DataPLANT

The review Ontologies for increasing the FAIRness of plant research data provides an overview and usage guidance for ontologies in plant research.

The table below is from the WG Ontology collection spreadsheet.

Source: /files/meta/Used_Ontologies_at_NFDI.xlsx (sheet: DataPLANT)

Ontology ID	Domain	License	Modularity	Format	developed / reused / only indexed / only evaluated	Ontology Name	Upper Level Ontology	References	Ontology Type	DataPlant Domains	Obofoundry <br/>domain	Ontology ID Bioportal	Bioportal category	Used in	OBO dependencies	Obofoundry	OLS Url	BioPortal	Some other URL	Type Sorting	TODO: Domain aufräumen
AGRO	Agronomic practices, techniques, and variables used in agronomic experiments.	CC BY 4.0	BFO	owl	only evaluated	AGRonomy Ontology	BFO	Devare et al. 2016	Plant specific ontologies	Agronomic experiments	agriculture			GARDIAN	bfo, envo, foodon, go, iao, ncbitaxon, obi, pato, peco, po, ro, to, uo, xco	https://obofoundry.org/ontology/agro.html	https://www.ebi.ac.uk/ols/ontologies/agro	https://bioportal.bioontology.org/ontologies/AGRO		1.0
FLOPO	Traits and phenotypes of flowering plants	CC0 1.0	None (?!), but rich mapping to other ontologies	owl	only evaluated	Flora Phenotype Ontology	None (?!), but rich mapping to other ontologies	Hoehndorf et al. 2016	Plant specific ontologies	Flora Ontology	phenotype		Phenotype, Plant			https://obofoundry.org/ontology/flopo.html	https://www.ebi.ac.uk/ols/ontologies/flopo	https://bioportal.bioontology.org/ontologies/FLOPO		1.0
PECO	Plant experimental conditions	CC BY 4.0	OBO-based	owl	reused	Plant Experimental Conditions Ontology	BFO	Cooper et al. 2018	Plant specific ontologies	Plant biology experiments.	investigations		Experimental Conditions, Phenotype, Plant			https://obofoundry.org/ontology/peco.html	https://www.ebi.ac.uk/ols/ontologies/peco	https://bioportal.bioontology.org/ontologies/PECO		1.0
PO	Plant anatomy, morphology and growth and development	CC BY 4.0	OBO-based, BFO_aligned	owl	reused	Plant Ontology	BFO	Walls et al. 2012;Walls et al. 2019;Cooper et al. 2013	Plant specific ontologies	Plant anatomy and development	anatomy and development		Plant Anatomy, Plant, Plant Development			https://obofoundry.org/ontology/po.html	http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PO	https://bioportal.bioontology.org/ontologies/PO		1.0
PPEO	Plant Phenotypes and Traits (implementation of the Minimal Information About Plant Phenotyping Experiment)	CC BY 4.0		owl	only evaluated	Plant Phenotype Experiment Ontology /	None	Papoutsoglou et al. 2020	Plant specific ontologies	Plant Phenotyping			NOT_ON_BIOPORTAL			---	---	---	https://agroportal.lirmm.fr/ontologies/PPEO , https://github.com/MIAPPE/MIAPPE-ontology , https://fairsharing.org/1234	1.0	Real plant Ontologies <= Neither complete, not accurate, but first attempt at "sorting" the ontologies by use / domain
PPO	Phenology of individual plants and populations of plants	CC BY 3.0	BFO aligned	owl	only evaluated	Plant Phenology Ontology	BFO	Stucky et al. 2018	Plant specific ontologies	Plant Phenology Ontology	phenotype					https://obofoundry.org/ontology/ppo.html	https://www.ebi.ac.uk/ols/ontologies/ppo	https://bioportal.bioontology.org/ontologies/PPO		1.0	TODO: welche ist in welcher enthalten, welche sind gepflegt und wo sind Altlasten ...; Soll Part eines Reviews werden, welches gerade in der Mache ist
PSO	Biotic and abiotic stresses that a plant may encounter	CC BY 3.0	BFO	owl	only evaluated	Plant Stress Ontology	BFO	Cooper et al. 2018	Plant specific ontologies		agriculture	PLANTSO	Plant		ro	https://obofoundry.org/ontology/pso.html	https://www.ebi.ac.uk/ols/ontologies/pso			1.0
TO	Phenotypic traits in plants	CC BY 4.0	BFO	owl	reused	Plant Trait Ontology	BFO	Jaiswal 2011	Plant specific ontologies	Phenotypic traits in plants	phenotype	PTO	Phenotype, Plant			https://obofoundry.org/ontology/to.html	https://www.ebi.ac.uk/ols/ontologies/to	https://bioportal.bioontology.org/ontologies/PTO		1.0
BAO	Biological screening assays and their results			owl	only evaluated	BioAssay Ontology	None	Abeyruwan et al., 2014	General Scientific ontologies				Molecule, Biological Process, Other, Subcellular, Chemical, Cell, Protein, Vocabularies, Physicochemical			---	https://www.ebi.ac.uk/ols/ontologies/bao	https://bioportal.bioontology.org/ontologies/BAO		2.0	(General / Omics) Experimental stuff
BCO	Support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys	CC0 1.0	BFO, DwC, RO, CARO, DC, NCBITAXON, OIO, OBI, DCTERMS, IAO, SO, RDFS, OWL, PR, PCO, UBERON, ENVO, CHEBI, GO, CL	owl	only evaluated	Biological Collections Ontology	BFO	Walls et al. 2014	General Scientific ontologies	Biodiversity	organisms		All Organisms			https://obofoundry.org/ontology/bco.html	https://www.ebi.ac.uk/ols/ontologies/bco	https://bioportal.bioontology.org/ontologies/BCO		2.0
BOF	Biodiversity, as developed by the National Institute for Amazonian Research			owl	only evaluated	Biodiversity Ontology	None	Albuquerque 2011	General Scientific ontologies	Biodiversity	--					---	---	https://bioportal.bioontology.org/ontologies/BOF		2.0
BTO	Source of an enzyme comprising tissues, cell lines, cell types and cell cultures	CC BY 4.0	IAO, RO, OIO	owl	only evaluated	BRENDA Tissue and Enzyme Source Ontology	None	Gremse et al., 2011	General Scientific ontologies		anatomy and development					https://obofoundry.org/ontology/bto.html	https://www.ebi.ac.uk/ols/ontologies/bto	https://bioportal.bioontology.org/ontologies/BTO		2.0	(General) Tissue and cellular thingies
CHEBI	Molecular entities of biological interest	CC BY 4.0		owl	reused	Chemical Entities of Biological Interest Ontology	None	Degtyarenko et al. 2008	General Scientific ontologies	Chemistry	chemistry and biochemistry		Chemical			https://obofoundry.org/ontology/chebi.html	https://www.ebi.ac.uk/ols/ontologies/chebi	https://bioportal.bioontology.org/ontologies/CHEBI		2.0	Molecular Biology things
CHMO	Methods used to collect data in chemical experiments	CC BY 4.0	BFO	owl	only evaluated	Chemical Methods Ontology	BFO	https://github.com/rsc-ontologies/rsc-cmo	General Scientific ontologies	Chemistry	health		Chemical			https://obofoundry.org/ontology/chmo.html	https://www.ebi.ac.uk/ols/ontologies/chmo	https://bioportal.bioontology.org/ontologies/CHMO		2.0
CO	Breeder’s traits and variables			owl	only evaluated	Crop Ontology		Shrestha et al., 2012; Arnaud et al., 2016; Arnaud et al., 2020
DPBO	To fill the ontology gap				developed	Data Plant Biology Ontology		https://github.com/nfdi4plants/nfdi4plants_ontology
EDAM	computational biology, bioinformatics and bioimage informatics			owl	only evaluated	EDAM bioinformatics operations, data types, formats, identifiers and topics	None	Ison et al., 2013	General Scientific ontologies	life-sciences & data management			All Organisms, Biomedical Resources, Genomic and Proteomic, Other, Vocabularies			---	https://www.ebi.ac.uk/ols/ontologies/edam	https://bioportal.bioontology.org/ontologies/EDAM		2.0	Bioinformatics stuff
EFO	Experimental variables	Apache license 2.0	ORDO, MONDO, CHEBI, GO, NCBITAXON, DC, NCIT, HP, FMA, OIO, OWL, UBERON, RO, PR, FBBT, OBI, OBA, IAO, SKOS, SO, BAO, DCTERMS, CLO, HANCESTRO, OGMS, PO, IDO, ZFA, RDFS, TO, CL, PATO, MPATH, DOID, FBDV, BFO, BTO, MA, MP, OMIT, UO, WBLS	owl	reused	Experimental Factor Ontology	BFO	Malone et al. 2010	General Scientific ontologies				Experimental Conditions, Biological Process			---	https://www.ebi.ac.uk/ols/ontologies/efo	https://bioportal.bioontology.org/ontologies/EFO		2.0
ENVO	Environmental systems, components and processes	CC0 1.0	CARO, CHEBI, RO, FOODON, GO, NCBITAXON, DC, UBERON, OIO, DCTERMS, IAO, SKOS, PCO, OBI, PO, RDFS, PATO, BFO, OWL, FAO, CL, SCHEMA	owl	reused	Environment Ontology	BFO	Buttigieg et al. 2013, 2016	General Scientific ontologies		environment		Experimental Conditions, Other, Physicochemical		chebi, foodon, go, ncbitaxon, pco, po, ro, uberon	https://obofoundry.org/ontology/envo.html	https://www.ebi.ac.uk/ols/ontologies/envo	https://bioportal.bioontology.org/ontologies/ENVO		2.0
GEOSPECIES	Integration of species concepts with species occurrences, gene sequences, images, references and geographical information		EO	owl	only evaluated	GeoSpecies Ontology	None	http://lod.geospecies.org/	General Scientific ontologies				Other			---	---	https://bioportal.bioontology.org/ontologies/GEOSPECIES		2.0
GO	Function of genes and gene products	CC BY 4.0	OIO, DC, IAO, DCTERMS, RDFS, RO, OWL	owl	only evaluated	Gene Ontology	None	Ashburner et al. 2000;Gene Ontology Consortium 2023	General Scientific ontologies	Biology	biological systems		Genomic and Proteomic		cl, go/extensions/go-bridge-to-nifstd.owl, ncbitaxon, ro, uberon	https://obofoundry.org/ontology/go.html	https://www.ebi.ac.uk/ols/ontologies/go			2.0
MMO	Methods used to make clinical and phenotype measurements	CC0 1.0		owl	only evaluated	Measurement Method Ontology	None	Smith et al., 2013	General Scientific ontologies		health		Phenotype			https://obofoundry.org/ontology/mmo.html	https://www.ebi.ac.uk/ols/ontologies/mmo	https://bioportal.bioontology.org/ontologies/MMO		2.0
MOD	Protein chemical modifications, classified by molecular structure or amino acid	CC BY 4.0		owl	reused	Protein modification (PSI-MOD)		Montecchi-Palazzi et al. 2008	General Scientific ontologies		chemistry and biochemistry					https://obofoundry.org/ontology/mod.html	https://www.ebi.ac.uk/ols/ontologies/mod			2.0
MS	proteomics mass spectrometry	CC BY 4.0		owl	reused	PSI Mass Spectrometry Ontology	None	Mayer et al., 2013	General Scientific ontologies	Chemistry	investigations		Experimental Conditions, Protein		pato, uo	https://obofoundry.org/ontology/ms.html	https://www.ebi.ac.uk/ols/ontologies/ms	https://bioportal.bioontology.org/ontologies/MS		2.0
MSIO	mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies		BFO	owl	only evaluated	Metabolomics Standards Initiative Ontology (MSIO)	BFO	Rocca-Serra, 2018	General Scientific ontologies				NOT_ON_BIOPORTAL			---	https://www.ebi.ac.uk/ols/ontologies/msio	---		2.0
NCBITAXON	NCBI organismal taxonomy	CC0 1.0	OIO, DCTERMS, IAO	owl	reused	National Center for Biotechnology Information (NCBI) Organismal Classification	None	Federhen 2012	General Scientific ontologies	Taxonomy	organisms		Taxonomic Classification			https://obofoundry.org/ontology/ncbitaxon.html	https://www.ebi.ac.uk/ols/ontologies/ncbitaxon	https://bioportal.bioontology.org/ontologies/NCBITAXON		2.0	(General) Taxonomy stuff Missing: full-blown Leipzig catalogue of vascular plants
NCIT	Broad coverage of the cancer domain	CC BY 4.0		owl	reused	National Cancer Institute Thesaurus	None ??	https://ncit.nci.nih.gov	General Scientific ontologies		health					https://obofoundry.org/ontology/ncit.html	https://www.ebi.ac.uk/ols/ontologies/ncit	https://bioportal.bioontology.org/ontologies/NCIT		2.0
OBI	Life-science and clinical investigations	CC BY 4.0	BFO	owl	reused	Ontology for Biomedical Investigations	BFO	Brinkman et al. 2010;<br/>Bandrowski et al. 2016	General Scientific ontologies	Biomedicine	investigations		Experimental Conditions			https://obofoundry.org/ontology/obi.html	https://www.ebi.ac.uk/ols/ontologies/obi	https://bioportal.bioontology.org/ontologies/OBI		2.0	(General) Experimental setup, descriptions
OMP	phenotypes observed in all microbes	CC BY 3.0	imports terms from PATO, CHEBI, GO	owl	reused	Ontology of Microbial Phenotypes			General Scientific ontologies	microbiology			Phenotype					https://bioportal.bioontology.org/ontologies/OMP
PATO	Phenotypic qualities (properties, attributes or characteristics)	CC BY 3.0	BFO	owl	reused	Phenotype And Trait Ontology	BFO	Gkoutos et al. 2018	General Scientific ontologies	Phenotypic Quality Ontology	phenotype		Phenotype			https://obofoundry.org/ontology/pato.html	https://www.ebi.ac.uk/ols/ontologies/pato	https://bioportal.bioontology.org/ontologies/PATO		2.0
PCO	Material entities, qualities, and processes related to collections of interacting organisms such as populations and communities	CC0 1.0	BFO	owl	only evaluated	Population and Community Ontology	BFO	Walls et al. 2014	General Scientific ontologies		environment		All Organisms, Other		bfo, caro, envo, go, iao, ncbitaxon, pato, ro	https://obofoundry.org/ontology/pco.html	https://www.ebi.ac.uk/ols/ontologies/pco	https://bioportal.bioontology.org/ontologies/PCO		2.0
STATO	statistical tests, conditions of application, and information needed or resulting from statistical methods		BFO	owl	only evaluated	Statistics Ontology	BFO	https://github.com/ISA-tools/stato	General Scientific ontologies		information technology		Biomedical Resources, Experimental Conditions			https://obofoundry.org/ontology/stato.html	https://www.ebi.ac.uk/ols/ontologies/stato	https://bioportal.bioontology.org/ontologies/STATO		2.0
SWO	software tools, their types, tasks, versions, provenance and associated data	CC BY 4.0	BFO, RO, OBI	owl	only evaluated	Software Ontology	BFO	Malone et al., 2014	General Scientific ontologies	life-sciences & data management	information technology		Experimental Conditions, Biomedical Resources			https://obofoundry.org/ontology/swo.html	https://www.ebi.ac.uk/ols/ontologies/swo			2.0
UO	Metrical units for use in conjunction with PATO	CC BY 3.0		owl	reused	Unit Ontology	None	Gkoutos et al. 2012	General Scientific ontologies	Scientific units	phenotype		Phenotype			https://obofoundry.org/ontology/uo.html	https://www.ebi.ac.uk/ols/ontologies/uo	https://bioportal.bioontology.org/ontologies/UO		2.0
BFO	Standardizes upper level structure of OBO ontologies	CC BY 4.0		owl	only evaluated	Basic Formal Ontology		Arp et al. 2015	Upper level ontologies		upper		Upper Level Ontology			https://obofoundry.org/ontology/ro.html		https://bioportal.bioontology.org/ontologies/BFO		3.0
RO	Standardizes relations in obo foundry ontologies	CC0 1.0		owl	reused	Relations Ontology		https://oborel.github.io/obo-relations/	Upper level ontologies		upper					https://obofoundry.org/ontology/ro.html	https://www.ebi.ac.uk/ols/ontologies/ro			3.0
EO		CC BY 4.0			only evaluated	Plant Environment Ontology, This ontology is deprecated! Consider using: peco			XXX Deprecated	This ontology is deprecated! Consider using: peco	environment		Other			https://obofoundry.org/ontology/eo.html				4.0	Environmental / Biodiversity like stuff
GAZ		CC0 1.0		owl	only evaluated	Gazetteer. This ontology is inactive.	None ??		XXX Deprecated		environment					https://obofoundry.org/ontology/gaz.html	https://www.ebi.ac.uk/ols/ontologies/gaz	https://bioportal.bioontology.org/ontologies/GAZ		4.0
NEWT					only evaluated	NEWT UniProt Taxonomy				Taxonomy	organisms		NOT_ON_BIOPORTAL			---	---	---		4.0
PAE					only evaluated	Plant Anatomy, REPLACED BY: Plant Ontology (PO).			XXX Deprecated	REPLACED BY: Plant Ontology (PO).			Plant Anatomy, Plant			---	---	https://bioportal.bioontology.org/ontologies/PAE		4.0