Soybean Ontology

Abbreviation: CO_336

General Information

The Soybean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.

Homepage http://www.cropontology.org/ontology/CO_336/Soybean

Countries that developed this resource United States

Created in 2015

Taxonomic range

Glycine max

Knowledge Domains

Subjects

User-defined Tags

Data standards

Plant Phenotypes and Traits

How to cite this record FAIRsharing.org: CO_336; Soybean Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j75srj; Last edited: Jan. 29, 2020, 2:49 p.m.; Last accessed: Nov 25 2020 4:38 p.m.

Record added: Jan. 18, 2018, 3:41 p.m.
Record updated: Jan. 29, 2020, 2:49 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.j75srj' by 'The FAIRsharing Team' at 14:49, 29 Jan 2020 (approved):

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			email|helpdesk@cropontology-curationtool.org
			forum|http://www.cropontology.org/feedback
			help|http://www.cropontology.org/help
			online documentation|http://agroportal.lirmm.fr/ontologies/CO_336
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			email|helpdesk@cropontology-curationtool.org
			forum|http://www.cropontology.org/feedback
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Edits to 'https://fairsharing.org/FAIRsharing.j75srj' by 'The FAIRsharing Team' at 09:54, 18 Dec 2019 (approved):

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			Agriculture
			Food
			Life Science
			Phenotype
			Plant Phenotypes and Traits
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			email|helpdesk@cropontology-curationtool.org
			forum|http://www.cropontology.org/feedback
			online documentation|http://agroportal.lirmm.fr/ontologies/CO_336
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			email|helpdesk@cropontology-curationtool.org
			forum|http://www.cropontology.org/feedback
			help|http://www.cropontology.org/help
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			Download RDF
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			Download OBO Format
			Download RDF
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			Annotation tool
			Add new terms
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			Browse
			Login 
			Annotation tool
			Add new terms
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Edits to 'https://fairsharing.org/FAIRsharing.j75srj' by 'The FAIRsharing Team' at 14:29, 25 Jan 2018 (approved):

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		After: http://www.cropontology.org/ontology/CO_336/Soybean

Support

General

support email	Crop Ontology Helpdesk
forum	Crop Ontology Forum
help	Video Tutorials

Additional Information

Contact

Elizabeth Arnaud ORCID

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 Curation

Annotation tool	http://www.cropontology.org/annotation-tool
Add new terms	http://www.cropontology.org/add-ontology

Data Access

Download OBO Format	http://www.cropontology.org/obo/CO_336
Download RDF	http://www.cropontology.org/ontology/CO_336/Soybean/nt
Browse	http://www.cropontology.org/ontology/CO_336/Soybean
Login	http://www.cropontology.org/ontology/CO_336/Soybean
AgroPortal: Browse / Download	http://agroportal.lirmm.fr/ontologies/CO_336

REST Web Services

Crop Ontology API

http://www.cropontology.org/api

Publications

No publications available

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Crop Ontology

Models and Formats

Web Ontology Language

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases (4)

SoyBase
SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. The quantitative trait loci (QTL) represent more than 18 years of QTL mapping of more than 90 unique traits. SoyBase also contains the well-annotated 'Williams 82' genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. SoyBase is the repository for controlled vocabularies for soybean growth, development and trait terms, which are also linked to the more general plant ontologies.

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.

AgroPortal
The AgroPortal project reuses the biomedical domain’s semantic tools and insights to serve agronomy, but also food, plant, agriculture and biodiversity sciences. We offer a portal that features ontology hosting, search, versioning, visualization, comment, and recommendation; enables semantic annotation; stores and exploits ontology alignments; and enables interoperation with the semantic web. The AgroPortal specifically satisfies requirements of the agronomy community in terms of ontology formats (e.g., SKOS vocabularies and trait dictionaries) and supported features (offering detailed metadata and advanced annotation capabilities). The AgroPortal content is automatically retrieved by FAIRsharing.org (https://fairsharing.org/) and the Agrisemantics Map of Data Standards (http://vest.agrisemantics.org/).

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

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

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Funds

CGIAR, Montpellier, France (Government body)

Maintains

International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria (Research institute)
CGIAR Research Program on Grain Legumes (Consortium)

Soybean Ontology

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