)])	Alves et al. 2027, Radiat. Phys. Chem. 250:114279, doi:10.1016/j.radphyschem.2026.114279	Both band ends are approximate: the source places the most favourable responses broadly between approximately 5 and 15 Gy across its endpoints, with the apparent maximum depending on variety, endpoint and sampling time.	The source irradiated doses from 2.5 to 20 Gy and scored germination, hypocotyl emergence and cotyledon liberation from 3 to 9 days after sowing, and seedling fresh weight at two and four weeks, in three varieties; where the window extends past the tested doses, the position is arithmetic only.
Nicotiana_tabacum_SeedlingPerformance_WithinFavourableBandDose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some [CotyledonFreeing, FreshMass, GerminationPercentage, GerminationRate, HypocotylEmergence] and atStage some [EarlySeedlingStage, GerminationStage] and doseGy some [minInclusive 5.0 and maxInclusive 15.0 (xsd:decimal, xsd:double)])	Alves et al. 2027, Radiat. Phys. Chem. 250:114279, doi:10.1016/j.radphyschem.2026.114279	Both band ends are approximate: the source places the most favourable responses broadly between approximately 5 and 15 Gy across its endpoints, with the apparent maximum depending on variety, endpoint and sampling time.	The source irradiated doses from 2.5 to 20 Gy and scored germination, hypocotyl emergence and cotyledon liberation from 3 to 9 days after sowing, and seedling fresh weight at two and four weeks, in three varieties; where the window extends past the tested doses, the position is arithmetic only.
Plukenetia_volubilis_SeedlingSurvival_AtOrAboveLD50Dose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_316893 and forEndpoint some SeedlingSurvival and atStage some EarlySeedlingStage and doseGy some [minInclusive 618.78 (xsd:decimal, xsd:double)])	Corazon-Guivin et al. 2023, Adv. Agric. 2023:9737125, doi:10.1155/2023/9737125	A logistic regression of mortality on dose (a generalized linear model) gives 618.78 Gy, inside the tested range of 500 to 900 Gy.	The source irradiated doses from 500 to 900 Gy and scored surviving plants per irradiated seed in a greenhouse sowing, with growth recorded 30 days after emergence; where the window extends past the tested doses, the position is arithmetic only.
Plukenetia_volubilis_SeedlingSurvival_BelowLD50Dose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_316893 and forEndpoint some SeedlingSurvival and atStage some EarlySeedlingStage and doseGy some [minExclusive 0.0 and maxExclusive 618.78 (xsd:decimal, xsd:double)])	Corazon-Guivin et al. 2023, Adv. Agric. 2023:9737125, doi:10.1155/2023/9737125	A logistic regression of mortality on dose (a generalized linear model) gives 618.78 Gy, inside the tested range of 500 to 900 Gy.	The source irradiated doses from 500 to 900 Gy and scored surviving plants per irradiated seed in a greenhouse sowing, with growth recorded 30 days after emergence; where the window extends past the tested doses, the position is arithmetic only.
Solanum_lycopersicum_SeedlingSurvival_BelowLD50Dose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4081 and forEndpoint some SeedlingSurvival and atStage some EarlySeedlingStage and doseGy some [minExclusive 0.0 and maxInclusive 120.0 (xsd:decimal, xsd:double)])	Indrayanti et al. 2024, Pak. J. Phytopathol. 36(2):267-280, doi:10.33866/phytopathol.036.02.1047	The source fits a quadratic to the number of seedlings alive four weeks after germination, relative to the control, and reports 132.49 Gy, above its highest dose of 120 Gy, at which 59 % of seedlings relative to the control were alive. 120 Gy is encoded as a lower bound on the LD50, so only the window below the LD50 is defined, and it includes 120 Gy.	The source irradiated doses from 50 to 120 Gy and scored seedlings alive four weeks after germination, relative to the unirradiated control; where the window extends past the tested doses, the position is arithmetic only.
Trigonella_foenum_graecum_SeedlingSurvival_BelowLD50Dose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_78534 and forEndpoint some SeedlingSurvival and atStage some EarlySeedlingStage and doseGy some [minExclusive 0.0 and maxInclusive 350.0 (xsd:decimal, xsd:double)])	Patel et al. 2017, J. AgriSearch 4(4):237-241, doi:10.21921/jas.v4i04.10200	The source states that the LD50 is close to 350 Gy, its highest dose, at which 64 % of seeds germinated and 56 % of seedlings survived, against 96 % and 90 % in the control. Survival above half at 350 Gy makes 350 Gy a lower bound on the LD50, so only the window below the LD50 is defined, and it includes 350 Gy.	The source irradiated doses from 150 to 350 Gy and scored plants alive 30 days after sowing in Petri dishes, as a percentage of the seeds sown; where the window extends past the tested doses, the position is arithmetic only.
Triticum_aestivum_SeedlingSurvival_AtOrAboveLD50Dose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4565 and forEndpoint some SeedlingSurvival and atStage some EarlySeedlingStage and doseGy some [minInclusive 278.61 (xsd:decimal, xsd:double)])	Chakraborty et al. 2023, Braz. Arch. Biol. Technol. 66:e23220294, doi:10.1590/1678-4324-2023220294	Probit estimates on survival for two varieties, 272.71 Gy (DBW 187) and 278.61 Gy (K 1006), inside the tested range of 200 to 450 Gy; the window below the LD50 ends below the lower estimate and the window at or above it starts at the higher.	The source irradiated doses from 200 to 450 Gy and scored viable seedlings 7 days after sowing, in two varieties; where the window extends past the tested doses, the position is arithmetic only.
Triticum_aestivum_SeedlingSurvival_BelowLD50Dose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4565 and forEndpoint some SeedlingSurvival and atStage some EarlySeedlingStage and doseGy some [minExclusive 0.0 and maxExclusive 272.71 (xsd:decimal, xsd:double)])	Chakraborty et al. 2023, Braz. Arch. Biol. Technol. 66:e23220294, doi:10.1590/1678-4324-2023220294	Probit estimates on survival for two varieties, 272.71 Gy (DBW 187) and 278.61 Gy (K 1006), inside the tested range of 200 to 450 Gy; the window below the LD50 ends below the lower estimate and the window at or above it starts at the higher.	The source irradiated doses from 200 to 450 Gy and scored viable seedlings 7 days after sowing, in two varieties; where the window extends past the tested doses, the position is arithmetic only.
Vigna_unguiculata_SeedlingSurvival_AtOrAboveLD50Dose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_3917 and forEndpoint some SeedlingSurvival and atStage some FloweringStage and doseGy some [minInclusive 250.0 (xsd:decimal, xsd:double)])	Gnankambary et al. 2019, Int. J. Genet. Mol. Biol. 11(2):29-33, doi:10.5897/IJGMB2019.0174	The source fits a straight line to survival against dose for each of three genotypes and reports LD50s of 129.8, 132.0 and 150.2 Gy, two of them below the lowest dose tested. Its observations bracket the LD50 of every genotype between 150 and 250 Gy: survival at 150 Gy, the lowest dose, was 56 to 71 %, and at 250 Gy it was zero in all three genotypes; at 200 Gy it was zero in two genotypes, and for the third the table prints 75.86 % in both the lethality and the survival column. The window below the LD50 runs up to 150 Gy and includes it, and the window at or above it starts at 250 Gy; doses above 150 Gy and below 250 Gy fall in no window.	The source irradiated doses from 150 to 300 Gy and scored plants alive at 50 % flowering, relative to the unirradiated control, in three genotypes; where the window extends past the tested doses, the position is arithmetic only.
Vigna_unguiculata_SeedlingSurvival_BelowLD50Dose	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_3917 and forEndpoint some SeedlingSurvival and atStage some FloweringStage and doseGy some [minExclusive 0.0 and maxInclusive 150.0 (xsd:decimal, xsd:double)])	Gnankambary et al. 2019, Int. J. Genet. Mol. Biol. 11(2):29-33, doi:10.5897/IJGMB2019.0174	The source fits a straight line to survival against dose for each of three genotypes and reports LD50s of 129.8, 132.0 and 150.2 Gy, two of them below the lowest dose tested. Its observations bracket the LD50 of every genotype between 150 and 250 Gy: survival at 150 Gy, the lowest dose, was 56 to 71 %, and at 250 Gy it was zero in all three genotypes; at 200 Gy it was zero in two genotypes, and for the third the table prints 75.86 % in both the lethality and the survival column. The window below the LD50 runs up to 150 Gy and includes it, and the window at or above it starts at 250 Gy; doses above 150 Gy and below 250 Gy fall in no window.	The source irradiated doses from 150 to 300 Gy and scored plants alive at 50 % flowering, relative to the unirradiated control, in three genotypes; where the window extends past the tested doses, the position is arithmetic only.

Classes 126

AbioticStressResistance

Stress resistance under an abiotic stress, such as salinity, drought or an extreme temperature.

label	abiotic stress resistance
subclass of	StressResistance
external alignment	close match obo:TO_0000168

AboveReportedFavourableBand

A dose assessment whose dose exceeds the upper end of the favourable band reported for its taxon, endpoint and stage.

label	above reported favourable band
subclass of	DoseAssessment

Am241

The radionuclide americium-241.

label	americium-241
subclass of	Isotope

AntioxidantActivity

The capacity of a tissue extract to scavenge free radicals or reactive oxygen species, measured in an assay such as DPPH radical scavenging.

label	antioxidant activity
subclass of	Endpoint
external alignment	close match obo:TO_0001143, related match obo:GO_0016209

AntioxidantIncrease

An increase in antioxidant content or antioxidant enzyme activity measured after irradiation, relative to the unirradiated control.

label	antioxidant increase
subclass of	BiochemicalChange
external alignment	broad match obo:TO_0001143

AtOrAboveReportedLD50

A dose assessment whose dose reaches or exceeds the LD50 reported for its taxon, endpoint and stage: the reported estimate, every estimate where the source reports one per genotype or setting, or an upper bound that the source's observations place on the LD50. An LD50 is a 50 % lethality statistic for one endpoint and scoring time.

label	at or above reported LD50
subclass of	DoseAssessment

BelowReportedFavourableBand

A dose assessment whose dose is below the lower end of the favourable band reported for its taxon, endpoint and stage.

label	below reported favourable band
subclass of	DoseAssessment

BelowReportedLD50

A dose assessment whose dose is below the LD50 reported for its taxon, endpoint and stage: below the reported estimate, below every estimate where the source reports one per genotype or setting, or at most a dose that the source's own observations place below the LD50.

label	below reported LD50
subclass of	DoseAssessment

BiochemicalChange

A biochemical characteristic measured after irradiation, such as the balance of reactive oxygen species, antioxidant content or an enzyme activity; the direction of the change is a result.

label	biochemical change
subclass of	Endpoint

BiochemicalEndpointCategory

The endpoint category of biochemical measurements, such as enzyme activities, metabolite contents and antioxidant capacity (EP2).

label	biochemical endpoint category
subclass of	EndpointCategory

BioticStressResistance

Stress resistance under a biotic stress, such as a pathogen or a pest.

label	biotic stress resistance
subclass of	StressResistance
external alignment	close match obo:TO_0000179

BrainCousensModel

The dose-response model of Brain and Cousens: an equation for dose responses with stimulation at low doses, which contains the common sigmoidal (log-logistic) curve as a special case.

label	Brain–Cousens model
definition source	Brain P, Cousens R (1989). An equation to describe dose responses where there is stimulation of growth at low doses. Weed Research 29:93-96, doi:10.1111/j.1365-3180.1989.tb00845.x
subclass of	DoseResponseModel

ChlorophyllContent

The amount of chlorophyll in leaf or seedling tissue, per unit mass or area.

label	chlorophyll content
subclass of	Endpoint
external alignment	close match obo:TO_0000495

Co60

The radionuclide cobalt-60, whose decay emits gamma photons of 1.17 and 1.33 MeV.

label	cobalt-60
subclass of	Isotope
external alignment	broad match obo:CHEBI_27638

Context

An experimental or environmental condition under which an outcome was observed.

label	context

CotyledonFreeing

The percentage of seedlings whose cotyledons are free of the seed coat at a stated time after sowing.

label	cotyledon freeing
subclass of	Endpoint
external alignment	related match obo:PO_0007049

Cs137

The radionuclide caesium-137, whose decay emits gamma photons of 0.662 MeV through its daughter barium-137m.

label	caesium-137
equivalent to	obo:CHEBI_196959
subclass of	Isotope
external alignment	equivalent to obo:CHEBI_196959

DoseAssessment

A record of one absorbed dose applied to a plant structure and considered for one endpoint and one life-cycle stage, which a reasoner places relative to the statistics reported for the taxon of the structure.

label	dose assessment
subclass of	obo:IAO_0000030
external alignment	subclass of obo:IAO_0000030

DoseCategory

A qualitative classification of an irradiation dose by the biological effect a curator asserts for it.

label	dose category
equivalent to	(HormeticDose or MutagenicDose or SterilizationDose)

DoseRange

The range of absorbed doses irradiated in a study, from its minimum to its maximum dose.

label	dose range
subclass of	maxDose some QuantityValue minDose some QuantityValue

DoseRateAbove100GyPerHour

An absorbed-dose rate above 100 Gy per hour.

label	dose rate above 100 Gy per hour
comment	The bound of 100 Gy per hour lies between the two groups of rates reported in the coded corpus, at most 84 and at least 135 Gy per hour.
subclass of	DoseRateCategory

DoseRateBelow100GyPerHour

An absorbed-dose rate below 100 Gy per hour.

label	dose rate below 100 Gy per hour
comment	The bound of 100 Gy per hour lies between the two groups of rates reported in the coded corpus, at most 84 and at least 135 Gy per hour.
subclass of	DoseRateCategory

DoseRateCategory

A category of absorbed-dose rate, named by the bound that delimits it.

label	dose-rate category

DoseResponseModel

A parametric model of how an endpoint varies with dose.

label	dose–response model

DryMass

The mass of a seedling, plant or organ after drying.

label	dry mass
subclass of	Endpoint
external alignment	broad match obo:PATO_0000125

EarlySeedlingStage

The stage from seedling emergence through the first weeks of growth, over which seedling survival and growth are scored, in the studies coded here from 7 days to about six weeks after sowing.

label	early seedling stage
comment	Matched to PO:0007131 seedling development stage by skos:closeMatch: the Plant Ontology seedling stage ends with the first true leaf, and radiosensitivity tests also score seedlings after it.
subclass of	LifecycleStage
external alignment	close match obo:PO_0007131

ElectronBeam

Radiation consisting of a beam of accelerated electrons.

label	electron beam
subclass of	RadiationType

EmergenceAndEarlyVigor

The endpoint category of seed germination, seedling emergence and early seedling vigour (code EP1 of the coded corpus).

label	emergence and early vigour
subclass of	EndpointCategory

Endpoint

A measurable characteristic of an irradiated plant structure, or of the plant grown from it, used to quantify the outcome of a treatment, such as germination, root length or mutation frequency.

label	endpoint
subclass of	obo:BFO_0000019
external alignment	subclass of obo:BFO_0000019

EndpointCategory

A coarse grouping of measured endpoints, as recorded by the coding scheme of a study corpus. Distinct from Endpoint, which names an individual measurable characteristic.

label	endpoint category

EnzymeActivityChange

A change in the activity of an enzyme measured after irradiation, relative to the unirradiated control.

label	enzyme activity change
subclass of	BiochemicalChange
external alignment	broad match obo:TO_0000599

FloweringStage

The stage at which the plant flowers. Radiosensitivity tests often score survival when half of the plants have flowered.

label	flowering stage
subclass of	LifecycleStage
external alignment	close match obo:PO_0007616

FreshMass

The mass of a seedling, plant or organ weighed fresh.

label	fresh mass
subclass of	Endpoint
external alignment	broad match obo:PATO_0000125

Gamma

Electromagnetic radiation emitted by an atomic nucleus in radioactive decay, such as the photons of cobalt-60 and caesium-137.

label	gamma
subclass of	RadiationType
external alignment	related match obo:PECO_0001022

GeneticEndpointCategory

The endpoint category of genetic measurements, such as mutation frequency, chromosomal aberrations and molecular markers (EP3).

label	genetic endpoint category
subclass of	EndpointCategory

GerminationPercentage

The percentage of sown seeds that germinate within the period of a germination test.

label	germination percentage
definition source	Plant Trait Ontology, TO:0010001 percent germination
subclass of	Endpoint
external alignment	close match obo:TO_0010001

GerminationRate

The speed of germination of a seed lot, measured as the time to a stated germination percentage or as a germination index.

label	germination rate
subclass of	Endpoint
external alignment	close match obo:TO_0000430

GerminationStage

The stage from the imbibition of a seed to the emergence of the radicle or of the seedling, over which germination is scored.

label	germination stage
subclass of	LifecycleStage
external alignment	close match obo:PO_0007057

HighDoseRate

OBSOLETE. A reported dose rate above 100 Gy per hour. Renamed after the bound that defines it.

label	obsolete high dose rate
replaced by	DoseRateAbove100GyPerHour

HormeticDose

A dose asserted by a curator to have a hormetic effect. Discouraged for new annotation: the category names a biological outcome, and the outcome of one absorbed dose depends on taxon, endpoint and stage. Retained because data that already carries a dose category reasons through its axioms. Record the category as an individual typed with this class; the general class inclusion reads that typing. For new curation, record the numeric dose as a DoseAssessment with doseGy, hasSubject, forEndpoint and atStage. [curation note] Kept active: an obsolete OBO term carries no logical axioms, and this class is the antecedent of a general class inclusion. DoseAssessment records where a numeric dose lies relative to the statistics reported for its taxon.

label	hormetic dose
subclass of	DoseCategory

HormeticResponse

A response observed as a biphasic dose-response: an endpoint exceeds its value in the unirradiated control over a range of low doses and falls below it at higher doses.

label	hormetic response
definition source	Calabrese EJ, Baldwin LA (2002). Defining hormesis. Human & Experimental Toxicology 21:91-97, doi:10.1191/0960327102ht217oa: hormesis is characterized by biphasic dose responses.
subclass of	Response

HypocotylEmergence

The percentage of seeds whose hypocotyl has emerged at a stated time after sowing.

label	hypocotyl emergence
subclass of	Endpoint
external alignment	related match obo:PO_0007043

InhibitoryResponse

A response in which an endpoint falls below its value in the unirradiated control, such as reduced germination, growth or seedling survival.

label	inhibitory response
subclass of	Response

Ir192

The radionuclide iridium-192.

label	iridium-192
subclass of	Isotope

Isotope

A radionuclide used as the source of a seed-irradiation treatment.

label	radioisotope

Lablab_purpureus_Germination_AtOrAboveLD50Dose

A dose assessment of Lablab purpureus for germination, at a dose of 304.1 Gy or more, at or above both probit estimates of the LD50 of Mahesha et al. (2023) and the 30 kR they adopt.

label	Lablab purpureus germination at or above LD50 dose
source statement	Probit analysis revealed that the LD50 value was 30kR. [...] Based on the percentage of germination both in petri plates and polybags, the LD50 value was calculated using probit analysis, which observed probit values being 34.67kR and 33.11kR, respectively
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_35936 and forEndpoint some GerminationPercentage and atStage some GerminationStage and doseGy some [minInclusive 304.1 (xsd:decimal, xsd:double)])
subclass of	AtOrAboveReportedLD50

Lablab_purpureus_Germination_BelowLD50Dose

A dose assessment of Lablab purpureus for germination, at a dose below 263.1 Gy (30 kR), the LD50 that Mahesha et al. (2023) adopt, and below both of their probit estimates.

label	Lablab purpureus germination below LD50 dose
source statement	Probit analysis revealed that the LD50 value was 30kR. [...] Based on the percentage of germination both in petri plates and polybags, the LD50 value was calculated using probit analysis, which observed probit values being 34.67kR and 33.11kR, respectively
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_35936 and forEndpoint some GerminationPercentage and atStage some GerminationStage and doseGy some [minExclusive 0.0 and maxExclusive 263.1 (xsd:decimal, xsd:double)])
subclass of	BelowReportedLD50

LifecycleStage

A stage in the life cycle of a plant at which an endpoint is scored.

label	life-cycle stage
subclass of	obo:PO_0009012
external alignment	subclass of obo:PO_0009012

LightCondition

The light under which seeds were germinated or plants grown: its intensity, quality or photoperiod.

label	light condition
subclass of	Context
external alignment	related match obo:PECO_0007224

LipidPeroxidation

The extent of oxidative degradation of membrane lipids, usually measured as malondialdehyde content.

label	lipid peroxidation
subclass of	Endpoint
external alignment	broad match obo:GO_0034440

LossOfViability

A response in which the irradiated propagule, or the plant grown from it, dies or fails to germinate or emerge.

label	loss of viability
subclass of	Response

LowDoseRate

OBSOLETE. A reported dose rate below 100 Gy per hour. Renamed after the bound that defines it.

label	obsolete low dose rate
replaced by	DoseRateBelow100GyPerHour

Magnolia_champaca_Germination_AtOrAboveLD50Dose

A dose assessment of Magnolia champaca for germination, at a dose of 40 Gy or more, at or above the LD50 that Zanzibar and Sudrajat (2016) place between 30 and 40 Gy.

label	Magnolia champaca germination at or above LD50 dose
source statement	Irradiation at dose higher than 30 Gy and below 40 Gy is considered being the lethal dosage (LD50) for M. champaca seeds
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_86757 and forEndpoint some GerminationPercentage and atStage some GerminationStage and doseGy some [minInclusive 40.0 (xsd:decimal, xsd:double)])
subclass of	AtOrAboveReportedLD50

Magnolia_champaca_Germination_BelowLD50Dose

A dose assessment of Magnolia champaca for germination, at a dose below 30 Gy, below the LD50 that Zanzibar and Sudrajat (2016) place between 30 and 40 Gy.

label	Magnolia champaca germination below LD50 dose
source statement	Irradiation at dose higher than 30 Gy and below 40 Gy is considered being the lethal dosage (LD50) for M. champaca seeds
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_86757 and forEndpoint some GerminationPercentage and atStage some GerminationStage and doseGy some [minExclusive 0.0 and maxExclusive 30.0 (xsd:decimal, xsd:double)])
subclass of	BelowReportedLD50

MorphologicalEndpointCategory

The endpoint category of morphological and anatomical measurements of plants and organs (EP4).

label	morphological endpoint category
subclass of	EndpointCategory

MutagenicDose

A dose asserted by a curator to have a mutagenic effect. Discouraged for new annotation: the category names a biological outcome, and the outcome of one absorbed dose depends on taxon, endpoint and stage. Retained because data that already carries a dose category reasons through its axioms. Record the category as an individual typed with this class; the general class inclusion reads that typing. For new curation, record the numeric dose as a DoseAssessment with doseGy, hasSubject, forEndpoint and atStage. [curation note] Kept active: an obsolete OBO term carries no logical axioms, and this class is the antecedent of a general class inclusion. DoseAssessment records where a numeric dose lies relative to the statistics reported for its taxon.

label	mutagenic dose
subclass of	DoseCategory

MutagenicOutcome

A treatment outcome that has a mutagenic response.

label	mutagenic outcome
equivalent to	(TreatmentOutcome and hasResponse some MutagenicResponse)

MutagenicResponse

A response in which irradiation induces heritable changes in the genetic material of the irradiated propagule, observed as mutations or chromosomal aberrations in the plant or its progeny.

label	mutagenic response
subclass of	Response

MutationFrequency

The frequency of mutants, or of mutations, among the plants or progeny raised from irradiated propagules.

label	mutation frequency
subclass of	Endpoint

Neutron

Radiation consisting of free neutrons.

label	neutron
subclass of	RadiationType
external alignment	related match obo:CHEBI_30222

Nicotiana_tabacum_AboveFavourableBandDose

OBSOLETE. A dose window of release 1.6.0 for Nicotiana tabacum, conditioned on the taxon alone. Replaced by a window that is also conditioned on the endpoint and the stage its source scored.

label	obsolete Nicotiana tabacum above favourable band dose
replaced by	Nicotiana_tabacum_SeedlingPerformance_AboveFavourableBandDose

Nicotiana_tabacum_BelowFavourableBandDose

OBSOLETE. A dose window of release 1.6.0 for Nicotiana tabacum, conditioned on the taxon alone. Replaced by a window that is also conditioned on the endpoint and the stage its source scored.

label	obsolete Nicotiana tabacum below favourable band dose
replaced by	Nicotiana_tabacum_SeedlingPerformance_BelowFavourableBandDose

Nicotiana_tabacum_SeedlingPerformance_AboveFavourableBandDose

A dose assessment of Nicotiana tabacum for germination or early seedling growth, at a dose above the favourable band of approximately 5 to 15 Gy that Alves et al. (2027) report.

label	Nicotiana tabacum seedling performance above favourable band dose
source statement	Across endpoints, the most favorable responses were concentrated broadly between approximately 5 and 15 Gy. The exact position of the apparent maximum depended on variety, endpoint, and sampling time, indicating that no single universal optimum should be assumed for all tobacco genotypes.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some [CotyledonFreeing, FreshMass, GerminationPercentage, GerminationRate, HypocotylEmergence] and atStage some [EarlySeedlingStage, GerminationStage] and doseGy some [minExclusive 15.0 (xsd:decimal, xsd:double)])
subclass of	AboveReportedFavourableBand

Nicotiana_tabacum_SeedlingPerformance_BelowFavourableBandDose

A dose assessment of Nicotiana tabacum for germination or early seedling growth, at a dose below the favourable band of approximately 5 to 15 Gy that Alves et al. (2027) report.

label	Nicotiana tabacum seedling performance below favourable band dose
source statement	Across endpoints, the most favorable responses were concentrated broadly between approximately 5 and 15 Gy. The exact position of the apparent maximum depended on variety, endpoint, and sampling time, indicating that no single universal optimum should be assumed for all tobacco genotypes.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some [CotyledonFreeing, FreshMass, GerminationPercentage, GerminationRate, HypocotylEmergence] and atStage some [EarlySeedlingStage, GerminationStage] and doseGy some [minExclusive 0.0 and maxExclusive 5.0 (xsd:decimal, xsd:double)])
subclass of	BelowReportedFavourableBand

Nicotiana_tabacum_SeedlingPerformance_CotyledonFreeing_EarlySeedlingStage_BandUpperEndProbe

A dose assessment of Nicotiana tabacum for cotyledon freeing at the early seedling stage, at the upper end of the favourable band reported for that taxon, 15 Gy. The class is unsatisfiable when that dose also lies at or above an LD50 reported for the same taxon, endpoint and stage, which flags a band that reaches its LD50 for a curator.

label	Nicotiana tabacum seedling performance cotyledon freeing early seedling stage band upper end probe
comment	A probe for the reasoner, one for each endpoint and stage of a favourable band: it is satisfiable while the band lies below every LD50 reported for the same taxon, endpoint and stage.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some CotyledonFreeing and atStage some EarlySeedlingStage and doseGy some [minInclusive 15.0 and maxInclusive 15.0 (xsd:double)])

Nicotiana_tabacum_SeedlingPerformance_CotyledonFreeing_GerminationStage_BandUpperEndProbe

A dose assessment of Nicotiana tabacum for cotyledon freeing at the germination stage, at the upper end of the favourable band reported for that taxon, 15 Gy. The class is unsatisfiable when that dose also lies at or above an LD50 reported for the same taxon, endpoint and stage, which flags a band that reaches its LD50 for a curator.

label	Nicotiana tabacum seedling performance cotyledon freeing germination stage band upper end probe
comment	A probe for the reasoner, one for each endpoint and stage of a favourable band: it is satisfiable while the band lies below every LD50 reported for the same taxon, endpoint and stage.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some CotyledonFreeing and atStage some GerminationStage and doseGy some [minInclusive 15.0 and maxInclusive 15.0 (xsd:double)])

Nicotiana_tabacum_SeedlingPerformance_FreshMass_EarlySeedlingStage_BandUpperEndProbe

A dose assessment of Nicotiana tabacum for fresh mass at the early seedling stage, at the upper end of the favourable band reported for that taxon, 15 Gy. The class is unsatisfiable when that dose also lies at or above an LD50 reported for the same taxon, endpoint and stage, which flags a band that reaches its LD50 for a curator.

label	Nicotiana tabacum seedling performance fresh mass early seedling stage band upper end probe
comment	A probe for the reasoner, one for each endpoint and stage of a favourable band: it is satisfiable while the band lies below every LD50 reported for the same taxon, endpoint and stage.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some FreshMass and atStage some EarlySeedlingStage and doseGy some [minInclusive 15.0 and maxInclusive 15.0 (xsd:double)])

Nicotiana_tabacum_SeedlingPerformance_FreshMass_GerminationStage_BandUpperEndProbe

A dose assessment of Nicotiana tabacum for fresh mass at the germination stage, at the upper end of the favourable band reported for that taxon, 15 Gy. The class is unsatisfiable when that dose also lies at or above an LD50 reported for the same taxon, endpoint and stage, which flags a band that reaches its LD50 for a curator.

label	Nicotiana tabacum seedling performance fresh mass germination stage band upper end probe
comment	A probe for the reasoner, one for each endpoint and stage of a favourable band: it is satisfiable while the band lies below every LD50 reported for the same taxon, endpoint and stage.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some FreshMass and atStage some GerminationStage and doseGy some [minInclusive 15.0 and maxInclusive 15.0 (xsd:double)])

Nicotiana_tabacum_SeedlingPerformance_GerminationPercentage_EarlySeedlingStage_BandUpperEndProbe

A dose assessment of Nicotiana tabacum for germination percentage at the early seedling stage, at the upper end of the favourable band reported for that taxon, 15 Gy. The class is unsatisfiable when that dose also lies at or above an LD50 reported for the same taxon, endpoint and stage, which flags a band that reaches its LD50 for a curator.

label	Nicotiana tabacum seedling performance germination percentage early seedling stage band upper end probe
comment	A probe for the reasoner, one for each endpoint and stage of a favourable band: it is satisfiable while the band lies below every LD50 reported for the same taxon, endpoint and stage.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some GerminationPercentage and atStage some EarlySeedlingStage and doseGy some [minInclusive 15.0 and maxInclusive 15.0 (xsd:double)])

Nicotiana_tabacum_SeedlingPerformance_GerminationPercentage_GerminationStage_BandUpperEndProbe

A dose assessment of Nicotiana tabacum for germination percentage at the germination stage, at the upper end of the favourable band reported for that taxon, 15 Gy. The class is unsatisfiable when that dose also lies at or above an LD50 reported for the same taxon, endpoint and stage, which flags a band that reaches its LD50 for a curator.

label	Nicotiana tabacum seedling performance germination percentage germination stage band upper end probe
comment	A probe for the reasoner, one for each endpoint and stage of a favourable band: it is satisfiable while the band lies below every LD50 reported for the same taxon, endpoint and stage.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some GerminationPercentage and atStage some GerminationStage and doseGy some [minInclusive 15.0 and maxInclusive 15.0 (xsd:double)])

Nicotiana_tabacum_SeedlingPerformance_GerminationRate_EarlySeedlingStage_BandUpperEndProbe

A dose assessment of Nicotiana tabacum for germination rate at the early seedling stage, at the upper end of the favourable band reported for that taxon, 15 Gy. The class is unsatisfiable when that dose also lies at or above an LD50 reported for the same taxon, endpoint and stage, which flags a band that reaches its LD50 for a curator.

label	Nicotiana tabacum seedling performance germination rate early seedling stage band upper end probe
comment	A probe for the reasoner, one for each endpoint and stage of a favourable band: it is satisfiable while the band lies below every LD50 reported for the same taxon, endpoint and stage.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some GerminationRate and atStage some EarlySeedlingStage and doseGy some [minInclusive 15.0 and maxInclusive 15.0 (xsd:double)])

Nicotiana_tabacum_SeedlingPerformance_GerminationRate_GerminationStage_BandUpperEndProbe

A dose assessment of Nicotiana tabacum for germination rate at the germination stage, at the upper end of the favourable band reported for that taxon, 15 Gy. The class is unsatisfiable when that dose also lies at or above an LD50 reported for the same taxon, endpoint and stage, which flags a band that reaches its LD50 for a curator.

label	Nicotiana tabacum seedling performance germination rate germination stage band upper end probe
comment	A probe for the reasoner, one for each endpoint and stage of a favourable band: it is satisfiable while the band lies below every LD50 reported for the same taxon, endpoint and stage.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some GerminationRate and atStage some GerminationStage and doseGy some [minInclusive 15.0 and maxInclusive 15.0 (xsd:double)])

Nicotiana_tabacum_SeedlingPerformance_HypocotylEmergence_EarlySeedlingStage_BandUpperEndProbe

A dose assessment of Nicotiana tabacum for hypocotyl emergence at the early seedling stage, at the upper end of the favourable band reported for that taxon, 15 Gy. The class is unsatisfiable when that dose also lies at or above an LD50 reported for the same taxon, endpoint and stage, which flags a band that reaches its LD50 for a curator.

label	Nicotiana tabacum seedling performance hypocotyl emergence early seedling stage band upper end probe
comment	A probe for the reasoner, one for each endpoint and stage of a favourable band: it is satisfiable while the band lies below every LD50 reported for the same taxon, endpoint and stage.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some HypocotylEmergence and atStage some EarlySeedlingStage and doseGy some [minInclusive 15.0 and maxInclusive 15.0 (xsd:double)])

Nicotiana_tabacum_SeedlingPerformance_HypocotylEmergence_GerminationStage_BandUpperEndProbe

A dose assessment of Nicotiana tabacum for hypocotyl emergence at the germination stage, at the upper end of the favourable band reported for that taxon, 15 Gy. The class is unsatisfiable when that dose also lies at or above an LD50 reported for the same taxon, endpoint and stage, which flags a band that reaches its LD50 for a curator.

label	Nicotiana tabacum seedling performance hypocotyl emergence germination stage band upper end probe
comment	A probe for the reasoner, one for each endpoint and stage of a favourable band: it is satisfiable while the band lies below every LD50 reported for the same taxon, endpoint and stage.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some HypocotylEmergence and atStage some GerminationStage and doseGy some [minInclusive 15.0 and maxInclusive 15.0 (xsd:double)])

Nicotiana_tabacum_SeedlingPerformance_WithinFavourableBandDose

A dose assessment of Nicotiana tabacum for germination or early seedling growth, at a dose within the favourable band of approximately 5 to 15 Gy that Alves et al. (2027) report, both ends included.

label	Nicotiana tabacum seedling performance within favourable band dose
source statement	Across endpoints, the most favorable responses were concentrated broadly between approximately 5 and 15 Gy. The exact position of the apparent maximum depended on variety, endpoint, and sampling time, indicating that no single universal optimum should be assumed for all tobacco genotypes.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4097 and forEndpoint some [CotyledonFreeing, FreshMass, GerminationPercentage, GerminationRate, HypocotylEmergence] and atStage some [EarlySeedlingStage, GerminationStage] and doseGy some [minInclusive 5.0 and maxInclusive 15.0 (xsd:decimal, xsd:double)])
subclass of	WithinReportedFavourableBand

Nicotiana_tabacum_WithinFavourableBandDose

OBSOLETE. A dose window of release 1.6.0 for Nicotiana tabacum, conditioned on the taxon alone. Replaced by a window that is also conditioned on the endpoint and the stage its source scored.

label	obsolete Nicotiana tabacum within favourable band dose
replaced by	Nicotiana_tabacum_SeedlingPerformance_WithinFavourableBandDose

NoDetectedResponseOutcome

A treatment outcome with no response: the endpoints measured did not differ from the unirradiated control.

label	no detected response outcome
comment	An outcome enters this class when it is asserted to have no response (hasResponse max 0). An outcome that records no response without that assertion stays unclassified, because OWL does not infer the absence of an unrecorded value.
equivalent to	(TreatmentOutcome and hasResponse max 0)

OtherPhysiologicalEndpointCategory

The endpoint category of physiological measurements other than germination and early vigour, such as growth, yield and photosynthetic traits (EP6).

label	other physiological endpoint category
subclass of	EndpointCategory

Plant

A whole plant.

label	plant
definition source	Plant Ontology (Cooper et al. 2013), checked on the EBI Ontology Lookup Service, PO:0000003 whole plant
subclass of	obo:BFO_0000040 obo:PO_0000003
external alignment	subclass of obo:BFO_0000040, subclass of obo:PO_0000003

PlantBulb

A bulb: a short underground shoot whose fleshy leaves or leaf bases store reserves, as in onion, shallot and tuberose. A garlic clove is a bulblet.

label	plant bulb
definition source	Plant Ontology (Cooper et al. 2013), checked on the EBI Ontology Lookup Service, PO:0025356 bulb
equivalent to	obo:PO_0025356
subclass of	PlantPart
external alignment	equivalent to obo:PO_0025356

PlantCallus

A plant callus: a mass of mostly parenchyma cells, formed on wounding or in tissue culture, irradiated as the propagule in in vitro mutagenesis.

label	plant callus
definition source	Plant Ontology (Cooper et al. 2013), checked on the EBI Ontology Lookup Service, PO:0005052 plant callus
equivalent to	obo:PO_0005052
subclass of	PlantPart
external alignment	equivalent to obo:PO_0005052

PlantHealthEndpointCategory

The endpoint category of plant health, such as disease incidence or resistance to a pathogen or pest (EP5).

label	plant health endpoint category
subclass of	EndpointCategory

PlantPart

A material plant structure that can be irradiated and observed: an organ, a tissue, or a propagule such as a seed, bulb, tuber, cutting or callus.

label	plant part
subclass of	obo:BFO_0000040 obo:PO_0025131
external alignment	subclass of obo:BFO_0000040, subclass of obo:PO_0025131

PlantSeed

A seed: the propagule of a seed plant, which generally develops from an ovule after fertilization.

label	plant seed
definition source	Plant Ontology (Cooper et al. 2013), checked on the EBI Ontology Lookup Service, PO:0009010 seed
equivalent to	obo:PO_0009010
subclass of	obo:BFO_0000040 PlantPart
external alignment	equivalent to obo:PO_0009010, subclass of obo:BFO_0000040

PlantTuber

A shoot axis tuber: a swollen stem that stores reserves, as in the potato.

label	plant tuber
definition source	Plant Ontology (Cooper et al. 2013), checked on the EBI Ontology Lookup Service, PO:0004543 shoot axis tuber
equivalent to	obo:PO_0004543
subclass of	PlantPart
external alignment	equivalent to obo:PO_0004543

Plukenetia_volubilis_SeedlingSurvival_AtOrAboveLD50Dose

A dose assessment of Plukenetia volubilis for seedling survival in the early seedling stage, at a dose at or above the LD50 of 618.78 Gy that Corazon-Guivin et al. (2023) estimate.

label	Plukenetia volubilis seedling survival at or above LD50 dose
source statement	A logistic regression between radiation doses and mortality was calculated to estimate the optimum LD50 using a generalized linear model. [...] the LD50 of the dosimetry assay was 618.78 Gy.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_316893 and forEndpoint some SeedlingSurvival and atStage some EarlySeedlingStage and doseGy some [minInclusive 618.78 (xsd:decimal, xsd:double)])
subclass of	AtOrAboveReportedLD50

Plukenetia_volubilis_SeedlingSurvival_BelowLD50Dose

A dose assessment of Plukenetia volubilis for seedling survival in the early seedling stage, at a dose below the LD50 of 618.78 Gy that Corazon-Guivin et al. (2023) estimate.

label	Plukenetia volubilis seedling survival below LD50 dose
source statement	A logistic regression between radiation doses and mortality was calculated to estimate the optimum LD50 using a generalized linear model. [...] the LD50 of the dosimetry assay was 618.78 Gy.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_316893 and forEndpoint some SeedlingSurvival and atStage some EarlySeedlingStage and doseGy some [minExclusive 0.0 and maxExclusive 618.78 (xsd:decimal, xsd:double)])
subclass of	BelowReportedLD50

PollenSterility

The percentage of pollen grains that are not viable in a viability test.

label	pollen sterility
subclass of	Endpoint
external alignment	close match obo:TO_0000437

Proton

Radiation consisting of accelerated protons.

label	proton
subclass of	RadiationType
external alignment	related match obo:CHEBI_24636

QuantityValue

A measured quantity with a numeric value and a unit given as a QUDT unit (absorbed dose in gray, dose rate in gray per hour or per minute, fluence in joule per square metre).

label	quantity value
comment	Dose and dose-rate values carry a typed qudt:hasUnit link; absorbed dose is in gray.
equivalent to	http://qudt.org/schema/qudt/QuantityValue

ROSBalanceShift

A change in the level of reactive oxygen species, or in the balance between their production and removal, measured after irradiation relative to the unirradiated control.

label	ROS balance shift
subclass of	BiochemicalChange
external alignment	related match obo:CHEBI_26523, related match obo:TO_0002657

RadiationType

A kind of radiation by which a seed-irradiation treatment is delivered.

label	radiation type

Response

A biological process in an irradiated plant structure, or in the plant grown from it, observed as a difference from the unirradiated control in one or more endpoints.

label	response
subclass of	obo:BFO_0000015
external alignment	related match obo:TO_0000161, subclass of obo:BFO_0000015

RootLength

The length of the primary root or of the root system of a seedling or plant.

label	root length
subclass of	Endpoint
external alignment	close match obo:TO_0000227

SeedIrradiationTreatment

A planned process in which seeds or other plant propagules (bulbs, tubers, cuttings, shoot cultures, callus) are exposed to radiation of a stated type and source, at a stated dose or dose range and, where reported, a stated dose rate.

label	seed irradiation treatment
comment	In the OnSIR ABox one treatment individual records the irradiations of one study: a study that irradiated several doses carries a DoseRange from its lowest to its highest dose, and a treatment at a single dose records that dose with hasDose.
subclass of	hasRadiationType some RadiationType (hasDose some QuantityValue or hasDoseRange some DoseRange or hasFluence some QuantityValue) obo:BFO_0000015 obo:OBI_0302889 SeedTreatment
external alignment	broad match obo:PECO_0007151, subclass of obo:BFO_0000015, subclass of obo:OBI_0302889

SeedStage

The stage at which the propagule is a quiescent seed, before imbibition.

label	seed stage
subclass of	LifecycleStage

SeedSterility

The percentage of flowers or spikelets that fail to set seed.

label	seed sterility
subclass of	Endpoint
external alignment	broad match obo:TO_0000485

SeedTreatment

A planned process applied to seeds or other plant propagules before sowing or planting.

label	seed treatment
subclass of	obo:BFO_0000015
external alignment	subclass of obo:BFO_0000015

Seedling

A young plant derived from a newly germinated seed, up to the development of its first true leaf.

label	seedling
definition source	Plant Ontology (Cooper et al. 2013), checked on the EBI Ontology Lookup Service, PO:0008037 seedling
equivalent to	obo:PO_0008037
subclass of	obo:BFO_0000040
external alignment	equivalent to obo:PO_0008037, subclass of obo:BFO_0000040

SeedlingSurvival

The percentage of irradiated propagules, or of the seedlings raised from them, alive at a stated time after sowing, often relative to the unirradiated control.

label	seedling survival
subclass of	Endpoint
external alignment	related match obo:PATO_0000169

SeedlingVigorIndex

An index of seedling vigour that combines germination with seedling growth, such as germination percentage multiplied by seedling length or dry mass.

label	seedling vigour index
subclass of	Endpoint
external alignment	close match obo:TO_0000280

ShootLength

The length of the shoot of a seedling or plant.

label	shoot length
subclass of	Endpoint
external alignment	close match obo:TO_0001158

SoilCondition

The soil in which plants were grown, or a property of it.

label	soil condition
subclass of	Context
external alignment	close match obo:PECO_0007049

Solanum_lycopersicum_SeedlingSurvival_BelowLD50Dose

A dose assessment of Solanum lycopersicum for seedling survival in the early seedling stage, at a dose of 120 Gy or less; at 120 Gy, the highest dose of Indrayanti et al. (2024), 59 % of seedlings relative to the control were alive.

label	Solanum lycopersicum seedling survival below LD50 dose
source statement	The analysis of the lethal dose showed a 50% reduction in plant growth of tomato cv. 'Timothy' F1 was obtained at 132.49 Gy.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4081 and forEndpoint some SeedlingSurvival and atStage some EarlySeedlingStage and doseGy some [minExclusive 0.0 and maxInclusive 120.0 (xsd:decimal, xsd:double)])
subclass of	BelowReportedLD50

SterilizationDose

A dose asserted by a curator to have a sterilizing effect. Discouraged for new annotation: the category names a biological outcome, and the outcome of one absorbed dose depends on taxon, endpoint and stage. Retained because data that already carries a dose category reasons through its axioms. Record the category as an individual typed with this class; the general class inclusion reads that typing. For new curation, record the numeric dose as a DoseAssessment with doseGy, hasSubject, forEndpoint and atStage. [curation note] Kept active: an obsolete OBO term carries no logical axioms, and this class is the antecedent of a general class inclusion. DoseAssessment records where a numeric dose lies relative to the statistics reported for its taxon.

label	sterilization dose
subclass of	DoseCategory

SterilizationResponse

A response in which irradiation reduces or abolishes the capacity of the plant grown from the irradiated propagule to produce viable gametes or seed.

label	sterilization response
subclass of	Response

StimulatoryOutcome

A treatment outcome that has a hormetic response.

label	stimulatory outcome
equivalent to	(TreatmentOutcome and hasResponse some HormeticResponse)

StressResistance

The capacity of a plant raised from an irradiated propagule to grow under a biotic or abiotic stress, measured against the unirradiated control.

label	stress resistance
subclass of	Endpoint
external alignment	close match obo:TO_0000164

Substrate

The medium on which seeds were germinated or plants grown, such as filter paper, agar, rock wool or a soil mix.

label	substrate
subclass of	Context
external alignment	close match obo:PECO_0007147

TemperatureCondition

The temperature at which seeds were germinated or plants grown.

label	temperature condition
subclass of	Context
external alignment	close match obo:PECO_0007175, related match obo:PATO_0000146

TreatmentOutcome

What was observed in a plant structure after a seed-irradiation treatment, recorded with the treatment, the subject and the response, endpoint or endpoint category observed.

label	treatment outcome
subclass of	hasTreatment some SeedIrradiationTreatment hasTreatment exactly 1 SeedIrradiationTreatment

Trigonella_foenum_graecum_BelowLD50Dose

OBSOLETE. A dose window of release 1.6.0 for Trigonella foenum-graecum, conditioned on the taxon alone. Replaced by a window that is also conditioned on the endpoint and the stage its source scored.

label	obsolete Trigonella foenum-graecum below LD50 dose
replaced by	Trigonella_foenum_graecum_SeedlingSurvival_BelowLD50Dose

Trigonella_foenum_graecum_SeedlingSurvival_BelowLD50Dose

A dose assessment of Trigonella foenum-graecum for seedling survival in the early seedling stage, at a dose of 350 Gy or less; at 350 Gy, the highest dose of Patel et al. (2017), 56 % of seedlings survived.

label	Trigonella foenum-graecum seedling survival below LD50 dose
source statement	The LD50 was closed to 350 on which 64 percent seed germination, 56% seedlings survival and a considerable reduction in seedlings growth were recorded.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_78534 and forEndpoint some SeedlingSurvival and atStage some EarlySeedlingStage and doseGy some [minExclusive 0.0 and maxInclusive 350.0 (xsd:decimal, xsd:double)])
subclass of	BelowReportedLD50

Triticum_aestivum_SeedlingSurvival_AtOrAboveLD50Dose

A dose assessment of Triticum aestivum for seedling survival in the early seedling stage, at a dose of 278.61 Gy or more, at or above the LD50 of both varieties that Chakraborty et al. (2023) estimate.

label	Triticum aestivum seedling survival at or above LD50 dose
source statement	The median lethal dose was recorded to be 272.71 Gy and 278.61 Gy in DBW 187 and K 1006 respectively.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4565 and forEndpoint some SeedlingSurvival and atStage some EarlySeedlingStage and doseGy some [minInclusive 278.61 (xsd:decimal, xsd:double)])
subclass of	AtOrAboveReportedLD50

Triticum_aestivum_SeedlingSurvival_BelowLD50Dose

A dose assessment of Triticum aestivum for seedling survival in the early seedling stage, at a dose below 272.71 Gy, below the LD50 of both varieties that Chakraborty et al. (2023) estimate.

label	Triticum aestivum seedling survival below LD50 dose
source statement	The median lethal dose was recorded to be 272.71 Gy and 278.61 Gy in DBW 187 and K 1006 respectively.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_4565 and forEndpoint some SeedlingSurvival and atStage some EarlySeedlingStage and doseGy some [minExclusive 0.0 and maxExclusive 272.71 (xsd:decimal, xsd:double)])
subclass of	BelowReportedLD50

UV_A

Ultraviolet radiation of wavelength from 315 to 400 nm.

label	UV-A
definition source	CIE ultraviolet spectral bands: UV-A 315-400 nm
subclass of	RadiationType
external alignment	related match obo:PECO_0007222

UV_B

Ultraviolet radiation of wavelength from 280 to 315 nm.

label	UV-B
definition source	CIE ultraviolet spectral bands: UV-B 280-315 nm
subclass of	RadiationType
external alignment	related match obo:PECO_0007222

UV_C

Ultraviolet radiation of wavelength from 100 to 280 nm.

label	UV-C
definition source	CIE ultraviolet spectral bands: UV-C 100-280 nm
subclass of	RadiationType
external alignment	related match obo:PECO_0007222

Vigna_unguiculata_AtOrAboveLD50Dose

OBSOLETE. A dose window of release 1.6.0 for Vigna unguiculata, conditioned on the taxon alone. Replaced by a window that is also conditioned on the endpoint and the stage its source scored.

label	obsolete Vigna unguiculata at or above LD50 dose
replaced by	Vigna_unguiculata_SeedlingSurvival_AtOrAboveLD50Dose

Vigna_unguiculata_BelowLD50Dose

OBSOLETE. A dose window of release 1.6.0 for Vigna unguiculata, conditioned on the taxon alone. Replaced by a window that is also conditioned on the endpoint and the stage its source scored.

label	obsolete Vigna unguiculata below LD50 dose
replaced by	Vigna_unguiculata_SeedlingSurvival_BelowLD50Dose

Vigna_unguiculata_SeedlingSurvival_AtOrAboveLD50Dose

A dose assessment of Vigna unguiculata for seedling survival scored at the flowering stage, at a dose of 250 Gy or more, at which Gnankambary et al. (2019) observed no survival in any genotype they tested.

label	Vigna unguiculata seedling survival at or above LD50 dose
source statement	Plant survival was recorded at 50% flowering. [...] The (LD50%) for each genotype was estimated through the simple linear regression model considering 100% of seed germination and survival rate of the control.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_3917 and forEndpoint some SeedlingSurvival and atStage some FloweringStage and doseGy some [minInclusive 250.0 (xsd:decimal, xsd:double)])
subclass of	AtOrAboveReportedLD50

Vigna_unguiculata_SeedlingSurvival_BelowLD50Dose

A dose assessment of Vigna unguiculata for seedling survival scored at the flowering stage, at a dose of 150 Gy or less; at 150 Gy, the lowest dose of Gnankambary et al. (2019), more than half of the plants of every genotype they tested survived.

label	Vigna unguiculata seedling survival below LD50 dose
source statement	Plant survival was recorded at 50% flowering. [...] The (LD50%) for each genotype was estimated through the simple linear regression model considering 100% of seed germination and survival rate of the control.
equivalent to	(DoseAssessment and hasSubject some obo:RO_0002162 some obo:NCBITaxon_3917 and forEndpoint some SeedlingSurvival and atStage some FloweringStage and doseGy some [minExclusive 0.0 and maxInclusive 150.0 (xsd:decimal, xsd:double)])
subclass of	BelowReportedLD50

WaterQuality

The water supplied to seeds or plants and its properties, such as its source, its salinity or the watering regime.

label	water quality
subclass of	Context
external alignment	related match obo:PECO_0007383

WithinReportedFavourableBand

A dose assessment whose dose lies within the favourable band reported for its taxon, endpoint and stage, both ends included: the band of doses in which the source reports its most favourable responses. [curation note] Declared disjoint from AtOrAboveReportedLD50, as is BelowReportedFavourableBand, on the assumption that a favourable band lies below the LD50 reported for the same taxon, endpoint and stage. A record coding a band that reaches that LD50 makes the probe class of the band for that endpoint and stage unsatisfiable, and is sent to a curator.

label	within reported favourable band
subclass of	DoseAssessment

XRay

Electromagnetic radiation of wavelength from about 5 pm to 10 nm produced outside the nucleus, as by an X-ray tube.

label	X-ray
definition source	Plant Experimental Conditions Ontology, PECO:0007628 X-ray exposure (5 pm to 10 nm)
subclass of	RadiationType
external alignment	related match obo:PECO_0007628

Xe133

The radionuclide xenon-133.

label	xenon-133
subclass of	Isotope

Object properties 26

atStage forEndpoint forTaxon hasBiochemicalChange hasContext hasDose hasDoseCategory hasDoseRange hasDoseRate hasDoseRateCategory hasEndpointCategory hasExposureTime hasFluence hasModel hasRadiationType hasResponse hasSourceIsotope hasSubject hasTaxon hasTreatment hasWavelength inducedBy induces isTreatmentOf maxDose minDose

atStage

Relates a dose assessment to the life-cycle stage at which its endpoint is scored.

label	at stage
domain	DoseAssessment
range	LifecycleStage
characteristics	owl:FunctionalProperty

forEndpoint

Relates a dose assessment or a treatment outcome to the endpoint it concerns.

label	for endpoint
domain	(DoseAssessment or TreatmentOutcome)
range	Endpoint
characteristics	owl:FunctionalProperty

forTaxon

OBSOLETE. Related a dose assessment to an individual standing for a taxon. A dose assessment now names the plant structure the dose is applied to with hasSubject, and the structure states its taxon with RO:0002162 in taxon some NCBITaxon class.

label	obsolete for taxon
consider	hasSubject, obo:RO_0002162

hasBiochemicalChange

Relates a treatment outcome to a biochemical change measured in it.

label	has biochemical change
domain	TreatmentOutcome
range	BiochemicalChange

hasContext

Relates a treatment outcome to a condition under which it was observed.

label	has context
domain	TreatmentOutcome
range	Context

hasDose

Relates a seed-irradiation treatment to the single absorbed dose it delivered.

label	has absorbed dose
domain	SeedIrradiationTreatment
range	http://qudt.org/schema/qudt/QuantityValue
characteristics	owl:FunctionalProperty

hasDoseCategory

Relates a treatment outcome to the dose category a curator asserts for its dose.

label	has dose category
domain	TreatmentOutcome
range	DoseCategory

hasDoseRange

Relates a seed-irradiation treatment that delivered several doses to their range.

label	has dose range
domain	SeedIrradiationTreatment
range	DoseRange

hasDoseRate

Relates a seed-irradiation treatment to the absorbed-dose rate at which it was delivered.

label	has dose rate
domain	SeedIrradiationTreatment
range	http://qudt.org/schema/qudt/QuantityValue
characteristics	owl:FunctionalProperty

hasDoseRateCategory

Relates a seed-irradiation treatment to the category of its dose rate.

label	has dose-rate category
domain	SeedIrradiationTreatment
range	DoseRateCategory

hasEndpointCategory

Relates a treatment outcome to the endpoint category its source corpus records for it.

label	has endpoint category
domain	TreatmentOutcome
range	EndpointCategory

hasExposureTime

Relates a seed-irradiation treatment to the duration of the exposure.

label	has exposure time
domain	SeedIrradiationTreatment
range	http://qudt.org/schema/qudt/QuantityValue

hasFluence

Relates a seed-irradiation treatment to its fluence, the radiant exposure in joule per square metre by which ultraviolet treatments are dosed.

label	has fluence
domain	SeedIrradiationTreatment
range	http://qudt.org/schema/qudt/QuantityValue

hasModel

Relates a treatment outcome to a dose-response model fitted to it.

label	has model
domain	TreatmentOutcome
range	DoseResponseModel

hasRadiationType

Relates a seed-irradiation treatment to the kind of radiation that delivered it.

label	has radiation type
domain	SeedIrradiationTreatment
range	RadiationType

hasResponse

Relates a treatment outcome to a response observed in it.

label	has response
domain	TreatmentOutcome
range	Response

hasSourceIsotope

Relates a seed-irradiation treatment to the radionuclide of its source.

label	has source isotope
domain	SeedIrradiationTreatment
range	Isotope

hasSubject

Relates a treatment outcome or a dose assessment to the plant structure that was irradiated or observed.

label	has subject
domain	(DoseAssessment or TreatmentOutcome)
range	PlantPart

hasTaxon

OBSOLETE. Related a plant structure to an individual standing for its taxon. A plant structure now states its taxon with RO:0002162 in taxon some NCBITaxon class.

label	obsolete has taxon
replaced by	obo:RO_0002162

hasTreatment

Relates a treatment outcome to the seed-irradiation treatment that produced it.

label	has treatment
domain	TreatmentOutcome
range	SeedIrradiationTreatment

hasWavelength

Relates a seed-irradiation treatment to the wavelength of the radiation, for ultraviolet treatments.

label	has wavelength
domain	SeedIrradiationTreatment
range	http://qudt.org/schema/qudt/QuantityValue

inducedBy

Relates a response to the seed-irradiation treatment that induced it; the inverse of induces.

label	induced by
domain	Response
range	SeedIrradiationTreatment
inverse of	induces

induces

Relates a seed-irradiation treatment to a response it induced.

label	induces
domain	SeedIrradiationTreatment
range	Response

isTreatmentOf

Relates a seed-irradiation treatment to an outcome it produced; the inverse of has treatment.

label	is treatment of
domain	SeedIrradiationTreatment
range	TreatmentOutcome
inverse of	hasTreatment

maxDose

Relates a dose range to its highest dose.

label	maximum dose
domain	DoseRange
range	http://qudt.org/schema/qudt/QuantityValue
characteristics	owl:FunctionalProperty

minDose

Relates a dose range to its lowest dose.

label	minimum dose
domain	DoseRange
range	http://qudt.org/schema/qudt/QuantityValue
characteristics	owl:FunctionalProperty

Datatype properties 11

bc_b bc_c bc_d bc_e bc_f doseGy germinationRateIncrease mutationFrequency numericValue rootGrowthStimulus sterilityRate

bc_b

The slope parameter b of a Brain-Cousens model, which sets the steepness of the decline.

label	Brain–Cousens parameter b
domain	DoseResponseModel
range	xsd:double

bc_c

The lower limit c of a Brain-Cousens model, the response at very high doses.

label	Brain–Cousens parameter c
domain	DoseResponseModel
range	xsd:double

bc_d

The upper limit d of a Brain-Cousens model, the response in the unirradiated control.

label	Brain–Cousens parameter d
domain	DoseResponseModel
range	xsd:double

bc_e

The dose parameter e of a Brain-Cousens model, which locates the decline on the dose axis.

label	Brain–Cousens parameter e
domain	DoseResponseModel
range	xsd:double

bc_f

The stimulation parameter f of a Brain-Cousens model, the rate of increase of the response at low doses.

label	Brain–Cousens parameter f
domain	DoseResponseModel
range	xsd:double

doseGy

The absorbed dose of a dose assessment, in gray.

label	dose in gray
domain	DoseAssessment
range	xsd:decimal, xsd:double
characteristics	owl:FunctionalProperty

germinationRateIncrease

The increase in germination relative to the control in a hormetic response, as a fraction.

label	germination rate increase
domain	HormeticResponse
range	xsd:double

mutationFrequency

The frequency of mutants or mutations in a mutagenic response, as a fraction.

label	mutation frequency
domain	MutagenicResponse
range	xsd:double

numericValue

The numeric value of a quantity value, in the unit given by its qudt:hasUnit link.

label	numeric value
domain	QuantityValue
range	xsd:double
characteristics	owl:FunctionalProperty

rootGrowthStimulus

The increase in root growth relative to the control in a hormetic response, as a fraction.

label	root growth stimulus
domain	HormeticResponse
range	xsd:double

sterilityRate

The fraction of sterile plants or gametes in a sterilization response.

label	sterility rate
domain	SterilizationResponse
range	xsd:double

Named individuals 3

Individual	Types
taxon_Nicotiana_tabacum
taxon_Trigonella_foenum_graecum
taxon_Vigna_unguiculata

Reproducibility

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