Environment Ontology
Abbreviation: ENVO
Homepage http://environmentontology.org/
Countries that developed this resource Germany , Kenya , United States
Created in 2007
Taxonomic range
Knowledge Domains
Subjects
How to cite this record FAIRsharing.org: ENVO; Environment Ontology; DOI: https://doi.org/10.25504/FAIRsharing.azqskx; Last edited: Dec. 16, 2020, 2:35 p.m.; Last accessed: Apr 12 2021 12:55 a.m.
Publication for citation The environment ontology: contextualising biological and biomedical entities. Buttigieg PL,Morrison N,Smith B,Mungall CJ,Lewis SE; J Biomed Semantics ; 2013; 10.1186/2041-1480-4-43;
Record updated: Dec. 16, 2020, 2:34 p.m. by The FAIRsharing Team.
contact form | Contact the Consortium |
forum | GitHub Issue Tracker |
online documentation | GitHub Repository |
online documentation | Annotation Guidelines |
online documentation | About |
online documentation | Annotation Guidelines |
@envoTweets |
Additional Information
Contact | Pier Luigi Buttigieg |
External Links
Bioportal | http://bioportal.bioontology.org/ontologies/ENVO |
OBO | http://obofoundry.org/ontology/envo.html |
No XSD schemas defined
Conditions of Use
Applies to: Data useData Access
Search Ontology | http://www.environmentontology.org/Browse-EnvO |
Download Ontology | https://sites.google.com/site/environmentontology/downloads |
Browse (via OLS) | https://www.ebi.ac.uk/ols/ontologies/envo |
AgroPortal: Browse / Download | http://agroportal.lirmm.fr/ontologies/ENVO |
Other Web Services
Persistent URL allowing access to the most recent version of ENVO in OWL format | http://purl.obolibrary.org/obo/envo.owl |
Persistent URL allowing access to the most recent version of ENVO in OBO format | http://purl.obolibrary.org/obo/envo.obo |
Persistent URL allowing access to the most recent, basic version of ENVO (only including ENVO terms and no imported terms) in OBO format | http://purl.obolibrary.org/obo/envo/subsets/envo-basic.obo |
Persistent URL allowing access to the most recent version of ENVO in JSON format | http://purl.obolibrary.org/obo/envo.json |
The environment ontology: contextualising biological and biomedical entities.
Buttigieg PL,Morrison N,Smith B,Mungall CJ,Lewis SE
J Biomed Semantics 2013
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.
Buttigieg PL,Pafilis E,Lewis SE,Schildhauer MP,Walls RL,Mungall CJ
J Biomed Semantics 2016
Emerging semantics to link phenotype and environment.
Thessen AE,Bunker DE,Buttigieg PL,Cooper LD,Dahdul WM,Domisch S,Franz NM,Jaiswal P,Lawrence-Dill CJ,Midford PE,Mungall CJ,Ramirez MJ,Specht CD,Vogt L,Vos RA,Walls RL,White JW,Zhang G,Deans AR,Huala E,Lewis SE,Mabee PM
PeerJ 2015
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.
Pafilis E,Buttigieg PL,Ferrell B,Pereira E,Schnetzer J,Arvanitidis C,Jensen LJ
Database (Oxford) 2016
View in BioPortal.
View in OBO Foundry.
Reporting Guidelines
Terminology Artifacts
- Chemical Entities of Biological Interest
- OBO ReLationship
- Phenotypic QualiTy Ontology
- NCBI Taxonomy
- Gene Ontology
- Basic Formal Ontology
- Agronomy Ontology
- Population and Community Ontology
- UBER anatomy ONtology
- Influenza Ontology
- Genomic Epidemiology Ontology
- OBO Relations Ontology
- Domain Resource Application Ontology
- Ontology of Prokaryotic Phenotypic and Metabolic Characters
Models and Formats
No syntax standards defined
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
The Genomes Online Database provides access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.
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.
Manually Curated Database of Rice Proteins
The Manually Curated Database of Rice Proteins (MCDRP) is a manually-curated database based on published experimental data. The database contains data for rice proteins curated from experiments drawn from research articles. The database stores information including gene name, plant type, tissue and developmental stage. The homepage for this resource could not be loaded. Please contact us if you have any information regarding the current status of this resource.
DataONE
DataONE is a community driven project providing access to data across multiple member repositories, supporting enhanced search and discovery of Earth and environmental data.
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.
Metabolomic Repository Bordeaux
MeRy-B is a plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants.
MAR databases
The MAR databases is a collection of manually curated marine microbial contextual and sequence databases, based at the Marine Metagenomics Portal. This was developed as a part of the ELIXIR EXCELERATE project in 2017 and is maintained by The Center for Bioinformatics (SfB) at the UiT The Arctic University of Norway. SfB is hosting the UiT node of ELIXIR Norway. The MarRef, MarDb, MarFun and MarCat contextual databases are built by compiling data from a number of public available sequence, taxonomy and literature databases in a semi-automatic fashion.
National Microbiome Data Collaborative
The National Microbiome Data Collaborative seeks to address fundamental roadblocks in microbiome data science and gaps in transdisciplinary collaboration. The NMDC's Phase I Pilot was launched in July 2019 funded by the Department of Energy’s (DOE) Office of Science, Biological and Environmental Research program, with two strategic priorities — infrastructure and engagement. The infrastructure goal is to democratize microbiome data science by providing access to multidisciplinary, multi-omics data (e.g., metagenomics and metaproteomics) through distributed data resources, with seamless integration to platforms that support reproducible, cross- study analyses. The engagement goal is to enable community-driven shared ownership of microbiome data that supports open science across research teams, funders, publishers, and societies. Currently, no data are available, as this project is still in the development stage. Please sign up for our Quarterly newsletter via the website (starting in Sep 2020) for updates, feature releases, and ways to get involved.
Scroll for more...
Record Maintainer
This record is maintained by plbuttigieg ORCID
Funds
Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research (AWI), Germany (Research institute)
Lawrence Berkeley National Laboratory (LBNL), CA, USA (Government body)
European Commission (Government body)
European Commission FP7 (Government body)
National Human Genome Research Institute (NHGRI), Bethesda, MD, USA (Government body)
Maintains
ENVO (Consortium)
Grant Number(s)
283359 (European Commission FP7)
287589 (European Commission)
HG004838 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)