The environment ontology: contextualising biological and biomedical entities

Journal of Biomedical Semantics

Suzanna E Lewis⁴  Christopher J Mungall⁴  Barry Smith¹  Norman Morrison²  Pier Luigi Buttigieg³ 

[1] Department of Philosophy, University at Buffalo, Buffalo, NY 14260-4150, USA;School of Computer Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK;HGF-MPG Research Group on Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven 27570, Germany;Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

关键词: Ontology;    Biome;    Ecosystem;    Environment;   

Others  :  806285
DOI  :  10.1186/2041-1480-4-43

 received in 2013-06-15, accepted in 2013-11-30,  发布年份 2013

【 摘 要 】

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO;http://www.environmentontology.org webcite) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, content, structure, adoption, and governance approach. The ontology is available fromhttp://purl.obolibrary.org/obo/envo.owl webcite - an OBO format version is also available by switching the file suffix to “obo”.

【 授权许可】

   
2013 Buttigieg et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 2.

【 参考文献 】

• [1]Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu DY, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-tillson H, Stewart C, Thorpe J, Freeman J, Andrews-pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-rosso G, Eguiarte LE, Karl DM, Sathyendranath S, et al.: The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 2007, 5:398-431.
• [2]Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, Raes J, Sullivan M, Arendt D, Benzoni F, Claverie J-M, Follows M, Gorsky G, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Krzic U, Not F, Ogata H, Pesant S, Reynaud EG, Sardet C, Sieracki ME, Speich S, Velayoudon D, Weissenbach J, Wincker P: A holistic approach to marine eco-systems biology. PLoS Biol 2011, 9:e1001177.
• [3]Kelling S, Hochachka WM, Fink D, Riedewald M, Caruana R, Ballard G, Hooker G: Data-intensive science: a new paradigm for biodiversity studies. Bioscience 2009, 59:613-620.
• [4]Flemons P, Guralnick R, Krieger J, Ranipeta A, Neufeld D: A web-based GIS tool for exploring the world’s biodiversity: The Global Biodiversity Information Facility Mapping and Analysis Portal Application (GBIF-MAPA). Ecol Inform 2007, 2:49-60.
• [5]Wilson EO: The encyclopedia of life. Trends Ecol Evol 2003, 18:77-80.
• [6]Abu-Asab MS, Chaouchi M, Alesci S, Galli S, Laassri M, Cheema AK, Atouf F, VanMeter J, Amri H: Biomarkers in the age of omics: time for a systems biology approach. OMICS 2011, 15:105-112.
• [7]Ley R, Turnbaugh P, Klein S, Gordon J: Microbial ecology: human gut microbes associated with obesity. Nature 2006, 444:1022-1023.
• [8]Knox SS: From “omics” to complex disease: a systems biology approach to gene-environment interactions in cancer. Cancer Cell Internat 2010, 10:11. BioMed Central Full Text
• [9]The Human Microbiome Project Consortium: Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214.
• [10]Eisenberg JNS, Desai MA, Levy K, Bates SJ, Liang S, Naumoff K, Scott JC: Environmental determinants of infectious disease: a framework for tracking causal links and guiding public health research. Environ Health Perspect 2007, 115:1216-1223.
• [11]Bengtsson L, Lu X, Thorson A, Garfield R, Von Schreeb J: Improved response to disasters and outbreaks by tracking population movements with mobile phone network data: a post-earthquake geospatial study in Haiti. PLoS Med 2011, 8:e1001083.
• [12]Field D: Working together to put molecules on the map. Nature 2008, 453:978.
• [13]Raskin R, Pan M: Knowledge representation in the semantic web for Earth and environmental terminology (SWEET). Comput Geosci 2005, 31:1119-1125.
• [14]Olsen LM, Major G, Shein K, Scialdone J, Ritz S, Stevens T, Morahan M, Aleman A, Vogel R, Leicester S, Weir H, Meaux M, Grebas S, Solomon C, Holland M, Northcutt T, Restrepo RA, Bilodeau R: NASA/Global Change Master Directory (GCMD) Earth Science Keywords. 2013. Version 8.0.0.0.0
• [15]Reimerink A, León-Araúz P, Magaña P: Ecolexicon: an environmental tkb. Valletta: Proceedings of the International Conference on Language Resources and Evaluation (LREC 2010); 2010.
• [16]van Der Werf D, Adamescu M, Ayromlou M, Bertrand N, Borovec J, Boussard H, Cazacu C, Van Daele T, Datcu S, Frenzel M, Hammen V, Karasti H, Kertesz M, Kuitunen P, Lane M, Lieskovsky J, Magagna B, Peterseil J, Rennie S, Schentz H, Schleidt K, Tuominen L: SERONTO: a Socio-Ecological Research and Observation oNTOlogy. In Proceedings of TDWG. Freemantle, Australia; 2008.
• [17]Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone S-A, Scheuermann RH, Shah N, Whetzel PL, Lewis S: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007, 25:1251-1255.
• [18]The Open Biomedical and Biological Ontologies Foundry http://obofoundry.org webcite
• [19]Basic Formal Ontology 2.0: Draft Specification and User’s Guide http://bfo.googlecode.com/svn/trunk/docs/bfo2-reference/BFO2-Reference.docx webcite
• [20]Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 2000, 25:25-29.
• [21]Laforest BJ, Winegardner AK, Zaheer OA, Jeffery NW, Boyle EE, Adamowicz SJ: Insights into biodiversity sampling strategies for freshwater microinvertebrate faunas through bioblitz campaigns and DNA barcoding. BMC Ecology 2013, 13:13. BioMed Central Full Text
• [22]The Environment Ontology Code Repository http://code.google.com/p/envo/ webcite
• [23]Bittner T: From top-level to domain ontologies : Ecosystem classifications as a case study. Berlin, Heidelberg: Springer-Verlag; 2007:61-77. [COSIT’07 Proceedings of the 8th international conference on Spatial information theory, Volume i]
• [24]Bennett B: Foundations for an Ontology of Environment and Habitat. In Formal Ontology in Information Systems, Proceedings of the Sixth International Conference (FOIS-2010). Edited by Galton A, Mizoguchi R. Amsterdam: IOS Press; 2010:31-44.
• [25]Marino B, Odum H: Biosphere 2. Introduction and research progress. Ecol Eng 1999, 13:3-14.
• [26]The Biosphere 2 Website http://www.b2science.org/ webcite
• [27]Holt RD: Bringing the Hutchinsonian niche into the 21st century: ecological and evolutionary perspectives. Proc Natl Acad Sci USA 2009, 106(Suppl):19659-19665.
• [28]Smith B, Varzi AC: The Niche. Nous 1999, 33:198-222.
• [29]Olson DM, Dinerstein E, Wikramanayake ED, Burgess ND, Powell GVN, Underwood EC, D’amico JA, Itoua I, Strand HE, Morrison JC, Loucks CJ, Allnutt TF, Ricketts TH, Kura Y, Lamoreux JF, Wettengel WW, Hedao P, Kassem KR: Terrestrial ecoregions of the world: a new map of life on earth. BioScience 2001, 51:933.
• [30]Ellis EC, Ramankutty N: Putting people in the map: anthropogenic biomes of the world. Front Ecol Environ 2008, 6:439-447.
• [31]Ellis EC, Klein Goldewijk K, Siebert S, Lightman D, Ramankutty N: Anthropogenic transformation of the biomes, 1700 to 2000. Glob Ecol Biogeogr 2010, 19:589-606.
• [32]Frew J, Freeston M, Freitas N, Hill L, Janée G, Lovette K, Nideffer R, Smith T, Zheng Q: The Alexandria Digital Library architecture. Int J Digit Libr 2000, 2:259-268.
• [33]The Alexandria Digital Library Feature Type Thesaurus http://www.alexandria.ucsb.edu/gazetteer//FeatureTypes/FTT2HTM/ webcite
• [34]The GeoNames Geographical Database http://www.geonames.org/ webcite
• [35]The Environment Ontology Issue Tracker https://code.google.com/p/envo/issues/list webcite
• [36]Frank JL, Coffan RA, Southworth D: Aquatic gilled mushrooms: Psathyrella fruiting in the Rogue River in southern Oregon. Mycologia 2009, 102:93-107.
• [37]The Environment Ontology Annotation Guidelines http://www.environmentontology.org/annotation-guidelines webcite
• [38]The environment ontology user list http://www.environmentontology.org/users webcite
• [39]Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PSG, Charlson E, Costello EK, Huot-Creasy H, et al.: Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol 2011, 29:415-420.
• [40]Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch-Mizrachi I, Klenk H-P, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone S-A, Schriml LM, Sterk P, Tatusova T, Ussery DW, White O, Wooley J: The Genomic Standards Consortium. PLoS Biol 2011, 9:e1001088.
• [41]Kottmann R, Kostadinov I, Duhaime MB, Buttigieg PL, Yilmaz P, Hankeln W, Waldmann J, Glöckner FO: Megx.net: integrated database resource for marine ecological genomics. Nucleic Acids Res 2010, 38(Database issue):D391-D395.
• [42]Hirschman L, Clark C, Cohen KB, Mardis S, Luciano J, Kottmann R, Cole J, Markowitz V, Kyrpides N, Morrison N: Habitat-Lite: a GSC case study based on free text terms for environmental metadata. OMICS 2008, 12:129-136.
• [43]An ENVO-lite Annotation of Microbial Genome Projects Available through Megx.net
• [44]The Visualization and Analysis of Microbial Populations Structures (VAMPS) Environmental Data Search Page http://vamps.mbl.edu/portals/icomm/subsets/ webcite
• [45]Gilbert JA, Bailey M, Field D, Fierer N, Fuhrman JA, Hu B, Jansson J, Knight R, Kowalchuk GA, Kyrpides NC, Meyer F, Stevens R, The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011. Stand Genomic Sci 2011, 5:243-247.
• [46]The Earth Microbiome Project Sample Breakdown http://www.microbio.me/emp/ webcite
• [47]Chaffron S, Rehrauer H, Pernthaler J, Von Mering C: A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res 2010, 20:947-959.
• [48]Dawyndt P, Vancanneyt M, De Meyer H, Swings J: Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources. IEEE Trans Knowl Data Eng 2005, 17:1111-1126.
• [49]StrainInfo.net http://www.straininfo.net webcite
• [50]Verslyppe B, De Smet W, De Vos P, De Baets B, Dawyndt P: Semantic integration of isolation habitat and location in StrainInfo. BMC Bioinformatics 2010, 11(Suppl 5):3.
• [51]The Environments-EOL Project http://envo.her.hcmr.gr/environments.html webcite
• [52]Parr CS, Parafiynyk A, Sachs J, Ding L, Dornbush S, Finin T, Wang D, Hollander A: Integrating ecoinformatics resources on the semantic web. New York, New York, USA: ACM Press; 2006:1073. [Proceedings of the 15th international conference on World Wide Web - WWW’06]
• [53]Schriml LM, Arze C, Nadendla S, Ganapathy A, Felix V, Mahurkar A, Phillippy K, Gussman A, Angiuoli S, Ghedin E, White O, Hall N: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. Nucleic Acids Res 2010, 38(Database issue):D754-D764.
• [54]The National Institute for Allergy and Infectious Diseases (NIAID): Bioinformatics Resource Centers (BRCs) for Infectious Diseases metadata standard. http://www.niaid.nih.gov/LabsAndResources/resources/dmid/Pages/metadatastandards.aspx webcite
• [55]The Environment Ontology Core Team http://www.environmentontology.org/core-team webcite
• [56]The Principles of the OBO Foundry http://www.obofoundry.org/crit.shtml webcite
• [57]Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA: Uberon, an integrative multi-species anatomy ontology. Genome Biol 2012, 13:R5. BioMed Central Full Text
• [58]Degtyarenko K, De Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M: ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res 2008, 36(Database issue):D344-D350.
• [59]The Genomic Standards Consortium Website http://gensc.org webcite
• [60]The environment ontology downloadable content page http://www.environmentontology.org/downloads webcite
• [61]GAZ: a First Step Towards an Open Source Gazetteer Constructed on Ontological Principles. http://purl.obolibrary.org/obo/gaz webcite
• [62]Pignatelli M, Moya A, Tamames J: EnvDB, a database for describing the environmental distribution of prokaryotic taxa. Environ Microbiol Rep 2009, 1:191-197.
• [63]The environment ontology contact page http://www.environmentontology.org/contact webcite
• [64]Day-Richter J, Harris MA, Haendel M, Lewis S: OBO-Edit–an ontology editor for biologists. Bioinformatics 2007, 23:2198-2200.
• [65]The OBO format description http://oboformat.org webcite
• [66]Kazakov Y, Krötzsch M, Simancík F: ELK Reasoner: Architecture and Evaluation. In Proceedings of the {OWL} Reasoner Evaluation Workshop (ORE’12). Edited by Horrocks I, Yatskevich M, Jimenez-Ruiz E. Manchester, UK: CEUR-WS.org; 2012.
• [67]An Introduction to the OBO Ontology Release Tool http://code.google.com/p/owltools/wiki/OortIntro webcite