{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,5]],"date-time":"2026-11-05T22:45:04Z","timestamp":1793918704453,"version":"4.8.0"},"reference-count":67,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2013,12,11]],"date-time":"2013-12-11T00:00:00Z","timestamp":1386720000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"},{"start":{"date-parts":[[2013,12,11]],"date-time":"2013-12-11T00:00:00Z","timestamp":1386720000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    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;\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.environmentontology.org\" ext-link-type=\"uri\">http:\/\/www.environmentontology.org<\/jats:ext-link>\n                    ) 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\u2019s motivation, content, structure, adoption, and governance approach. The ontology is available from\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/purl.obolibrary.org\/obo\/envo.owl\" ext-link-type=\"uri\">http:\/\/purl.obolibrary.org\/obo\/envo.owl<\/jats:ext-link>\n                    - an OBO format version is also available by switching the file suffix to \u201cobo\u201d.\n                  <\/jats:p>","DOI":"10.1186\/2041-1480-4-43","type":"journal-article","created":{"date-parts":[[2013,12,11]],"date-time":"2013-12-11T05:01:49Z","timestamp":1386738109000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":295,"title":["The environment ontology: contextualising biological and biomedical entities"],"prefix":"10.1186","volume":"4","author":[{"given":"Pier Luigi","family":"Buttigieg","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norman","family":"Morrison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barry","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher J","family":"Mungall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suzanna E","family":"Lewis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"the ENVO Consortium","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2013,12,11]]},"reference":[{"key":"222_CR1","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1371\/journal.pbio.0050077","volume":"5","author":"DB Rusch","year":"2007","unstructured":"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.","journal-title":"PLoS Biol"},{"key":"222_CR2","doi-asserted-by":"publisher","first-page":"e1001177","DOI":"10.1371\/journal.pbio.1001177","volume":"9","author":"E Karsenti","year":"2011","unstructured":"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: e1001177-10.1371\/journal.pbio.1001177.","journal-title":"PLoS Biol"},{"key":"222_CR3","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1525\/bio.2009.59.7.12","volume":"59","author":"S Kelling","year":"2009","unstructured":"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. 10.1525\/bio.2009.59.7.12.","journal-title":"Bioscience"},{"key":"222_CR4","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/j.ecoinf.2007.03.004","volume":"2","author":"P Flemons","year":"2007","unstructured":"Flemons P, Guralnick R, Krieger J, Ranipeta A, Neufeld D: A web-based GIS tool for exploring the world\u2019s biodiversity: The Global Biodiversity Information Facility Mapping and Analysis Portal Application (GBIF-MAPA). Ecol Inform. 2007, 2: 49-60. 10.1016\/j.ecoinf.2007.03.004.","journal-title":"Ecol Inform"},{"key":"222_CR5","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/S0169-5347(02)00040-X","volume":"18","author":"EO Wilson","year":"2003","unstructured":"Wilson EO: The encyclopedia of life. Trends Ecol Evol. 2003, 18: 77-80. 10.1016\/S0169-5347(02)00040-X.","journal-title":"Trends Ecol Evol"},{"key":"222_CR6","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1089\/omi.2010.0023","volume":"15","author":"MS Abu-Asab","year":"2011","unstructured":"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. 10.1089\/omi.2010.0023.","journal-title":"OMICS"},{"key":"222_CR7","doi-asserted-by":"publisher","first-page":"1022","DOI":"10.1038\/4441022a","volume":"444","author":"R Ley","year":"2006","unstructured":"Ley R, Turnbaugh P, Klein S, Gordon J: Microbial ecology: human gut microbes associated with obesity. Nature. 2006, 444: 1022-1023. 10.1038\/4441022a.","journal-title":"Nature"},{"key":"222_CR8","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/1475-2867-10-11","volume":"10","author":"SS Knox","year":"2010","unstructured":"Knox SS: From \u201comics\u201d to complex disease: a systems biology approach to gene-environment interactions in cancer. Cancer Cell Internat. 2010, 10: 11-10.1186\/1475-2867-10-11.","journal-title":"Cancer Cell Internat"},{"key":"222_CR9","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature11234","volume":"486","author":"The Human Microbiome Project Consortium","year":"2012","unstructured":"The Human Microbiome Project Consortium: Structure, function and diversity of the healthy human microbiome. Nature. 2012, 486: 207-214. 10.1038\/nature11234.","journal-title":"Nature"},{"key":"222_CR10","doi-asserted-by":"publisher","first-page":"1216","DOI":"10.1289\/ehp.9806","volume":"115","author":"JNS Eisenberg","year":"2007","unstructured":"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. 10.1289\/ehp.9806.","journal-title":"Environ Health Perspect"},{"key":"222_CR11","doi-asserted-by":"publisher","first-page":"e1001083","DOI":"10.1371\/journal.pmed.1001083","volume":"8","author":"L Bengtsson","year":"2011","unstructured":"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: e1001083-10.1371\/journal.pmed.1001083.","journal-title":"PLoS Med"},{"key":"222_CR12","doi-asserted-by":"publisher","first-page":"978","DOI":"10.1038\/453978b","volume":"453","author":"D Field","year":"2008","unstructured":"Field D: Working together to put molecules on the map. Nature. 2008, 453: 978-","journal-title":"Nature"},{"key":"222_CR13","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1016\/j.cageo.2004.12.004","volume":"31","author":"R Raskin","year":"2005","unstructured":"Raskin R, Pan M: Knowledge representation in the semantic web for Earth and environmental terminology (SWEET). Comput Geosci. 2005, 31: 1119-1125. 10.1016\/j.cageo.2004.12.004.","journal-title":"Comput Geosci"},{"key":"222_CR14","volume-title":"NASA\/Global Change Master Directory (GCMD) Earth Science Keywords","author":"LM Olsen","year":"2013","unstructured":"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"},{"key":"222_CR15","volume-title":"Ecolexicon: an environmental tkb","author":"A Reimerink","year":"2010","unstructured":"Reimerink A, Le\u00f3n-Ara\u00faz P, Maga\u00f1a P: Ecolexicon: an environmental tkb. 2010, Valletta: Proceedings of the International Conference on Language Resources and Evaluation (LREC 2010)"},{"key":"222_CR16","volume-title":"Proceedings of TDWG","author":"D van Der Werf","year":"2008","unstructured":"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. Proceedings of TDWG. 2008, Freemantle, Australia"},{"key":"222_CR17","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1038\/nbt1346","volume":"25","author":"B Smith","year":"2007","unstructured":"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. 10.1038\/nbt1346.","journal-title":"Nat Biotechnol"},{"key":"222_CR18","unstructured":"The Open Biomedical and Biological Ontologies Foundry. http:\/\/obofoundry.org,"},{"key":"222_CR19","unstructured":"Basic Formal Ontology 2.0: Draft Specification and User\u2019s Guide. http:\/\/bfo.googlecode.com\/svn\/trunk\/docs\/bfo2-reference\/BFO2-Reference.docx,"},{"key":"222_CR20","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"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. 10.1038\/75556.","journal-title":"Nat Genet"},{"key":"222_CR21","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1472-6785-13-13","volume":"13","author":"BJ Laforest","year":"2013","unstructured":"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: 13-10.1186\/1472-6785-13-13.","journal-title":"BMC Ecology"},{"key":"222_CR22","unstructured":"The Environment Ontology Code Repository. http:\/\/code.google.com\/p\/envo\/,"},{"key":"222_CR23","first-page":"61","volume-title":"From top-level to domain ontologies\u202f: Ecosystem classifications as a case study","author":"T Bittner","year":"2007","unstructured":"Bittner T: COSIT\u201907 Proceedings of the 8th international conference on Spatial information theory, Volume i. From top-level to domain ontologies\u202f: Ecosystem classifications as a case study. 2007, Berlin, Heidelberg: Springer-Verlag, 61-77."},{"key":"222_CR24","first-page":"31","volume-title":"Formal Ontology in Information Systems, Proceedings of the Sixth International Conference (FOIS-2010)","author":"B Bennett","year":"2010","unstructured":"Bennett B: Foundations for an Ontology of Environment and Habitat. Formal Ontology in Information Systems, Proceedings of the Sixth International Conference (FOIS-2010). Edited by: Galton A, Mizoguchi R. 2010, Amsterdam: IOS Press, 31-44."},{"key":"222_CR25","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/S0925-8574(98)00088-3","volume":"13","author":"B Marino","year":"1999","unstructured":"Marino B, Odum H: Biosphere 2. Introduction and research progress. Ecol Eng. 1999, 13: 3-14.","journal-title":"Ecol Eng"},{"key":"222_CR26","unstructured":"The Biosphere 2 Website. http:\/\/www.b2science.org\/,"},{"issue":"Suppl","key":"222_CR27","doi-asserted-by":"publisher","first-page":"19659","DOI":"10.1073\/pnas.0905137106","volume":"106","author":"RD Holt","year":"2009","unstructured":"Holt RD: Bringing the Hutchinsonian niche into the 21st century: ecological and evolutionary perspectives. Proc Natl Acad Sci USA. 2009, 106 (Suppl): 19659-19665.","journal-title":"Proc Natl Acad Sci USA"},{"key":"222_CR28","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1111\/0029-4624.00151","volume":"33","author":"B Smith","year":"1999","unstructured":"Smith B, Varzi AC: The Niche. Nous. 1999, 33: 198-222.","journal-title":"Nous"},{"key":"222_CR29","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1641\/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2","volume":"51","author":"DM Olson","year":"2001","unstructured":"Olson DM, Dinerstein E, Wikramanayake ED, Burgess ND, Powell GVN, Underwood EC, D\u2019amico 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: 933-10.1641\/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2.","journal-title":"BioScience"},{"key":"222_CR30","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1890\/070062","volume":"6","author":"EC Ellis","year":"2008","unstructured":"Ellis EC, Ramankutty N: Putting people in the map: anthropogenic biomes of the world. Front Ecol Environ. 2008, 6: 439-447. 10.1890\/070062.","journal-title":"Front Ecol Environ"},{"key":"222_CR31","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1111\/j.1466-8238.2010.00540.x","volume":"19","author":"EC Ellis","year":"2010","unstructured":"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.","journal-title":"Glob Ecol Biogeogr"},{"key":"222_CR32","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1007\/s007990050004","volume":"2","author":"J Frew","year":"2000","unstructured":"Frew J, Freeston M, Freitas N, Hill L, Jan\u00e9e G, Lovette K, Nideffer R, Smith T, Zheng Q: The Alexandria Digital Library architecture. Int J Digit Libr. 2000, 2: 259-268. 10.1007\/s007990050004.","journal-title":"Int J Digit Libr"},{"key":"222_CR33","unstructured":"The Alexandria Digital Library Feature Type Thesaurus. http:\/\/www.alexandria.ucsb.edu\/gazetteer\/\/FeatureTypes\/FTT2HTM\/,"},{"key":"222_CR34","unstructured":"The GeoNames Geographical Database. http:\/\/www.geonames.org\/,"},{"key":"222_CR35","unstructured":"The Environment Ontology Issue Tracker. https:\/\/code.google.com\/p\/envo\/issues\/list,"},{"key":"222_CR36","doi-asserted-by":"publisher","first-page":"93","DOI":"10.3852\/07-190","volume":"102","author":"JL Frank","year":"2009","unstructured":"Frank JL, Coffan RA, Southworth D: Aquatic gilled mushrooms: Psathyrella fruiting in the Rogue River in southern Oregon. Mycologia. 2009, 102: 93-107.","journal-title":"Mycologia"},{"key":"222_CR37","unstructured":"The Environment Ontology Annotation Guidelines. http:\/\/www.environmentontology.org\/annotation-guidelines,"},{"key":"222_CR38","unstructured":"The environment ontology user list. http:\/\/www.environmentontology.org\/users,"},{"key":"222_CR39","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/nbt.1823","volume":"29","author":"P Yilmaz","year":"2011","unstructured":"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. 10.1038\/nbt.1823.","journal-title":"Nat Biotechnol"},{"key":"222_CR40","doi-asserted-by":"publisher","first-page":"e1001088","DOI":"10.1371\/journal.pbio.1001088","volume":"9","author":"D Field","year":"2011","unstructured":"Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Gl\u00f6ckner 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: e1001088-10.1371\/journal.pbio.1001088.","journal-title":"PLoS Biol"},{"issue":"Database issue","key":"222_CR41","doi-asserted-by":"publisher","first-page":"D391","DOI":"10.1093\/nar\/gkp918","volume":"38","author":"R Kottmann","year":"2010","unstructured":"Kottmann R, Kostadinov I, Duhaime MB, Buttigieg PL, Yilmaz P, Hankeln W, Waldmann J, Gl\u00f6ckner FO: Megx.net: integrated database resource for marine ecological genomics. Nucleic Acids Res. 2010, 38 (Database issue): D391-D395.","journal-title":"Nucleic Acids Res"},{"key":"222_CR42","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1089\/omi.2008.0016","volume":"12","author":"L Hirschman","year":"2008","unstructured":"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. 10.1089\/omi.2008.0016.","journal-title":"OMICS"},{"key":"222_CR43","unstructured":"An ENVO-lite Annotation of Microbial Genome Projects. Available through Megx.net"},{"key":"222_CR44","unstructured":"The Visualization and Analysis of Microbial Populations Structures (VAMPS) Environmental Data Search Page. http:\/\/vamps.mbl.edu\/portals\/icomm\/subsets\/,"},{"key":"222_CR45","doi-asserted-by":"publisher","first-page":"243","DOI":"10.4056\/sigs.2134923","volume":"5","author":"JA Gilbert","year":"2011","unstructured":"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. 10.4056\/sigs.2134923.","journal-title":"Stand Genomic Sci"},{"key":"222_CR46","unstructured":"The Earth Microbiome Project Sample Breakdown. http:\/\/www.microbio.me\/emp\/,"},{"key":"222_CR47","doi-asserted-by":"publisher","first-page":"947","DOI":"10.1101\/gr.104521.109","volume":"20","author":"S Chaffron","year":"2010","unstructured":"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. 10.1101\/gr.104521.109.","journal-title":"Genome Res"},{"key":"222_CR48","doi-asserted-by":"publisher","first-page":"1111","DOI":"10.1109\/TKDE.2005.131","volume":"17","author":"P Dawyndt","year":"2005","unstructured":"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.","journal-title":"IEEE Trans Knowl Data Eng"},{"key":"222_CR49","unstructured":"StrainInfo.net. http:\/\/www.straininfo.net,"},{"issue":"Suppl 5","key":"222_CR50","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/1471-2105-11-S5-P3","volume":"11","author":"B Verslyppe","year":"2010","unstructured":"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-","journal-title":"BMC Bioinformatics"},{"key":"222_CR51","unstructured":"The Environments-EOL Project. http:\/\/envo.her.hcmr.gr\/environments.html,"},{"key":"222_CR52","first-page":"1073","volume-title":"Integrating ecoinformatics resources on the semantic web","author":"CS Parr","year":"2006","unstructured":"Parr CS, Parafiynyk A, Sachs J, Ding L, Dornbush S, Finin T, Wang D, Hollander A: Proceedings of the 15th international conference on World Wide Web - WWW\u201906. Integrating ecoinformatics resources on the semantic web. 2006, New York, New York, USA: ACM Press, 1073-"},{"issue":"Database issue","key":"222_CR53","doi-asserted-by":"publisher","first-page":"D754","DOI":"10.1093\/nar\/gkp832","volume":"38","author":"LM Schriml","year":"2010","unstructured":"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.","journal-title":"Nucleic Acids Res"},{"key":"222_CR54","unstructured":"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,"},{"key":"222_CR55","unstructured":"The Environment Ontology Core Team. http:\/\/www.environmentontology.org\/core-team,"},{"key":"222_CR56","unstructured":"The Principles of the OBO Foundry. http:\/\/www.obofoundry.org\/crit.shtml,"},{"key":"222_CR57","doi-asserted-by":"publisher","first-page":"R5","DOI":"10.1186\/gb-2012-13-1-r5","volume":"13","author":"CJ Mungall","year":"2012","unstructured":"Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA: Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012, 13: R5-10.1186\/gb-2012-13-1-r5.","journal-title":"Genome Biol"},{"issue":"Database issue","key":"222_CR58","first-page":"D344","volume":"36","author":"K Degtyarenko","year":"2008","unstructured":"Degtyarenko K, De Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alc\u00e1ntara 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.","journal-title":"Nucleic Acids Res"},{"key":"222_CR59","unstructured":"The Genomic Standards Consortium Website. http:\/\/gensc.org,"},{"key":"222_CR60","unstructured":"The environment ontology downloadable content page. http:\/\/www.environmentontology.org\/downloads,"},{"key":"222_CR61","unstructured":"GAZ: a First Step Towards an Open Source Gazetteer Constructed on Ontological Principles. http:\/\/purl.obolibrary.org\/obo\/gaz,"},{"key":"222_CR62","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1111\/j.1758-2229.2009.00030.x","volume":"1","author":"M Pignatelli","year":"2009","unstructured":"Pignatelli M, Moya A, Tamames J: EnvDB, a database for describing the environmental distribution of prokaryotic taxa. Environ Microbiol Rep. 2009, 1: 191-197. 10.1111\/j.1758-2229.2009.00030.x.","journal-title":"Environ Microbiol Rep"},{"key":"222_CR63","unstructured":"The environment ontology contact page. http:\/\/www.environmentontology.org\/contact,"},{"key":"222_CR64","doi-asserted-by":"publisher","first-page":"2198","DOI":"10.1093\/bioinformatics\/btm112","volume":"23","author":"J Day-Richter","year":"2007","unstructured":"Day-Richter J, Harris MA, Haendel M, Lewis S: OBO-Edit\u2013an ontology editor for biologists. Bioinformatics. 2007, 23: 2198-2200. 10.1093\/bioinformatics\/btm112.","journal-title":"Bioinformatics"},{"key":"222_CR65","unstructured":"The OBO format description. http:\/\/oboformat.org,"},{"key":"222_CR66","volume-title":"Proceedings of the {OWL} Reasoner Evaluation Workshop (ORE\u201912)","author":"Y Kazakov","year":"2012","unstructured":"Kazakov Y, Kr\u00f6tzsch M, Simanc\u00edk F: ELK Reasoner: Architecture and Evaluation. Proceedings of the {OWL} Reasoner Evaluation Workshop (ORE\u201912). Edited by: Horrocks I, Yatskevich M, Jimenez-Ruiz E. 2012, Manchester, UK: CEUR-WS.org"},{"key":"222_CR67","unstructured":"An Introduction to the OBO Ontology Release Tool. http:\/\/code.google.com\/p\/owltools\/wiki\/OortIntro,"}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/2041-1480-4-43.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/2041-1480-4-43","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/2041-1480-4-43.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:26:38Z","timestamp":1790036798000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/2041-1480-4-43"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,12,11]]},"references-count":67,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2013,12]]}},"alternative-id":["222"],"URL":"https:\/\/doi.org\/10.1186\/2041-1480-4-43","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,12,11]]},"assertion":[{"value":"15 June 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 November 2013","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 December 2013","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"43"}}