{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T19:29:47Z","timestamp":1768591787811,"version":"3.49.0"},"reference-count":51,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"published-print":{"date-parts":[[2016,12]]},"DOI":"10.1186\/s13326-016-0060-6","type":"journal-article","created":{"date-parts":[[2016,4,14]],"date-time":"2016-04-14T08:33:58Z","timestamp":1460622838000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions"],"prefix":"10.1186","volume":"7","author":[{"given":"Carrine E.","family":"Blank","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong","family":"Cui","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lisa R.","family":"Moore","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramona L.","family":"Walls","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,4,12]]},"reference":[{"issue":"27","key":"60_CR1","doi-asserted-by":"crossref","first-page":"11436","DOI":"10.1073\/pnas.0611525104","volume":"105","author":"CA Lozupone","year":"2007","unstructured":"Lozupone CA, Knight R. Global patterns in bacterial diversity. Proc Natl Acad Sci U S A. 2007;105(27):11436\u201340.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"60_CR2","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nrmicro2482","volume":"9","author":"R Cavicchioli","year":"2011","unstructured":"Cavicchioli R. Archaea - timeline of the third domain. Nature Rev Microbiol. 2011;9(1):51\u201361.","journal-title":"Nature Rev Microbiol"},{"issue":"3","key":"60_CR3","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.jare.2014.10.005","volume":"6","author":"NH Youssef","year":"2015","unstructured":"Youssef NH, Couger MB, McCully AL, Criado AEG, Elshahed MS. Assessing the global phylum level diversity within the bacterial domain: A review. J Adv Res. 2015;6(3):269\u201382.","journal-title":"J Adv Res"},{"key":"60_CR4","doi-asserted-by":"crossref","first-page":"6578","DOI":"10.1073\/pnas.95.12.6578","volume":"95","author":"WB Whitman","year":"1998","unstructured":"Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A. 1998;95:6578\u201383.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"60_CR5","doi-asserted-by":"crossref","first-page":"9824","DOI":"10.1073\/pnas.1307701110","volume":"110","author":"P Flombaum","year":"2013","unstructured":"Flombaum P, Gallegos JL, Gordillo RA, Rinc\u00f3n J, Zabala LL, Jiao N, et al. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc Natl Acad Sci U S A. 2013;110:9824\u20139.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"60_CR6","volume-title":"The Prokaryotes. Prokaryotic Physiology and Biochemistry","author":"E Rosenberg","year":"2013","unstructured":"Rosenberg E, Delong EF, Stackebrandt E, Lory S, Thompson F. The Prokaryotes. Prokaryotic Physiology and Biochemistry. 4th ed. Berlin Heidelberg: Springer; 2013.","edition":"4"},{"key":"60_CR7","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1111\/j.1472-4669.2009.00219.x","volume":"7","author":"CE Blank","year":"2009","unstructured":"Blank CE. Not so old Archaea \u2013 The antiquity of biogeochemical processes in the archaeal domain of life. Geobiology. 2009;7:495\u2013514.","journal-title":"Geobiology"},{"key":"60_CR8","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1016\/j.bbagen.2011.03.010","volume":"1810","author":"CS Henry","year":"2011","unstructured":"Henry CS, Overbeek R, Xia FF, Best AA, Glass E, Gilbert J, et al. Connecting genotype to phenotype in the era of high-throughput sequencing. Biochim Biophys Acta-Gen Subjects. 2011;1810:967\u201377. SI).","journal-title":"Biochim Biophys Acta-Gen Subjects"},{"key":"60_CR9","author":"CE Blank","year":"2012","unstructured":"Blank CE. Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time. Archaea. 2012. doi: 10.1155\/2012\/843539 .","journal-title":"Archaea"},{"key":"60_CR10","doi-asserted-by":"crossref","first-page":"628","DOI":"10.1007\/s00248-011-9933-5","volume":"63","author":"A Bressan","year":"2012","unstructured":"Bressan A, Terlizzi F, Credi R. Independent origins of vectored plant pathogenic bacteria from arthropod-associated Arsenophonus endosymbionts. Microb Ecol. 2012;63:628\u201338.","journal-title":"Microb Ecol"},{"key":"60_CR11","doi-asserted-by":"crossref","first-page":"1040","DOI":"10.1111\/jpy.12111","volume":"49","author":"CE Blank","year":"2013","unstructured":"Blank CE. Origin and early evolution of photosynthetic eukaryotes in freshwater environments \u2013 reinterpreting proterozoic paleobiology and biogeochemical processes in light of trait evolution. J Phycol. 2013;49:1040\u201355.","journal-title":"J Phycol"},{"key":"60_CR12","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1093\/bfgp\/elt008","volume":"12","author":"BE Dutilh","year":"2013","unstructured":"Dutilh BE, Backus L, Edwards RA, Wels M, Bayjanov JR, van Hijum SAFT. Explaining microbial phenotypes on a genomic scale: GWAS for microbes. Brief Funct Genomics. 2013;12:366\u201380. SI.","journal-title":"Brief Funct Genomics"},{"key":"60_CR13","doi-asserted-by":"crossref","first-page":"20132146","DOI":"10.1098\/rspb.2013.2146","volume":"281","author":"JL Sachs","year":"2014","unstructured":"Sachs JL, Skophammer RG, Bansal N, Stajich JE. Evolutionary origins and diversification of proteobacterial mutualists. Proc R Soc London B. 2014;281:20132146.","journal-title":"Proc R Soc London B"},{"key":"60_CR14","unstructured":"AVAToL Natural Language Processing, Overview. http:\/\/avatol.org\/ngp\/nlp\/overview-2\/ . Accessed 30 Nov 2015."},{"key":"60_CR15","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1099\/ijs.0.03008-0","volume":"54","author":"A Oren","year":"2004","unstructured":"Oren A. A proposal for further integration of the cyanobacteria under the Bacteriological Code. Int J Syst Evol Microbiol. 2004;54:1895\u2013902.","journal-title":"Int J Syst Evol Microbiol"},{"key":"60_CR16","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1099\/ijs.0.018838-0","volume":"61","author":"A Oren","year":"2011","unstructured":"Oren A. 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. Int J Syst Evol Microbiol. 2011;61:10\u20135.","journal-title":"Int J Syst Evol Microbiol"},{"key":"60_CR17","doi-asserted-by":"crossref","unstructured":"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.","DOI":"10.1186\/s12866-014-0294-3"},{"key":"60_CR18","unstructured":"Microbial Phenotypes Wiki. http:\/\/microbialphenotypes.org\/wiki\/index.php\/Main_Page . Accessed 30 Nov 2015."},{"key":"60_CR19","doi-asserted-by":"crossref","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, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000;25:25\u20139.","journal-title":"Nat Genet"},{"key":"60_CR20","doi-asserted-by":"crossref","first-page":"235","DOI":"10.2174\/157489306777011941","volume":"1","author":"GV Gkoutos","year":"2006","unstructured":"Gkoutos GV. Towards a phenotypic semantic web. Curr Bioinform. 2006;1:235\u201346.","journal-title":"Curr Bioinform"},{"key":"60_CR21","doi-asserted-by":"crossref","unstructured":"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\u201363.","DOI":"10.1093\/nar\/gks1146"},{"key":"60_CR22","isbn-type":"print","volume-title":"Guidelines for the construction, format, and management of monolingual controlled vocabularies","author":"ANSI\/NISO Z39.19-2005","year":"2005","unstructured":"ANSI\/NISO Z39.19-2005. Guidelines for the construction, format, and management of monolingual controlled vocabularies. Bethesda: National Information Standards Organization, NISO Press; 2005. ISBN 1-880124-65-3.","ISBN":"https:\/\/id.crossref.org\/isbn\/1880124653"},{"key":"60_CR23","unstructured":"Protege. Copyrighted by the Stanford Center for Biomedical Informatics Research. http:\/\/protege.stanford.edu\/products.php . Accessed 30 Nov 2015"},{"key":"60_CR24","first-page":"20","volume-title":"Ontologies in medicine","author":"P Grenon","year":"2004","unstructured":"Grenon P, Smith B, Goldberg L. Biodynamic ontology: Applying BFO in the biomedical domain. In: Pisanelli DM, editor. Ontologies in medicine. Amsterdam: Ios Press; 2004. p. 20\u201338. Academic."},{"key":"60_CR25","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1038\/nbt1346","volume":"25","author":"B Smith","year":"2007","unstructured":"Smith B, Ashburner A, Rosse C, Bard J, Bug W, Ceusters W, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnol. 2007;25:1251\u20135.","journal-title":"Nature Biotechnol"},{"key":"60_CR26","volume-title":"AlgaeBase","author":"MD Guiry","year":"2015","unstructured":"Guiry MD, Guiry GM. AlgaeBase. Galway: National University of Ireland; 2015. http:\/\/www.algaebase.org . Accessed 30 Nov 2015."},{"key":"60_CR27","unstructured":"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."},{"key":"60_CR28","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1186\/1756-0500-3-175","volume":"3","author":"Z Xiang","year":"2010","unstructured":"Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. OntoFox: web-based support for ontology reuse. BMC Res Notes. 2010;3:175.","journal-title":"BMC Res Notes"},{"key":"60_CR29","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1002\/cfg.496","volume":"6","author":"P Jaiswal","year":"2005","unstructured":"Jaiswal P, Avraham S, Ilic K, Kellogg EA, McCouch S, Pujar A, et al. Plant ontology (PO): a controlled vocabulary of plant structures and growth stages. Comp Funct Genomics. 2005;6:388\u201397.","journal-title":"Comp Funct Genomics"},{"key":"60_CR30","doi-asserted-by":"crossref","unstructured":"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.","DOI":"10.1186\/gb-2005-6-5-r46"},{"key":"60_CR31","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1186\/2041-1480-1-S1-S7","volume":"1","author":"RR Brinkman","year":"2010","unstructured":"Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, et al. Modeling biomedical experimental processes with OBI. J Biomed Semant. 2010;1:S7.","journal-title":"J Biomed Semant"},{"key":"60_CR32","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1186\/1471-2105-11-441","volume":"11","author":"R Hoehndorf","year":"2010","unstructured":"Hoehndorf R, Oellrich A, Dumontier M, Kelso J, Rebholz-Schuhmann D, Herre H. Relations as patterns: bridging the gap between OBO and OWL. BMC Bioinformatics. 2010;11:441.","journal-title":"BMC Bioinformatics"},{"key":"60_CR33","doi-asserted-by":"crossref","unstructured":"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.","DOI":"10.1186\/1471-2105-12-6"},{"key":"60_CR34","doi-asserted-by":"crossref","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.","journal-title":"Genome Biol"},{"key":"60_CR35","doi-asserted-by":"crossref","first-page":"D8","DOI":"10.1093\/nar\/gks1189","volume":"41","author":"A Acland","year":"2013","unstructured":"Acland A, Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, et al. Database resources of the National Center for Biotechnology Information. Nuc Acids Res. 2013;41:D8\u2013D20.","journal-title":"Nuc Acids Res"},{"key":"60_CR36","doi-asserted-by":"crossref","unstructured":"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.","DOI":"10.1186\/2041-1480-5-34"},{"key":"60_CR37","unstructured":"Chemical Methods Ontology. http:\/\/obofoundry.org\/ontology\/chmo.html . Accessed 30 Nov 2015."},{"key":"60_CR38","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.jbi.2010.03.012","volume":"44","author":"P Topalis","year":"2011","unstructured":"Topalis P, Dialynas E, Mitraka E, Deligianni E, Siden-Kiamos I, Louis C. A set of ontologies to drive tools for the control of vector-borne diseases. J Biomed Inform. 2011;44:42\u20137.","journal-title":"J Biomed Inform"},{"key":"60_CR39","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/2041-1480-4-43","volume":"4","author":"PL Buttigieg","year":"2013","unstructured":"Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE. The Environment Ontology: contextualising biological and biomedical entities. J Biomed Semant. 2013;4:43.","journal-title":"J Biomed Semant"},{"key":"60_CR40","unstructured":"Gene Ontology Consortium, Ontology Structure. http:\/\/geneontology.org\/page\/ontology-structure . Accessed 30 Nov 2015."},{"key":"60_CR41","unstructured":"Purl address for MicrO. http:\/\/purl.obolibrary.org\/obo\/MicrO.owl . Accessed 1 Dec 2015."},{"key":"60_CR42","unstructured":"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."},{"key":"60_CR43","unstructured":"The OBO Foundry - prokaryotic phenotypic and metabolic characters. http:\/\/www.obofoundry.org\/ontology\/micro.html . Accessed 30 Nov 2015."},{"key":"60_CR44","unstructured":"Creative Commons, Attribution 2.0 Generic. http:\/\/creativecommons.org\/licenses\/by\/2.0 . Accessed 30 Nov 2015."},{"key":"60_CR45","doi-asserted-by":"crossref","unstructured":"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\u2013media pairings. Nat Commun. 2015;6:8493.","DOI":"10.1038\/ncomms9493"},{"key":"60_CR46","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1007\/978-1-4419-1327-2_19","volume-title":"Infectious Disease Informatics","author":"LG Cowell","year":"2010","unstructured":"Cowell LG, Smith B. Infectious Disease Ontology. In: Sintchenko V, editor. Infectious Disease Informatics. New York: Springer; 2010. p. 373\u201395."},{"key":"60_CR47","doi-asserted-by":"crossref","unstructured":"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\u20136.","DOI":"10.1093\/nar\/gkr972"},{"key":"60_CR48","doi-asserted-by":"crossref","first-page":"D1071","DOI":"10.1093\/nar\/gku1011","volume":"43","author":"WA Kibbe","year":"2015","unstructured":"Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, et al. Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nuc Acids Res. 2015;43:D1071\u20138.","journal-title":"Nuc Acids Res"},{"key":"60_CR49","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1016\/j.tree.2007.03.013","volume":"22","author":"PM Mabee","year":"2007","unstructured":"Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. 2007;22:345\u201350.","journal-title":"Trends Ecol Evol"},{"key":"60_CR50","doi-asserted-by":"crossref","first-page":"e1002033","DOI":"10.1371\/journal.pbio.1002033","volume":"13","author":"AR Deans","year":"2015","unstructured":"Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, et al. Finding our way through phenotypes. PLoS Biol. 2015;13:e1002033.","journal-title":"PLoS Biol"},{"key":"60_CR51","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1093\/sysbio\/syv031","volume":"64","author":"TA Dececchi","year":"2015","unstructured":"Dececchi TA, Balhoff JP, Lapp H, Mabee PM. Toward synthesizing our knowledge of morphology: Using ontologies and machine reasoning to extract presence\/absence evolutionary phenotypes across studies. Syst Biol. 2015;64:936\u201352.","journal-title":"Syst Biol"}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-016-0060-6","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,24]],"date-time":"2017-06-24T10:56:01Z","timestamp":1498301761000},"score":1,"resource":{"primary":{"URL":"http:\/\/jbiomedsem.biomedcentral.com\/articles\/10.1186\/s13326-016-0060-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,4,12]]},"references-count":51,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2016,12]]}},"alternative-id":["60"],"URL":"https:\/\/doi.org\/10.1186\/s13326-016-0060-6","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,4,12]]},"article-number":"18"}}