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We're happy to announce that a description of ENVO has been published in the Biomedical Ontologies series of the Journal of Biomedical Semantics. ENVO users may now cite:
Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE, and the ENVO Consortium (2013) The environment ontology: contextualising biological and biomedical entities. J Biomed Semant.4:43.
In May 2nd's release, EnvO's "terrestrial biome" hierarchy has been consolidated and terms which subsume several potential biome classes (e.g. "Mediterranean forests, woodlands, and shrub biome") have been split for better semantic resolution. Previous biome classes have been obsoleted and "replaced_by" or "consider" relations added between obsolete terms and new classes where possible. Some definitions are still being formulated and will be added soon along with synonyms.
Additionally, an "anthropogenic biome" class has been created and will be populated in the near future.
As always, feedback, input, and suggestions are welcome and are best submitted via EnvO's Google Code issue tracker.
Funded by the Encyclopedia of Life's (EOL) 2013 Rubenstein Research Fellowship program, the project “ENVIRONMENTS: Discovering habitat terms in EOL Contents” (Environments-EOL) has begun and will make extensive use of EnvO.
Environments-EOL aims to identify environmental descriptors across EOL's Taxon pages and map them to structured resources. The project's approaches and progress can be monitored via its blog. As an example of the tools in development, "ENVIRONMENTS", uses a dictionary based on EnvO's content to identify environments described in EOL pages and tag these pages with relevant EnvO terms. This dictionary serves as an intermediary between EnvO terms and their free text variations (e.g. plurals), a theme that will be further explored by the project.
The performance of ENVIRONMENTS and its counterparts in the ENVIRONMENTS-EOL project will be evaluated through comparison to a gold standard, also being created by the project team. Further, a suite of other tools which facilitate annotation using EnvO and assist annotators in requesting new terms is also in development.
We're looking forward to input from ENVIRONMENTS-EOL and to supporting this initiative!
From the 27-29th September, 2012, a COST-funded hackathon entitled "From Signals to Environmentally Tagged Sequences" was held at the Crete outstation of the Hellenic Center for Marine Research (HCMR). This hackathon aimed to develop automated approaches to annotate microbial sequences with environmental descriptors using a combination of sequence analysis, text-mining, and statistical analysis. EnvO, introduced and discussed via electronic-attendance, was used as a point-of-reference to map descriptors found in processed literature to a semantic framework. The results of systematic literature-mining exercises will be central in guiding the future development of EnvO. Feedback and requests from the text-mining community are always welcome! Please use our Contact page to get in touch.
After this hackathon's success, a follow-up hackathon will take place in June 2013 at the HCMR Crete, Greece.
Please contact Evangelos Pafilis for more information.
Sponsored by the National Bioscience Database Centre / Database Centre for Life Sciences (NBDC / DBCLS), Japan, the BioHackathon 2012 was an opportunity for semantic researchers to "hack" together new tools and solutions for use in the life science domain and to enhance existing resources.
Pier Luigi Buttigieg introduced EnvO during the event's symposium and participated in the ontology working group during the subsequent hackathon. During the hackathon, discussion centred on the potential interfaces between EnvO, GAZ, and the Metagenome Environment Ontology (MEO). The principles of ontology design and the development of an ontology for incomplete enzyme reactions were other main points of discussion. A wiki summarising these discussions can be found here.