EnvO Project
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Workshops: Inaugural EnvO Workshop -> Second EnvO CSHL workshop -> Third EnvO_Manchester_workshop
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[edit] Background
[edit] What is an environment?
For the purposes of this project we define an environment as the totality of circumstances external to a definable entity.
A biological sample is a kind of definable entity that can be comprised of one or more organism(s), or parts thereof. Examples include: a species of plant or animal, a tissue biopsy or a community of bacteria. A biological sample may also include a physical material as a component part. Examples include: soil, sediment, seawater or ice-core samples.
[edit] What’s the difference between an Environment and a Habitat?
A habitat is the environment where an organism, community or population of organisms lives.
[edit] What is an ontology?
An ontology is a controlled structured vocabulary developed to represent the types of entities in a given domain and the relations between them. - Adapted from Smith et al., 2006.
An ontology may take a variety of forms, but necessarily it will include a vocabulary of terms, and some specification of their meaning. This includes definitions and an indication of how the terms are inter-related which constrains logically possible interpretations.
[edit] What’s the point of an Environment Ontology?
A computer does not know that environments such as coral reef atol and deep sea thermal vent are both types of marine environment. Thus a query such as: “retrieve all data from samples taken from marine environments, between +/- 10 degrees of the equator” would fail to return samples annotated as such, unless they were terms explicitly included in the search.
An ontology provides a format that can be read and used by software agents, thus permitting them to find, share and integrate information that ordinarily would have required human intervention.
[edit] Aim
To develop a community based ontology for describing the environment of an organism or biological sample.
[edit] Scope
We see the new Environment Ontology (EnvO) bringing similar benefits to those that can already be achieved with the Gene Ontology (GO); through consistent annotation grounded in an ontological framework, we hope to facilitate the semantic retrieval of any biological record anchored to EnvO. For example, those contained in sequence databases, omic data repositories, tissue banks and museum collections.
The focus of our effort will be to develop an ontology that supports the annotation of the environment of any organism or biological sample. However, we hope that EnvO will also be used for the annotation of ANY record that has an environmental component. For example, you might like to tag an environmental descriptor to a picture that you took at the weekend or provide information on the general environment where some remote sensing devices are currently capturing data.
We hope that the community will adopt and contribute to this work, as wide acceptance of standardised terms is key to integration and federated searching of environmental data.
[edit] Workshops
As EnvO is community-driven, its development depends on the ability of developers and potential users to meet face to face.
- Inaugural EnvO Workshop - Report in Word Report as pdf
- Second EnvO CSHL workshop
- Third EnvO Manchester workshop
- Photos from the EnvO Meetings at the EnvO Consortium flickr site
[edit] Essential URLS
[edit] Home page, Downloading EnvO and Gaz, Term Trackers
The Environment Ontology Consortium is using an infrastructure similar to that for OBO/GO.
- Future homepage: http://www.environmentontology.org
- EnvO mailing list: https://lists.sourceforge.net/lists/listinfo/obo-envo
- Latest versions of EnvO and gaz:
http://obo.cvs.sourceforge.net/obo/obo/ontology/environmental/envo.obo/
http://obo.cvs.sourceforge.net/obo/obo/ontology/environmental/gaz.obo/
- Tracker for EnvO: https://sourceforge.net/tracker/?group_id=76834&atid=934923
Food Ontology Project http://gensc.org/gc_wiki/index.php/Food_Ontology_Project
[edit] Case Studies
An integral part of the development of EnvO will be the application of this ontology to real datasets.
- The beinning of the GSC EnvO Case Study was presented at the inaugural EnvO Workshop meeting in Oxford and has since been expanded upon. It involves a range of databases run by members of the GSC, all of which already use descriptions of habitat or plan to in the near future.
[edit] Related projects
- What Am I Eating.com : http://www.whatamieating.com/
- SWEET Ontologies: http://sweet.jpl.nasa.gov/ontology/
- Alexandria Digital Library: http://www.alexandria.ucsb.edu/
- Getty Thesaurus of Geographic Names: http://www.alexandria.ucsb.edu/
- Science Environment for Ecological Knowledge (SEEK): http://seek.ecoinformatics.org/
- Goddard Space Flight Centre: http://gcmd.nasa.org
- Ecoinformatics: http://www.ecoinformatics.org/
- www.mip.berkeley.edu/ecal/gazeteer/ftt_hier2.html
- EUNIS habitat taxonomy: (EUNIS system began with a nature conservation perspective) - The EEA website gives the EUNIS habitat taxonomy, for example: http://eunis.eea.europa.eu/habitats-code-browser.jsp?level=2&habCode=E
- Anthropogenic biomes: http://www.eoearth.org/article/Anthropogenic_biomes (Background to this radical new way of describing ecosystems on earth: http://biopact.com/2007/11/environmental-researchers-propose.html)
- NERC Data Grid Vocabulary Server - contains a large number of term lists in use in the environmental sciences. List of terms: http://vocab.ndg.nerc.ac.uk/clients/whatLists Background to project: http://www.bodc.ac.uk/products/web_services/vocab/
- Incubator Group Reports: Geospatial Vocabulary and Geospatial Ontologies: http://www.w3.org/News/2007#item234
- Geography markup language (XML describing geographic features): http://www.opengeospatial.org/standards/gml
- Digital Earth Project: http://www.ai.sri.com/digitalearth/
- Glossary of Geological and other Scientific terms used in Principles of Geology: http://en.wikisource.org/wiki/Glossary_of_Geological_and_other_Scientific_terms_used_in_Principles_of_Geology
[edit] References
Papers on the Ontology of Environments and of Ecological Niches by Barry Smith.
Smith, B., Kusnierczyk, W., Schober, D., Ceusters, Werner (2006) Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain, in: O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222
Return to the Main Page - Inaugural EnvO Workshop (29th - 31st August, 2007)
