TY - JOUR AU - Lozupone, C. A. AU - Knight, R. PY - 2007 DA - 2007// TI - Global patterns in bacterial diversity JO - Proc Natl Acad Sci U S A VL - 105 UR - https://doi.org/10.1073/pnas.0611525104 DO - 10.1073/pnas.0611525104 ID - Lozupone2007 ER - TY - JOUR AU - Cavicchioli, R. PY - 2011 DA - 2011// TI - Archaea - timeline of the third domain JO - Nature Rev Microbiol VL - 9 UR - https://doi.org/10.1038/nrmicro2482 DO - 10.1038/nrmicro2482 ID - Cavicchioli2011 ER - TY - JOUR AU - Youssef, N. H. AU - Couger, M. B. AU - McCully, A. L. AU - Criado, A. E. G. AU - Elshahed, M. S. PY - 2015 DA - 2015// TI - Assessing the global phylum level diversity within the bacterial domain: A review JO - J Adv Res VL - 6 UR - https://doi.org/10.1016/j.jare.2014.10.005 DO - 10.1016/j.jare.2014.10.005 ID - Youssef2015 ER - TY - JOUR AU - Whitman, W. B. AU - Coleman, D. C. AU - Wiebe, W. J. PY - 1998 DA - 1998// TI - Prokaryotes: the unseen majority JO - Proc Natl Acad Sci U S A VL - 95 UR - https://doi.org/10.1073/pnas.95.12.6578 DO - 10.1073/pnas.95.12.6578 ID - Whitman1998 ER - TY - JOUR AU - Flombaum, P. AU - Gallegos, J. L. AU - Gordillo, R. A. AU - Rincón, J. AU - Zabala, L. L. AU - Jiao, N. PY - 2013 DA - 2013// TI - Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus JO - Proc Natl Acad Sci U S A VL - 110 UR - https://doi.org/10.1073/pnas.1307701110 DO - 10.1073/pnas.1307701110 ID - Flombaum2013 ER - TY - BOOK AU - Rosenberg, E. AU - Delong, E. F. AU - Stackebrandt, E. AU - Lory, S. AU - Thompson, F. PY - 2013 DA - 2013// TI - The Prokaryotes. Prokaryotic Physiology and Biochemistry PB - Springer CY - Berlin Heidelberg ID - Rosenberg2013 ER - TY - JOUR AU - Blank, C. E. PY - 2009 DA - 2009// TI - Not so old Archaea – The antiquity of biogeochemical processes in the archaeal domain of life JO - Geobiology VL - 7 UR - https://doi.org/10.1111/j.1472-4669.2009.00219.x DO - 10.1111/j.1472-4669.2009.00219.x ID - Blank2009 ER - TY - JOUR AU - Henry, C. S. AU - Overbeek, R. AU - Xia, F. F. AU - Best, A. A. AU - Glass, E. AU - Gilbert, J. PY - 2011 DA - 2011// TI - Connecting genotype to phenotype in the era of high-throughput sequencing JO - Biochim Biophys Acta-Gen Subjects VL - 1810 UR - https://doi.org/10.1016/j.bbagen.2011.03.010 DO - 10.1016/j.bbagen.2011.03.010 ID - Henry2011 ER - TY - JOUR AU - Blank, C. E. PY - 2012 DA - 2012// TI - Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time JO - Archaea ID - Blank2012 ER - TY - JOUR AU - Bressan, A. AU - Terlizzi, F. AU - Credi, R. PY - 2012 DA - 2012// TI - Independent origins of vectored plant pathogenic bacteria from arthropod-associated Arsenophonus endosymbionts JO - Microb Ecol VL - 63 UR - https://doi.org/10.1007/s00248-011-9933-5 DO - 10.1007/s00248-011-9933-5 ID - Bressan2012 ER - TY - JOUR AU - Blank, C. E. PY - 2013 DA - 2013// TI - Origin and early evolution of photosynthetic eukaryotes in freshwater environments – reinterpreting proterozoic paleobiology and biogeochemical processes in light of trait evolution JO - J Phycol VL - 49 UR - https://doi.org/10.1111/jpy.12111 DO - 10.1111/jpy.12111 ID - Blank2013 ER - TY - JOUR AU - Dutilh, B. E. AU - Backus, L. AU - Edwards, R. A. AU - Wels, M. AU - Bayjanov, J. R. AU - Hijum, S. A. F. T. PY - 2013 DA - 2013// TI - Explaining microbial phenotypes on a genomic scale: GWAS for microbes JO - Brief Funct Genomics VL - 12 UR - https://doi.org/10.1093/bfgp/elt008 DO - 10.1093/bfgp/elt008 ID - Dutilh2013 ER - TY - JOUR AU - Sachs, J. L. AU - Skophammer, R. G. AU - Bansal, N. AU - Stajich, J. E. PY - 2014 DA - 2014// TI - Evolutionary origins and diversification of proteobacterial mutualists JO - Proc R Soc London B VL - 281 UR - https://doi.org/10.1098/rspb.2013.2146 DO - 10.1098/rspb.2013.2146 ID - Sachs2014 ER - TY - STD TI - AVAToL Natural Language Processing, Overview. http://avatol.org/ngp/nlp/overview-2/. Accessed 30 Nov 2015. UR - http://avatol.org/ngp/nlp/overview-2/ ID - ref14 ER - TY - JOUR AU - Oren, A. PY - 2004 DA - 2004// TI - A proposal for further integration of the cyanobacteria under the Bacteriological Code JO - Int J Syst Evol Microbiol VL - 54 UR - https://doi.org/10.1099/ijs.0.03008-0 DO - 10.1099/ijs.0.03008-0 ID - Oren2004 ER - TY - JOUR AU - Oren, A. PY - 2011 DA - 2011// TI - Cyanobacterial systematics and nomenclature as featured in the International Bulletin of Bacteriological Nomenclature and Taxonomy/International Journal of Systematic Bacteriology/International Journal of Systematic and Evolutionary Microbiology JO - Int J Syst Evol Microbiol VL - 61 UR - https://doi.org/10.1099/ijs.0.018838-0 DO - 10.1099/ijs.0.018838-0 ID - Oren2011 ER - TY - STD TI - Chibucos M, Zweifel AE, Herrera JC, Meza W, Shabnam E, Uetz P, Siegele DA, Hu JC, Giglio MG. An ontology for microbial phenotypes. BMC Microbiol. 2014;14:292. ID - ref17 ER - TY - STD TI - Microbial Phenotypes Wiki. http://microbialphenotypes.org/wiki/index.php/Main_Page. Accessed 30 Nov 2015. UR - http://microbialphenotypes.org/wiki/index.php/Main_Page ID - ref18 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. PY - 2000 DA - 2000// TI - Gene Ontology: tool for the unification of biology JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - JOUR AU - Gkoutos, G. V. PY - 2006 DA - 2006// TI - Towards a phenotypic semantic web JO - Curr Bioinform VL - 1 UR - https://doi.org/10.2174/157489306777011941 DO - 10.2174/157489306777011941 ID - Gkoutos2006 ER - TY - STD TI - Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res. 2013;41:D456–63. ID - ref21 ER - TY - BOOK PY - 2005 DA - 2005// TI - Guidelines for the construction, format, and management of monolingual controlled vocabularies PB - National Information Standards Organization, NISO Press CY - Bethesda ID - ref22 ER - TY - STD TI - Protege. Copyrighted by the Stanford Center for Biomedical Informatics Research. http://protege.stanford.edu/products.php. Accessed 30 Nov 2015 UR - http://protege.stanford.edu/products.php ID - ref23 ER - TY - CHAP AU - Grenon, P. AU - Smith, B. AU - Goldberg, L. ED - Pisanelli, D. M. PY - 2004 DA - 2004// TI - Biodynamic ontology: Applying BFO in the biomedical domain BT - Ontologies in medicine PB - Ios Press CY - Amsterdam ID - Grenon2004 ER - TY - JOUR AU - Smith, B. AU - Ashburner, A. AU - Rosse, C. AU - Bard, J. AU - Bug, W. AU - Ceusters, W. PY - 2007 DA - 2007// TI - The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration JO - Nature Biotechnol VL - 25 UR - https://doi.org/10.1038/nbt1346 DO - 10.1038/nbt1346 ID - Smith2007 ER - TY - BOOK AU - Guiry, M. D. AU - Guiry, G. M. PY - 2015 DA - 2015// TI - AlgaeBase PB - National University of Ireland CY - Galway ID - Guiry2015 ER - TY - STD TI - Xiang Z, Mungall C, Ruttenberg A, He Y. Ontobee. A Linked Data Server and Browser for Ontology Terms. Proceedings of the 2nd International Conference on Biomedical Ontologies (ICBO), July 28-30, 2011, Buffalo, NY, USA. Pages 279-281. URL: http://ceur-ws.org/Vol-833/paper48.pdf. Accessed 6 Apr 2016. UR - http://ceur-ws.org/Vol-833/paper48.pdf ID - ref27 ER - TY - JOUR AU - Xiang, Z. AU - Courtot, M. AU - Brinkman, R. R. AU - Ruttenberg, A. AU - He, Y. PY - 2010 DA - 2010// TI - OntoFox: web-based support for ontology reuse JO - BMC Res Notes VL - 3 UR - https://doi.org/10.1186/1756-0500-3-175 DO - 10.1186/1756-0500-3-175 ID - Xiang2010 ER - TY - JOUR AU - Jaiswal, P. AU - Avraham, S. AU - Ilic, K. AU - Kellogg, E. A. AU - McCouch, S. AU - Pujar, A. PY - 2005 DA - 2005// TI - Plant ontology (PO): a controlled vocabulary of plant structures and growth stages JO - Comp Funct Genomics VL - 6 UR - https://doi.org/10.1002/cfg.496 DO - 10.1002/cfg.496 ID - Jaiswal2005 ER - TY - STD TI - Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C. Relations in biomedical ontologies. Genome Biol. 2005;6:R46. ID - ref30 ER - TY - JOUR AU - Brinkman, R. R. AU - Courtot, M. AU - Derom, D. AU - Fostel, J. M. AU - He, Y. AU - Lord, P. PY - 2010 DA - 2010// TI - Modeling biomedical experimental processes with OBI JO - J Biomed Semant VL - 1 UR - https://doi.org/10.1186/2041-1480-1-S1-S7 DO - 10.1186/2041-1480-1-S1-S7 ID - Brinkman2010 ER - TY - JOUR AU - Hoehndorf, R. AU - Oellrich, A. AU - Dumontier, M. AU - Kelso, J. AU - Rebholz-Schuhmann, D. AU - Herre, H. PY - 2010 DA - 2010// TI - Relations as patterns: bridging the gap between OBO and OWL JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-441 DO - 10.1186/1471-2105-11-441 ID - Hoehndorf2010 ER - TY - STD TI - Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD. Logical development of the Cell Ontology. BMC Bioinformatics. 2011;12:6. ID - ref33 ER - TY - JOUR AU - Mungall, C. J. AU - Torniai, C. AU - Gkoutos, G. V. AU - Lewis, S. E. AU - Haendel, M. A. PY - 2012 DA - 2012// TI - Uberon, an integrative multi-species anatomy ontology JO - Genome Biol VL - 13 UR - https://doi.org/10.1186/gb-2012-13-1-r5 DO - 10.1186/gb-2012-13-1-r5 ID - Mungall2012 ER - TY - JOUR AU - Acland, A. AU - Agarwala, R. AU - Barrett, T. AU - Beck, J. AU - Benson, D. A. AU - Bollin, C. PY - 2013 DA - 2013// TI - Database resources of the National Center for Biotechnology Information JO - Nuc Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1189 DO - 10.1093/nar/gks1189 ID - Acland2013 ER - TY - STD TI - Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. J Biomed Semant. 2014;5:34. ID - ref36 ER - TY - STD TI - Chemical Methods Ontology. http://obofoundry.org/ontology/chmo.html. Accessed 30 Nov 2015. UR - http://obofoundry.org/ontology/chmo.html ID - ref37 ER - TY - JOUR AU - Topalis, P. AU - Dialynas, E. AU - Mitraka, E. AU - Deligianni, E. AU - Siden-Kiamos, I. AU - Louis, C. PY - 2011 DA - 2011// TI - A set of ontologies to drive tools for the control of vector-borne diseases JO - J Biomed Inform VL - 44 UR - https://doi.org/10.1016/j.jbi.2010.03.012 DO - 10.1016/j.jbi.2010.03.012 ID - Topalis2011 ER - TY - JOUR AU - Buttigieg, P. L. AU - Morrison, N. AU - Smith, B. AU - Mungall, C. J. AU - Lewis, S. E. PY - 2013 DA - 2013// TI - The Environment Ontology: contextualising biological and biomedical entities JO - J Biomed Semant VL - 4 UR - https://doi.org/10.1186/2041-1480-4-43 DO - 10.1186/2041-1480-4-43 ID - Buttigieg2013 ER - TY - STD TI - Gene Ontology Consortium, Ontology Structure. http://geneontology.org/page/ontology-structure. Accessed 30 Nov 2015. UR - http://geneontology.org/page/ontology-structure ID - ref40 ER - TY - STD TI - Purl address for MicrO. http://purl.obolibrary.org/obo/MicrO.owl. Accessed 1 Dec 2015. UR - http://purl.obolibrary.org/obo/MicrO.owl ID - ref41 ER - TY - STD TI - MicrO - A microbial ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. https://github.com/carrineblank/MicrO. Accessed 30 Nov 2015. UR - https://github.com/carrineblank/MicrO ID - ref42 ER - TY - STD TI - The OBO Foundry - prokaryotic phenotypic and metabolic characters. http://www.obofoundry.org/ontology/micro.html. Accessed 30 Nov 2015. UR - http://www.obofoundry.org/ontology/micro.html ID - ref43 ER - TY - STD TI - Creative Commons, Attribution 2.0 Generic. http://creativecommons.org/licenses/by/2.0. Accessed 30 Nov 2015. UR - http://creativecommons.org/licenses/by/2.0 ID - ref44 ER - TY - STD TI - Oberhardt MA, Zarecki R, Gronow S, Lang E, Klenk H-P, Gophna U, Ruppin E. Harnessing the landscape of microbial culture media to predict new organism–media pairings. Nat Commun. 2015;6:8493. ID - ref45 ER - TY - CHAP AU - Cowell, L. G. AU - Smith, B. ED - Sintchenko, V. PY - 2010 DA - 2010// TI - Infectious Disease Ontology BT - Infectious Disease Informatics PB - Springer CY - New York UR - https://doi.org/10.1007/978-1-4419-1327-2_19 DO - 10.1007/978-1-4419-1327-2_19 ID - Cowell2010 ER - TY - STD TI - Schriml LM, Arze C, Nadendla S, Chang YWW, Mazaitis M, Felix V, Feng G, Kibbe WA. Disease ontology: a backbone for disease semantic integration. Nuc Acids Res. 2012;40:D940–6. ID - ref47 ER - TY - JOUR AU - Kibbe, W. A. AU - Arze, C. AU - Felix, V. AU - Mitraka, E. AU - Bolton, E. AU - Fu, G. PY - 2015 DA - 2015// TI - Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data JO - Nuc Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1011 DO - 10.1093/nar/gku1011 ID - Kibbe2015 ER - TY - JOUR AU - Mabee, P. M. AU - Ashburner, M. AU - Cronk, Q. AU - Gkoutos, G. V. AU - Haendel, M. AU - Segerdell, E. AU - Mungall, C. AU - Westerfield, M. PY - 2007 DA - 2007// TI - Phenotype ontologies: the bridge between genomics and evolution JO - Trends Ecol Evol VL - 22 UR - https://doi.org/10.1016/j.tree.2007.03.013 DO - 10.1016/j.tree.2007.03.013 ID - Mabee2007 ER - TY - JOUR AU - Deans, A. R. AU - Lewis, S. E. AU - Huala, E. AU - Anzaldo, S. S. AU - Ashburner, M. PY - 2015 DA - 2015// TI - Finding our way through phenotypes JO - PLoS Biol VL - 13 UR - https://doi.org/10.1371/journal.pbio.1002033 DO - 10.1371/journal.pbio.1002033 ID - Deans2015 ER - TY - JOUR AU - Dececchi, T. A. AU - Balhoff, J. P. AU - Lapp, H. AU - Mabee, P. M. PY - 2015 DA - 2015// TI - Toward synthesizing our knowledge of morphology: Using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies JO - Syst Biol VL - 64 UR - https://doi.org/10.1093/sysbio/syv031 DO - 10.1093/sysbio/syv031 ID - Dececchi2015 ER -