Plant Trait Ontology

Abbreviation: TO

General Information

A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part. The TO is part of the Planteome Project.

Homepage http://browser.planteome.org/amigo/term/TO:0000387#display-lineage-tab

Countries that developed this resource United States

Created in 2017

Taxonomic range

Viridiplantae

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: TO; Plant Trait Ontology; DOI: https://doi.org/10.25504/FAIRsharing.w69t6r; Last edited: Jan. 29, 2020, 10:39 a.m.; Last accessed: Mar 31 2020 9:17 p.m.

This record is maintained by cooperl09

Record updated: Jan. 29, 2020, 10:38 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.w69t6r' by 'The FAIRsharing Team' at 10:38, 29 Jan 2020 (approved):

	'yearOfCreation' has been modified:
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		After: 2017

	'dataProcesses' has been modified:
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			Ontology release (OWL)
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Edits to 'https://fairsharing.org/FAIRsharing.w69t6r' by 'The FAIRsharing Team' at 13:32, 23 Jan 2020 (approved):

	'organizations' has been modified:
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			Gene Ontology Consortium|http://www.geneontology.org/|Maintains
			Oregon State University, USA|http://cgrb.oregonstate.edu|Maintains
		After:
			New York Botanical Garden|http://www.nybg.org|Maintains
			Oregon State University, USA|http://cgrb.oregonstate.edu|Maintains
			Lawrence Berkeley National Laboratory (LBNL), CA, USA|http://www.lbl.gov/about/|Maintains
			Biodiversity International, Montpellier, France|https://www.bioversityinternational.org/|Maintains
			Aberystwyth University, Wales, UK|http://www.aber.ac.uk/en/ibers/|Maintains
		Added:
			New York Botanical Garden|http://www.nybg.org|Maintains
			Lawrence Berkeley National Laboratory (LBNL), CA, USA|http://www.lbl.gov/about/|Maintains
			Biodiversity International, Montpellier, France|https://www.bioversityinternational.org/|Maintains
			Aberystwyth University, Wales, UK|http://www.aber.ac.uk/en/ibers/|Maintains
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			Gene Ontology Consortium|http://www.geneontology.org/|Maintains

	'supportLinks' has been modified:
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			contact form|http://planteome.org/contact
			forum|https://github.com/Planteome/plant-trait-ontology/issues
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			contact form|http://planteome.org/contact
			email|jaiswalp@science.oregonstate.edu
			forum|https://github.com/Planteome/plant-trait-ontology/issues
			online documentation|https://github.com/Planteome/plant-trait-ontology
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			email|jaiswalp@science.oregonstate.edu
			online documentation|https://github.com/Planteome/plant-trait-ontology
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			Creative Commons Attribution 4.0 International (CC BY 4.0)|https://creativecommons.org/licenses/by/4.0/|Data
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			phenotype
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			Life Science
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			Life Science
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	'related_standards' has been modified:
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			Thesaurus of Plant Characteristics
			Plant Ontology
			Castor Bean Ontology
			Crop Ontology
			SoyOntology
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			Thesaurus of Plant Characteristics
			Plant Ontology
			Castor Bean Ontology
			Crop Ontology
			SoyOntology
			Gene Ontology
			Chemical Entities of Biological Interest
			Phenotypic QualiTy Ontology
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			Gene Ontology
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			The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.|Cooper L,Meier A,Laporte MA,Elser JL,Mungall C,Sinn BT,Cavaliere D,Carbon S,Dunn NA,Smith B,Qu B,Preece J,Zhang E,Todorovic S,Gkoutos G,Doonan JH,Stevenson DW,Arnaud E,Jaiswal P|Nucleic Acids Res|2017
		Added:
			The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.|Cooper L,Meier A,Laporte MA,Elser JL,Mungall C,Sinn BT,Cavaliere D,Carbon S,Dunn NA,Smith B,Qu B,Preece J,Zhang E,Todorovic S,Gkoutos G,Doonan JH,Stevenson DW,Arnaud E,Jaiswal P|Nucleic Acids Res|2017
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	'homepage' has been modified:
		Before: http://browser.planteome.org/amigo
		After: http://browser.planteome.org/amigo/term/TO:0000387#display-lineage-tab

Edits to 'https://fairsharing.org/FAIRsharing.w69t6r' by 'The FAIRsharing Team' at 13:31, 02 Jul 2019 (approved):

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	'organizations' has been modified:
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			Gene Ontology Consortium|http://www.geneontology.org/|Maintains
			Oregon State University, USA|http://cgrb.oregonstate.edu|Undefined
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			Gene Ontology Consortium|http://www.geneontology.org/|Maintains
			Oregon State University, USA|http://cgrb.oregonstate.edu|Maintains
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			Oregon State University, USA|http://cgrb.oregonstate.edu|Maintains
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			Oregon State University, USA|http://cgrb.oregonstate.edu|Undefined

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			contact form|http://planteome.org/contact
			help|https://github.com/Planteome/plant-trait-ontology/issues
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			contact form|http://planteome.org/contact
			forum|https://github.com/Planteome/plant-trait-ontology/issues
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			forum|https://github.com/Planteome/plant-trait-ontology/issues
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			help|https://github.com/Planteome/plant-trait-ontology/issues

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			Life Sciences
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			Castor Bean Ontology
			Crop Ontology
			SoyOntology
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			Castor Bean Ontology
			Crop Ontology
			SoyOntology
			Plant Ontology
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			Plant Ontology
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			phenotype
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	'dataProcesses' has been modified:
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Edits to 'https://fairsharing.org/FAIRsharing.w69t6r' by 'The FAIRsharing Team' at 11:31, 04 May 2017 (approved):

	'bioportal_abbreviation' has been modified:
		Before: PTO
		After: PTO Domain list has changed:  Previous values: Phenotype|information content entity|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2087 Trait|| New values:  Phenotype|information content entity|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2087 Trait|| Life Science|domain|

Edits to 'https://fairsharing.org/FAIRsharing.w69t6r' by 'cooperl' at 18:26, 03 May 2017 (approved):

	'homepage' has been modified:
		Before: http://purl.bioontology.org/ontology/TO
		After: http://browser.planteome.org/amigo

Support

General

contact form	Planteome Contact Form
support email	Pankaj Jaiswal
forum	GitHub Issue Tracker
online documentation	GitHub Project

Additional Information

Contact

Laurel Cooper ORCID

External Links

Bioportal	http://bioportal.bioontology.org/ontologies/PTO
OBO	http://obofoundry.org/ontology/to.html

Tools

No tools defined

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons Attribution 4.0 International (CC BY 4.0)

Data Release

Ontology release (OWL)	http://purl.obolibrary.org/obo/to.owl
Ontology release (OBO)	http://purl.obolibrary.org/obo/to.obo

Data Access

AgroPortal: Browse / Download

http://agroportal.lirmm.fr/ontologies/TO

Publications

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.

Cooper L,Meier A,Laporte MA,Elser JL,Mungall C,Sinn BT,Cavaliere D,Carbon S,Dunn NA,Smith B,Qu B,Preece J,Zhang E,Todorovic S,Gkoutos G,Doonan JH,Stevenson DW,Arnaud E,Jaiswal P
Nucleic Acids Res 2017

View Paper (PubMed) View Publication

PTO Ontology Display

View in BioPortal.

Disclaimer: This widget assumes the availability of the ontology resources in the NCBO BioPortal.

View in OBO Foundry.

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Models and Formats

Thesaurus of Plant Characteristics

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Implementing Databases (14)

Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants
Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other plant species. It represents a broad spectrum of species ranging from unicellular photo-autotrophs, algae, monocots, dicots and other important taxonomic clades. Within Plant Reactome, a database portal of Gramene, there are over 60 plant genomes as well as pathways for more than 80 species.

Maize Genetics and Genomics Database
MaizeGDB is the maize research community's central repository for genetics and genomics information.

Oryzabase
The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. The Oryzabase consists of five parts, (1) genetic resource stock information, (2) gene dictionary, (3) chromosome maps, (4) mutant images, and (5) fundamental knowledge of rice science.

Genome Database for Rosaceae
The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database providing centralized access to Rosaceae genomics and genetics data and analysis tools to facilitate cross-species utilization of data.

Manually Curated Database of Rice Proteins
‘Manually Curated Database of Rice Proteins’ (MCDRP) is a unique manually curated database based on published experimental data. Currently, the database has data for over 1800 rice proteins curated from > 4000 different experiments of over 400 research articles. Since every aspect of the experiment such as gene name, plant type, tissue and developmental stage has been digitized, experimental data can be rapidly accessed and integrated.

The Triticeae Toolbox
The Triticeae Toolbox (T3) is a repository for public wheat data generated by the Wheat Coordinated Agricultural Project (Wheat CAP). Funding is provided by the National Institute for Food and Agriculture (NIFA) and the United States Department of Agriculture (USDA). The current project is funded through NIFA's International Wheat Yield Partnership (IWYP) and part of the Agriculture and Food Research Initiative (AFRI).

Planteome
A resource providing data on bioentities and their associated ontology terms for Plant Biology. The database provides access to ontology-based annotations of genes, phenotypes and germplasms from about 90 plant species. A number of internal and external ontologies are used to annotate the biological data available from this resource.

OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.

Brassica Information Portal
The Brassica Information Portal is a web repository for population and trait scoring information related to the Brassica breeding community. It provides information about quantitative trait loci and links curated Brassica phenotype experimental data with genotype information stored in external data sources. Advanced data submission capabilities and APIs enable users to store and publish their own study results in BIP. The repository can be easily browsed thanks to a set of user-friendly query interfaces.

Metabolomic Repository Bordeaux
MeRy-B is a plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants.

DES-TOMATO
DES-TOMATO is a topic-specific literature exploration system developed to allow the exploration of information related to tomato. The information provided in DES-TOMATO is obtained through the text-mining of available scientific literature, namely full-length articles in PubMed Central and titles and abstracts in PubMed.

Agronomic Linked Data
The Agronomic Linked Data (AgroLD) is a knowledge-based system relying on Semantic Web technologies and exploiting standard domain ontologies, which integrates data about plant species of high interest for the plant science community. AgroLD is an RDF knowledge base of 100M triples created by annotating and integrating more than 50 datasets from 10 data sources and linked using 10 ontologies.

LEAFDATA
The LEAFDATA resource collects information from primary research articles focusing on Arabidopsis leaf growth and development. The result section of selected papers is manually annotated and organized into distinct categories. Text fragments of the manuscripts are displayed with links to the original papers on PubMed.

GWAS Atlas
The GWAS Atlas is a manually curated resource of genome-wide variant-trait associations for a wide range of species.

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Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by cooperl09

Maintains

New York Botanical Garden (Research institute)
Oregon State University, USA (University)
Lawrence Berkeley National Laboratory (LBNL), CA, USA (Lab)
Biodiversity International, Montpellier, France (Research institute)
Aberystwyth University, Wales, UK (University)

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