The environment ontology in 2016: Bridging domains with increased scope, semantic density, and interoperation

Journal of Biomedical Semantics

Volumn 7, Issue 1, 2016, Pages

  Buttigieg, Pier Luigi ^a   Pafilis, Evangelos ^b   Lewis, Suzanna E ^c   Schildhauer, Mark P ^d   Walls, Ramona L ^e   Mungall, Christopher J ^c  

^a ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH   (Germany)

^b INSTITUTE OF OCEANOGRAPHY   (Greece)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d NATIONAL CENTER FOR ECOLOGICAL ANALYSIS AND SYNTHESIS   (United States)

^e Thomas J Keating Bioresearch Building   (United States)

Author keywords

Anthropogenic environment; Ecosystem; Environmental semantics; Habitat; Indoor environment; Ontology; Sustainable development

Indexed keywords

EID: 84988625177     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/s13326-016-0097-6     Document Type: Article

References (82)

1. Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE. The environment ontology: contextualising biological and biomedical entities. J Biomed Semant. 2013;4:43.
2. 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.
3. Pesant S, Not F, Picheral M, Kandels-Lewis S, Le Bescot N, Gorsky G, Iudicone D, Karsenti E, Speich S, Troublé R, Dimier C, Searson S. Open science resources for the discovery and analysis of Tara Oceans data. Sci Data. 2015;2(Lmd):150023.
4. Savio D, Sinclair L, Ijaz UZ, Parajka J, Reischer GH, Stadler P, Blaschke AP, Blöschl G, Mach RL, Kirschner AKT, Farnleitner AH, Eiler A. Bacterial diversity along a 2600 km river continuum. Environ Microbiol. 2015;17(12):4994-5007.
5. Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, Fernandez-Guerra A, Jeanthon C, Rahav E, Ullrich M, Wichels A, Gerdts G, Polymenakou P, Kotoulas G, Siam R, Abdallah RZ, Sonnenschein EC, Cariou T, O'Gara F, Jackson S, Orlic S, Steinke M, Busch J, Duarte B, Caçador I, Canning-Clode J, Bobrova O, Marteinsson V, Reynisson E, Loureiro CM, et al. The ocean sampling day consortium. Gigascience. 2015;4:27.
6. Leung MHY, Wilkins D, Li EKT, Kong FKF, Lee PKH. Indoor-air microbiome in an urban subway network: diversity and dynamics. Appl Env Microbiol. 2014;80:6760-70.
7. Hartmann M, Niklaus PA, Zimmermann S, Schmutz S, Kremer J, Abarenkov K, Lüscher P, Widmer F, Frey B. Resistance and resilience of the forest soil microbiome to logging-associated compaction. ISME J. 2014;8:226-44.
8. Meyer F, Paarmann D, D'souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;19:386.
9. iMicrobe metagenomic record annotations with ENVO [https://github.com/hurwitzlab/imicrobe-lib/blob/master/docs/mapping_files/CameraMetadata_ENVO_working_copy.csv ]. Accessed 14 Sept 2016.
10. 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;25:1251-5.
11. Deck J, Barker K, Beaman R, Buttigieg PL, Dröge G, Miller C, Tuama ÉÓ, Murrell Z, Parr C, Robbins B. Clarifying Concepts and Terms in Biodiversity Informatics. Stand Genomic Sci. 2013;8:352-9.
12. Walls RL, Guralnick R, Deck J, Buntzman A, Buttigieg PL, Davies N, Denslow MW, Gallery RE, Parnell JJ, Osumi-sutherland D, Robbins RJ. Meeting report: advancing practical applications of biodiversity ontologies. Stand Genomic Sci. 2014;9:1-10.
13. Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-dill CJ, Midford PE, Mungall CJ, Ram J, Zhang G, Deans AR, Huala E, Lewis SE. Emerging semantics to link phenotype and environment. Peer J. 2015;3:e1470.
14. Walls RL, Deck J, Guralnick R, Baskauf S, Beaman R, Blum S, Bowers S, Buttigieg PL, Davies N, Endresen D, Gandolfo MA, Hanner R, Janning A, Krishtalka L, Matsunaga A, Midford P, Morrison N, Tuama ÉÓ, Schildhauer M, Smith B, Stucky BJ, Thomer A, Wieczorek J, Whitacre J, Wooley J. Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies. PLoS ONE. 2014;9:e89606.
15. Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, Neumann S, Sterk P, Tong W, Sansone S-A. ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics. 2010;26:2354-6.
16. Wieczorek J, Bloom D, Guralnick R, Blum S, Döring M, Giovanni R, Robertson T, Vieglais D. Darwin Core: an evolving community-developed biodiversity data standard. PLoS ONE. 2012;7:e29715.
17. Wieczorek J, Bánki O, Blum S, Deck J, Döring M, Dröge G, Endresen D, Goldstein P, Leary P, Krishtalka L, Tuama ÉÓ, Robbins RJ, Robertson T, Yilmaz P. Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013). Stand Genomic Sci. 2014;9:585-98.
18. Henschel A, Anwar MZ, Manohar V. Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities. PLoS Comput Biol. 2015;11:e1004468.
19. Parr CS, Wilson N, Schulz K, Leary P, Hammock J, Rice J, Corrigan Jr. RJ. TraitBank: Practical semantics for organism attribute data. Semant Web - Interoperability, Usability, Appl 2014, 650-1860.
20. Poelen JH, Simons JD, Mungall CJ. Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets. Ecol Inf. 2014;24:148-59.
21. Xiang Z, Mungall CJ, Ruttenberg A, He Y. Ontobee: A Linked Data Server and Browser for Ontology Terms. In Proceedings of the 2nd International Conference on Biomedical Ontologies (ICBO). Volume 1. Buffalo: CEUR Workshop Proceedings (CEUR-WS.org); 2011. p. 279-281. http://ceur-ws.org/Vol-833/.
22. Day-Richter J, Harris MA, Haendel M, Lewis S. OBO-Edit--an ontology editor for biologists. Bioinformatics. 2007;23:2198-200.
23. The Relations Ontology Code repository [https://github.com/oborel/obo-relations ]. Accessed 14 Sept 2016.
24. Basic Formal Ontology 2.0: Draft Specification and User's Guide [https://github.com/BFO-ontology/BFO/raw/master/docs/bfo2-reference/BFO2-Reference.pdf ]. Accessed 14 Sept 2016.
25. The Environment Ontology Issue Tracker [https://github.com/EnvironmentOntology/envo/issues ]. Accessed 14 Sept 2016.
26. Overton JA, Dietze H, Essaid S, Osumi-sutherland D, Mungall CJ. ROBOT: A command-line tool for ontology development. In Proceedings of the International Conference on Biomedical Ontology (ICBO). Lisbon: CEUR Workshop Proceedings (CEUR-WS.org); 2015. p. 131-132. http://ceur-ws.org/Vol-1515/.
27. Courtot M, Gibson F, Lister AL, Malone J, Schober D, Brinkman RR, Ruttenberg A. MIREOT: the Minimum Information to Reference an External Ontology Term Institute of Medical Biometry and Medical Informatics (IMBI), University Medical. Appl Ontol. 2011;6:23-33.
28. Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA. Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012;13:R5.
29. 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):D344-50.
30. Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall CJ. TermGenie - a web-application for pattern-based ontology class generation. J Biomed Semant. 2014;5:48.
31. Pafilis E, Frankild SP, Schnetzer J, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou K, Leary P, Hammock J, Schulz K, Parr CS, Arvanitidis C, Jensen LJ. ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. Bioinformatics. 2015;31:1872-4.
32. 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;29:415-20.
33. Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME J. 2014;8:1-3.
34. ten Hoopen P, Amid C, Buttigieg PL, Pafilis E, Bravakos P, Cerdeño-Tárraga AM, Gibson R, Kahlke T, Legaki A, Murthy KN, Papastefanou G, Pereira E, Rossello M, Toribio AL, Cochrane G. Value, but high costs in post-deposition data curation. Database 2016:1-10. doi: 10.1093/database/bav126.
35. Lund HG. What is a forest? Definitions do make a difference: An example from Turkey. Avrasya Terim Derg. 2014;2:1-8.
36. Sasaki N, Putz FE. Critical need for new definitions of "forest" and "forest degradation" in global climate change agreements. Conserv Lett. 2009;2:226-32.
37. Sexton JO, Noojipady P, Song X-P, Feng M, Song D-X, Kim D-H, Anand A, Huang C, Channan S, Pimm SL, Townshend JR. Conservation policy and the measurement of forests. Nat Clim Chang. 2015;6(October):1-6.
38. Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. Cross-product extensions of the Gene Ontology. J Biomed Semant Inf. 2011;44:80-6.
39. Parr CS, Wilson N, Leary P, Schulz KS, Lans K, Walley L, Hammock JA, Goddard A, Rice J, Studer M, Holmes JTG, Corrigan RJ. The encyclopedia of life v2: providing global access to knowledge about life on earth. Biodiv Data J. 2014;29(2):e1079.
40. The Tree of Life Web Project [http://tolweb.org ]. Accessed 14 Sept 2016.
41. Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Marcet-Houben M, Gabaldon T. PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res. 2014;42:D897-902.
42. Piel WH, Donoghue MJ, Sanderson MJ. TreeBASE: a database of phylogenetic knowledge. In: Shimura J, Wilson KL, Gordon D, editors. To the interoperable "Catalog of Life" with partners Species 2000 Asia Oceanea. Research report no. 171. Tsukuba, Japan: The National Institute for Environmental Studies; 2002. p. 41-7.
43. Vos R, Lapp H, Piel W, Tannen V. TreeBASE2: Rise of the Machines. Available from Nature Precedings; 2010.
44. IUCN: The IUCN Red List of Threatened Species. Version 2015-4 2015: http://www.iucnredlist.org. Accessed 14 Sept 2016.
45. The Environment Ontology's experimental habitat branch [https://github.com/EnvironmentOntology/envo-habitats ]. Accessed 14 Sept 2016.
46. Experimental ENVO Habitat Classes Derived from ENVIRONMENTS-EOL [http://dx.doi.org/ 10.5281/zenodo.35393 ]. Accessed 14 Sept 2016.
47. Groom QJ. Piecing together the biogeographic history of Chenopodium vulvaria L. using botanical literature and collections. Peer J. 2015;3:e723.
48. Elith J, Leathwick JR. Species distribution models: ecological explanation and prediction across space and time. Ann Rev Ecol Evol Syst. 2009;40:677-97.
49. Hall LS, Krausman PR, Morrison ML. The habitat concept and a plea for standard terminology. Wildl Soc Bull. 1997;25:173-82.
50. Kearney M. Habitat, environment and niche: What are we modelling? Oikos. 2006;115:186-91.
51. Schmidt TSB, Matias Rodrigues JF, von Mering C. Limits to robustness and reproducibility in thedemarcation of operational taxonomic units. Env Microbiol. 2014;17:1689-706.
52. Schmidt TSB, Matias Rodrigues JF, von Mering C. Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale. PLoS Comput Biol. 2014;10:e1003594.
53. Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. Swarm: robust and fast clustering method for amplicon-based studies. Peer J. 2014;2:e593.
54. Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG, Sogin ML. Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol Evol. 2013;4:1111-9.
55. Eren a M, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML. Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J. 2014;9:968-79.
56. Ellis EC, Ramankutty N. Putting people in the map: anthropogenic biomes of the world. Front Ecol Env. 2008;6:439-47.
57. Talisuna A, Adibaku S, Dorsey G, Kamya MR, Rosenthal PJ. Malaria in Uganda: challenges to control on the long road to elimination. II. The path forward. Acta Trop. 2012;121:196-201.
58. Wanzirah H, Tusting LS, Arinaitwe E, Katureebe A, Maxwell K, Rek J, Bottomley C, Staedke SG, Kamya M, Dorsey G, Lindsay SW. Mind the gap: house structure and the risk of malaria in Uganda. PLoS ONE. 2015;10:e0117396.
59. Pletscher-Frankild S, Pallejà A, Tsafou K, Binder JX, Jensen LJ. DISEASES: Text mining and data integration of disease-gene associations. Methods. 2014;74:83-9.
60. Groza T, Köhler S, Doelken S, Collier N, Oellrich A, Smedley D, Couto FM, Baynam G, Zankl A, Robinson PN. Automatic concept recognition using the human phenotype ontology reference and test suite corpora. Database (Oxford). 2015;2015:1-13.
61. Tringe SG, Zhang T, Liu X, Yu Y, Lee WH, Yap J, Yao F, Suan ST, Ing SK, Haynes M, Rohwer F, Wei CL, Tan P, Bristow J, Rubin EM, Ruan Y. The Airborne Metagenome in an Indoor Urban Environment. PLoS ONE. 2008;3:10.
62. Hospodsky D, Qian J, Nazaroff WW, Yamamoto N, Bibby K, Rismani-Yazdi H, Peccia J. Human occupancy as a source of indoor airborne bacteria. PLoS ONE. 2012;7:e34867.
63. Adams RI, Bateman AC, Bik HM, Meadow JF. Microbiota of the indoor environment: a meta-analysis. Microbiome. 2015;3:49.
64. Flores GE, Bates ST, Knights D, Lauber CL, Stombaugh J, Knight R, Fierer N. Microbial biogeography of public restroom surfaces. PLoS ONE. 2011;6:e28132.
65. Dunn RR, Fierer N, Henley JB, Leff JW, Menninger HL. Home life: factors structuring the bacterial diversity found within and between homes. PLoS ONE. 2013;8:e64133.
66. Hastings J, Jeliazkova N, Owen G, Tsiliki G, Munteanu CR, Steinbeck C, Willighagen E. eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. J Biomed Semantics. 2015;6:10.
67. Lovett GM, Tear TH, Evers DC, Findlay SEG, Cosby BJ, Dunscomb JK, Driscoll CT, Weathers KC. Effects of air pollution on ecosystems and biological diversity in the eastern United States. Ann N Y Acad Sci. 2009;1162:99-135.
68. The Sustainable Development Goals Interface Ontology (SDGIO) Code Repository [https://github.com/SDG-InterfaceOntology/sdgio ]. Accessed 14 Sept 2016.
69. Colglazier W. SUSTAINABILITY. Sustainable development agenda: 2030. Sci (80-). 2015;349:1048-50.
70. UNEP. Embedding the Environment in Sustainable Development Goals. UNEP Post-2015 Discussion Paper 1. Nairobi: United Nations Environment Programme (UNEP); 2013.
71. United Nations. Transforming our world: the 2030 agenda for sustainable development. 2015:A/RES/70/1.
72. General Multilingual Environmental Thesaurus (GEMET). 2012:version 3.1. http://www.eionet.europa.eu/gemet/. Accessed 14 Sept 2016.
73. Schmitt CB, Belokurov A, Besançon C, Boisrobert L, Burgess ND, Campbell A, Coad L, Fish L, Gliddon D, Humphries K, Kapos V, Loucks C, Lysenko I, Miles L, Mills C, Minnemeyer S, Pistorius T, Ravilious C, Steininger M, Winkel G. Global Ecological Forest Classification and Forest Protected Area Gap Analysis. Analyses and Recommendations in View of the 10% Target for Forest Protection under the Convention on Biological Diversity (CBD). 2nd ed. Freiburg: University Press; 2009.
74. Soltwedel T, Schauer U, Boebel O, Nothig EM, Bracher A, Metfies K, Schewe I, Boetius A, Klages M. FRAM - FRontiers in Arctic marine Monitoring Visions for permanent observations in a gateway to the Arctic Ocean. In OCEANS 2013 MTS/IEEE: The Challenges of the Northern Dimension. Bergen: IEEE; 2013. http://ieeexplore.ieee.org/document/6608008/?arnumber=6608008.
75. The Principles of the OBO Foundry [http://www.obofoundry.org/principles/fp-000-summary.html ]. Accessed 14 Sept 2016.
76. The Food Ontology (FOODON) Code Repository [https://github.com/FoodOntology/foodon ]. Accessed 14 Sept 2016.
77. The Agrononomy Ontology (AgrO) code repository [https://github.com/AgriculturalSemantics/agro ].
78. CEM-IUCN, Provita. IUCN Red List of Ecosystems. Caracas, Venez: Com Ecosyst Manag Int Union Conserv Nat Provita; 2012. http://www.iucnredlistofecosystems.org.
79. Hardisty A, Roberts D, Biodiversity Informatics Community. A decadal view of biodiversity informatics: challenges and priorities. BMC Ecol. 2013;13:16.
80. Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten J-W, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, 't Hoen PA, Hooft R, Kuhn T, Kok R, Kok J, et al. The FAIR guiding principles for scientific data management and stewardship. Sci Data. 2016;3:160018.
81. Shaping the semantic layer by mining digitised data: an encounter between iDigBio's plant records and the Environment Ontology (ENVO) [https://www.idigbio.org/content/webinar-shaping-semantic-layer-mining-digitised-data-encounter-between-idigbios-plant ]. Accessed 14 Sept 2016.
82. The Environment Ontology (OWL representation) [http://purl.obolibrary.org/obo/envo.owl ]. Accessed 14 Sept 2016.