Table 3.

Result of an Ontological Term Selection to Annotate Datasets about Submergence Tolerance of Rice Varieties for the Flood-Prone Lowlands in Nigeria

	Dataset Terms	Selected Ontology Terms	Definition	Source Ontologies	URI for Data Annotation
Crop	Rice	Oryza sativa	(Rice), species, monocots	NCBI taxonomy	http://purl.obolibrary.org/obo/NCBITaxon_4530
Variety Traits
Genotype	Germplasm with the submergence tolerance “Sub1” gene	Response to flooding	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating flooding, short-term immersion in water	Gene Ontology	http://purl.obolibrary.org/obo/GO_0009413
Phenotype	Submergence tolerance	Rice submergence tolerance trait Submergence sensitivity	The ability of plants to survive a period of submergence Measure of sensitivity of a plant if placed under submergence condition	Crop Ontology (CO) Trait Ontology (TO)	http://www.cropontology.org/rdf/CO_320:0000067a http://purl.obolibrary.org/obo/TO_0000286
Field practices	Manual weeding	Hand picking weeding process	A mechanical weeding process in which unwanted organisms are removed by hands	Agronomy Ontology	http://purl.obolibrary.org/obo/AGRO_00002057
	Herbicide treatment	Chemical weeding process	A weeding process in which chemical is used to manage unwanted weeds	Agronomy Ontology	http://purl.obolibrary.org/obo/AGRO_00002053
	Weeding application date			Term not found
Farming system	Rain-fed rice production system	Rain-fed farming	Arable cultivation relying solely on rainfall	AGROVOC	http://aims.fao.org/aos/agrovoc/c_6436
Abiotic stress	Flood-prone region exposure	Flood-prone region exposure Lowland region exposure	A treatment in terms of a plant's exposure to the regional conditions found in the vicinity of the water bodies, such as sea, river, lake. Growth conditions may include aerobic to anaerobic soil, salinity or toxicity in tidal areas. Treatment may include standing or flash flooding Treatment involving the plant, or the populations grown in regions where the land level is slightly steep, noncontinuous flooding of variable depth and duration. Alternating conditions of aerobic to anaerobic soil	Plant Experimental Conditions Ontology (PECO)	http://purl.obolibrary.org/obo/PECO_0007396b http://purl.obolibrary.org/obo/PECO_0007391
Geography	Bangladesh	Bangladesh		Gazetteer	http://purl.obolibrary.org/obo/GAZ_00000912
Agro-ecosystem	Lowland region	Lowland	None	AGROVOC	http://aims.fao.org/aos/agrovoc/c_4453
Socio-economy	Farmers' income	Household income Agricultural income	A demographic parameter indicating the amount of earnings made by a family Quantified household income using the sales information of agricultural products. This is gross income	NCI thesaurus in Socio-economic ontology Socio-Economic Ontology	http://purl.obolibrary.org/obo/NCIT_C70811 http://purl.obolibrary.org/obo/SURVO_00000200
	Fertilizer costs			Term not found

Annotation performed by Dr. Berta Miro, IRRI with the support of the CoP ontology experts.

^aCO term is mapped to a TO term so annotations using one or another are valid. CO will provide the format the variables measuring in the field the effect of the flood on the rice varieties.

^bPECO term is mapped to ENVO term “Floods (EO:0007172)” that has the definition: an unusual accumulation of water above the ground caused by high tide, heavy rain, melting snow, or rapid runoff from paved areas.