Who's using EnvO?

The list below features current users of the Environment Ontology. Please let us know if you're using EnvO and have not been mentioned or if you know of any other users!

Showing 20 items
NCBO Annotator  A Web service that tags free text with ontology concepts. NCBO uses these Web services to annotate resources in the NCBO Resource Index to create an ontology index of these resources. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Our service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards. Click here 
NCBO Resource Index The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data resources related to particular concepts. A set of annotations is generated automatically and presented through integration with BioPortal, enabling researchers to search for biomedical resources associated (annotated) with specific ontology terms. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. Click here 
megx.net Megx.net allows access to integrated environmental and (meta)genomic data intended for use in marine microbial ecology Click here 
iMicrobe The iMicrobe project extends the CyVerse infrastructure to create a data commons for microbial data sets taken from diverse environments. Researchers at iMicrobe are also developing methods for scientists to find, tag and reuse data sets based on standard terms and ontology, and develop Apps for analyzing metagenomic samples (see protocols.io). This project strives to enhance the use of shared microbial data sets and computational infrastructure and code to promote large-scale studies of microbial ecology to understand the Earth system. http://imicrobe.us/ 
MG-RAST MG-RAST is an open source web application server that suggests automatic phylogenetic and functional analysis of metagenomes. The application is high-throughput and as for April 21, 2016 holds 243,322 metagenome analyses.  https://metagenomics.anl.gov/ 
EukRef: The Eukaryote Reference Database EukRef is a community-based initiative to curate 18S ribosomal data sets. The project has incorporated EnvO into its annotation guides to better control the description of isolation environments. www.eukref.org 
Nature: Scientific Data Scientific Data is a peer-reviewed, open-access journal for descriptions of scientifically valuable datasets, and research that advances the sharing and reuse of scientific data. ENVO descriptors are used to improve data discoverability through the ISA Explorer software used by this journal. http://scientificdata.isa-explorer.org/ 
Environments-EOL This project processed the Encyclopedia of Life's (EOL) Taxon pages to extract descriptions of their environmental context. Such input will subsequently employed to answer integrative large-scale biological questions (Funded by the EOL Rubenstein Fellows Program) http://environments-eol.blogspot.gr/ 
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications The minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) standards developed by the Genomic Standards Consortium (GSC) are designed to provide tailored checklists for describing the environment from which a biological sample originates. These standards aim to enhance the ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere. Publication 
International Census of Marine Microbes (ICoMM) The International Census of Marine Microbes (ICoMM) will facilitate the inventory of marine microbial diversity developing a strategy to (1) catalogue all known diversity of single-cell organisms inclusive of the Bacteria, Archaea, Protista and associated viruses, (2) to explore and discover unknown microbial diversity, and (3) to place that knowledge into appropriate ecological and evolutionary contexts. http://icomm.mbl.edu/index.html 
ISA software suite  An open source ISA software suite and an extensible hierarchical data structure implemented by a growing number of international public resources. It caters to data as diverse as stem cell, toxicogenomics, environmental gene surveys, microbial diversity studies, and a variety of metabolomics and metagenomics-based studies. But it maintains cross-domain compatibility in the way the experimental context is described.  http://isa-tools.org/ 
Influenza Ontology The Influenza Ontology is an application ontology covering the numerous aspects if influenza virus basic research, and surveillance. The influenza ontology extends the Infectious Disease Ontology (IDO). View the ontology 
Gramene As an information resource, Gramene's purpose is to provide added value to data sets available within the public sector, which will facilitate researchers' ability to understand the grass genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other grass species. http://www.gramene.org/ 
PANGAEA PANGAEA, a data publisher for Earth and environmental science, uses ENVO to enrich its metadata and data archives.  http://www.pangaea.de 
Darwin Core A key project of the TDWG community, Darwin Core is a widely used standard to structure observational data in ecology. Efforts are underway to control the semantics of the DwC:habitat field with ENVO. View publication 
European Nucleotide Archive (ENA) The European Nucleotide Archive is a repository providing free and unrestricted access to annotated DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of sequence assembly and other metadata related to sequencing projects. The ENA's metagenomics portal is exploring further use of ENVO in structuring its archived data.  See this publication for illustration 
The United Nations Environment Programme (UNEP) UNEP has begun to use ontologies to improve knowledge management and information archiving, particularly in projects pertaining to the Sustainable Development Agenda for 2030. ENVO is a key component in the Sustainable Development Goals Interface Ontology (SDGIO) being developed for this purpose. http://uneplive.org/portal#ontologies 
Program for Resistance, Immunology, Surveillance and Modeling of Malaria in Uganda (PRISM) Researchers from PRISM - one of the International Centers for Excellence in Malaria Research - have worked with us to develop content useful to describing the natural and anthropogenic environments which are central to understanding the dynamics of malaria.  More information 
Centre for the Synthesis and Analysis of Biodiversity CESAB, a centre developed by the Foundation for Research on Biodiversity (http://www.fondationbiodiversite.fr/en/), is developing a project-driven thesaurus for multiple working groups. This will interface with ENVO, providing a deeper level of semantic support for their thesaurus efforts. Click here 
PlutoF A fully-fledged biodiversity platform for creating, managing, sharing, analysing and publishing biology-related databases and projects. PlutoF is developing its EnvO implementation to promote effective ecoinformatics. Homepage 
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