Plant Environmental Ontology

Abbreviation: EO

General Information

This record was deprecated on Feb. 14, 2019 for the following reason(s): This resource has been deprecated and is no longer maintained.

EO is a structured, controlled vocabulary for the representation of plant environmental conditions. EO has now been replaced by PECO. If you are using classes like EO:nnnnnn then you should be able to substitute this for PECO:nnnnnn, as all of the numeric parts of the ID are preserved. For a more robust mechanism, peco.obo contains alt_ids, and peco.owl contains the equivalent replaced_by assertions, which point from an obsoleted EO class to the corresponding PECO class.

This record is replaced by:

Plant Experimental Condition Ontology

Homepage http://browser.planteome.org/amigo/term/EO:0007359

Countries that developed this resource United States

Created in 2008

Taxonomic range

Plantae

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: EO; Plant Environmental Ontology; DOI: https://doi.org/10.25504/FAIRsharing.w7a76x; Last edited: Jan. 30, 2020, 11:20 a.m.; Last accessed: Apr 03 2020 5:42 a.m.

Record updated: Jan. 30, 2020, 11:20 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.w7a76x' by 'The FAIRsharing Team' at 11:20, 30 Jan 2020 (approved):

	'supportLinks' has been modified:
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			online documentation|http://agroportal.lirmm.fr/ontologies/EO
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		Removed:
			online documentation|http://agroportal.lirmm.fr/ontologies/EO

	'dataProcesses' has been modified:
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			Browse Ontology (OLS)
		After:
			Browse Ontology (OLS)
			AgroPortal: Browse / Download
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			AgroPortal: Browse / Download
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Edits to 'https://fairsharing.org/FAIRsharing.w7a76x' by 'The FAIRsharing Team' at 10:05, 08 Jan 2020 (approved):

	'supportLinks' has been modified:
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		After:
			online documentation|http://agroportal.lirmm.fr/ontologies/EO
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			online documentation|http://agroportal.lirmm.fr/ontologies/EO
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Edits to 'https://fairsharing.org/FAIRsharing.w7a76x' by 'The FAIRsharing Team' at 11:36, 21 Jun 2019 (approved):

	'miriam_id' has been modified:
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Edits to 'https://fairsharing.org/FAIRsharing.w7a76x' by 'The FAIRsharing Team' at 13:32, 14 Feb 2019 (approved):

	'status' has been modified:
		Before: RDY
		After: DEP

	'miriam_id' has been modified:
		Before: 
		After: None

Edits to 'https://fairsharing.org/FAIRsharing.w7a76x' by 'The FAIRsharing Team' at 13:28, 14 Feb 2019 (approved):

	'supportLinks' has been modified:
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			contact form|http://planteome.org/contact
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		Removed:
			contact form|http://planteome.org/contact

	'description' has been modified:
		Before: The Plant Environment Ontology describes the treatments, growing conditions, and/or study types used in various types of plant biology experiments. The subjects of the studies may also include in vitro plant structures (PO:0000004). A plant treatment is the most specific,and may be a component of a plant growing condition, and the plant study type. The broadest classes are the plant study types where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own and it may also involve instances of biotic and abiotic treatments and different growing conditions.
		After: EO is a structured, controlled vocabulary for the representation of plant environmental conditions. EO has now been replaced by PECO. If you are using classes like EO:nnnnnn then you should be able to substitute this for PECO:nnnnnn, as all of the numeric parts of the ID are preserved. For a more robust mechanism, peco.obo contains alt_ids, and peco.owl contains the equivalent replaced_by assertions, which point from an obsoleted EO class to the corresponding PECO class.

	'onto_disciplines' has been modified:
		Before:
			Environmental Sciences
		After:
			Botany
			Environmental Sciences
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			Botany
		Removed:

	'onto_domains' has been modified:
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		After:
			Experiment report
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			Experiment report
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	'miriam_id' has been modified:
		Before: None
		After: 

	'dataProcesses' has been modified:
		Before:
		After:
			Browse Ontology (OLS)
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			Browse Ontology (OLS)
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	'shortname' has been modified:
		Before: PECO
		After: EO

	'homepage' has been modified:
		Before: http://browser.planteome.org/amigo/term/EO:0007359#display-lineage-tab
		After: http://browser.planteome.org/amigo/term/EO:0007359

Edits to 'https://fairsharing.org/FAIRsharing.w7a76x' by 'The FAIRsharing Team' at 14:34, 09 May 2017 (approved):

	'homepage' has been modified:
		Before: http://purl.bioontology.org/ontology/PECO
		After: http://browser.planteome.org/amigo/term/EO:0007359#display-lineage-tab

Edits to 'https://fairsharing.org/FAIRsharing.w7a76x' by 'The FAIRsharing Team' at 14:19, 21 Nov 2016 (approved):

	'name' has been modified:
		Before: plant Environmental conditions Ontology
		After: Plant Environmental conditions Ontology Countries have changed:  Previous values: USA New values:  United States of America Organisations have changed:  Previous values: EO administrators Oregon State University New values:  EO administrators Oregon State University|USA

Edits to 'https://fairsharing.org/FAIRsharing.w7a76x' by 'The FAIRsharing Team' at 12:37, 12 Oct 2016 (approved):

	'description' has been modified:
		Before: "plant Environmental conditions Ontology" is a standard, specialising in the fields described under "scope and data types", below. Until this entry is claimed, more information on this project can be found at http://purl.bioontology.org/ontology/EO. This text was generated automatically. If you work on the project responsible for "plant Environmental conditions Ontology" then please consider helping us  by claiming this record  and updating it appropriately.
		After: The Plant Environment Ontology describes the treatments,growing conditions, and/or study types used in various types of plant biology experiments.

Support

No support information provided.

Additional Information

Contact

Pankaj Jaiswal

External Links

OBO	http://obofoundry.org/ontology/eo.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

Browse Ontology (OLS)

https://www.ebi.ac.uk/ols/ontologies/eo

Data Access

AgroPortal: Browse / Download

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

Publications

No publications available

EO Ontology Display

View in OBO Foundry.

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Castor Bean Ontology

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Implementing Databases (7)

Golm Metabolome Database
The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discovery of novel metabolic biomarkers.

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.

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.

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.

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.

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Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is in need of a maintainer. If you login, you'll be able to claim this record.

Funds

National Science Foundation (NSF), USA (Government body)

Maintains

Oregon State University, USA (University) Lead

Grant Number(s)

IOS:1340112 award (National Science Foundation (NSF), USA)

Plant Environmental Ontology

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