{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T06:35:05Z","timestamp":1787639705909,"version":"build-2736575974"},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2014,11,30]],"date-time":"2014-11-30T00:00:00Z","timestamp":1417305600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Microbiol"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/s12866-014-0294-3","type":"journal-article","created":{"date-parts":[[2014,11,29]],"date-time":"2014-11-29T14:01:57Z","timestamp":1417269717000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["An ontology for microbial phenotypes"],"prefix":"10.1186","volume":"14","author":[{"given":"Marcus C","family":"Chibucos","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrienne E","family":"Zweifel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan C","family":"Herrera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William","family":"Meza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shabnam","family":"Eslamfam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Uetz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah A","family":"Siegele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James C","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle G","family":"Giglio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2014,11,30]]},"reference":[{"issue":"1","key":"294_CR1","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/j.cell.2010.11.052","volume":"144","author":"RJ Nichols","year":"2011","unstructured":"Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA: Phenotypic landscape of a bacterial cell. Cell. 2011, 144 (1): 143-156. 10.1016\/j.cell.2010.11.052.","journal-title":"Cell"},{"issue":"6894","key":"294_CR2","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1038\/418244a","volume":"418","author":"GJ Hannon","year":"2002","unstructured":"Hannon GJ: RNA interference. Nature. 2002, 418 (6894): 244-251. 10.1038\/418244a.","journal-title":"Nature"},{"key":"294_CR3","volume-title":"Bergey\u2019s Manual of Determinative Microbiology","author":"JG Holt","year":"1994","unstructured":"Holt JG: Bergey\u2019s Manual of Determinative Microbiology. 1994, Lippincott Williams & Wilkins, Hagerstown, MD, 9","edition":"9"},{"issue":"11","key":"294_CR4","doi-asserted-by":"crossref","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 SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007, 25 (11): 1251-1255. 10.1038\/nbt1346.","journal-title":"Nat Biotechnol"},{"key":"294_CR5","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1186\/1471-2164-9-495","volume":"9","author":"EJ Blom","year":"2008","unstructured":"Blom EJ, Breitling R, Hofstede KJ, Roerdink JB, Van Hijum SA, Kuipers OP: Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources. BMC Genomics. 2008, 9: 495-10.1186\/1471-2164-9-495.","journal-title":"BMC Genomics"},{"issue":"10","key":"294_CR6","doi-asserted-by":"crossref","first-page":"e1000160","DOI":"10.1371\/journal.pcbi.1000160","volume":"4","author":"M Punta","year":"2008","unstructured":"Punta M, Ofran Y: The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PLoS Comput Biol. 2008, 4 (10): e1000160-10.1371\/journal.pcbi.1000160.","journal-title":"PLoS Comput Biol"},{"key":"294_CR7","doi-asserted-by":"crossref","first-page":"bau075","DOI":"10.1093\/database\/bau075","volume":"2014","author":"MC Chibucos","year":"2014","unstructured":"Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M: Standardized description of scientific evidence using the Evidence Ontology (ECO). Database. 2014, 2014: bau075-10.1093\/database\/bau075.","journal-title":"Database"},{"issue":"12","key":"294_CR8","doi-asserted-by":"crossref","first-page":"1905","DOI":"10.1084\/jem.20050112","volume":"201","author":"E Bille","year":"2005","unstructured":"Bille E, Zahar JR, Perrin A, Morelle S, Kriz P, Jolley KA, Maiden MC, Dervin C, Nassif X, Tinsley CR: A chromosomally integrated bacteriophage in invasive meningococci. J Exp Med. 2005, 201 (12): 1905-1913. 10.1084\/jem.20050112.","journal-title":"J Exp Med"},{"issue":"3","key":"294_CR9","doi-asserted-by":"crossref","first-page":"R29","DOI":"10.1186\/gb-2005-6-3-r29","volume":"6","author":"TF Hayamizu","year":"2005","unstructured":"Hayamizu TF, Mangan M, Corradi JP, Kadin JA, Ringwald M: The adult mouse anatomical dictionary: a tool for annotating and integrating data. Genome Biol. 2005, 6 (3): R29-10.1186\/gb-2005-6-3-r29.","journal-title":"Genome Biol"},{"issue":"Database issue","key":"294_CR10","doi-asserted-by":"crossref","first-page":"D484","DOI":"10.1093\/nar\/gkj068","volume":"34","author":"G Grumbling","year":"2006","unstructured":"Grumbling G, Strelets V: FlyBase: anatomical data, images and queries. Nucleic Acids Res. 2006, 34 (Database issue): D484-D488. 10.1093\/nar\/gkj068.","journal-title":"Nucleic Acids Res"},{"key":"294_CR11","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/1471-2105-12-32","volume":"12","author":"G Schindelman","year":"2011","unstructured":"Schindelman G, Fernandes JS, Bastiani CA, Yook K, Sternberg PW: Worm phenotype ontology: integrating phenotype data within and beyond the C. Elegans community. BMC Bioinformatics. 2011, 12: 32-10.1186\/1471-2105-12-32.","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"294_CR12","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/2041-1480-5-12","volume":"5","author":"CE Van Slyke","year":"2014","unstructured":"Van Slyke CE, Bradford YM, Westerfield M, Haendel MA: The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. J Biomedical Semantics. 2014, 5 (1): 12-10.1186\/2041-1480-5-12.","journal-title":"J Biomedical Semantics"},{"issue":"2","key":"294_CR13","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1104\/pp.106.092825","volume":"143","author":"K Ilic","year":"2007","unstructured":"Ilic K, Kellogg EA, Jaiswal P, Zapata F, Stevens PF, Vincent LP, Avraham S, Reiser L, Pujar A, Sachs MM, Whitman NT, McCouch SR, Schaeffer ML, Ware DH, Stein LD, Rhee SY: The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol. 2007, 143 (2): 587-599. 10.1104\/pp.106.092825.","journal-title":"Plant Physiol"},{"issue":"13","key":"294_CR14","doi-asserted-by":"crossref","first-page":"1671","DOI":"10.1093\/bioinformatics\/btt266","volume":"29","author":"MA Harris","year":"2013","unstructured":"Harris MA, Lock A, Bahler J, Oliver SG, Wood V: FYPO: the fission yeast phenotype ontology. Bioinformatics. 2013, 29 (13): 1671-1678. 10.1093\/bioinformatics\/btt266.","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"294_CR15","doi-asserted-by":"crossref","first-page":"D433","DOI":"10.1093\/nar\/gkp917","volume":"38","author":"SR Engel","year":"2010","unstructured":"Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM:Saccharomyces genome database provides mutant phenotype data. Nucleic Acids Res. 2010, 38 (Database issue): D433-D436. 10.1093\/nar\/gkp917.","journal-title":"Nucleic Acids Res"},{"key":"294_CR16","unstructured":"Microbial Phenotypes Wiki. [ http:\/\/microbialphenotypes.org ]"},{"key":"294_CR17","unstructured":"Ontology of Microbial Phenotypes open source development site. [ http:\/\/purl.obolibrary.org\/obo\/omp\/devel\/ ]"},{"issue":"1","key":"294_CR18","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/0092-8674(81)90272-5","volume":"23","author":"SD Emr","year":"1981","unstructured":"Emr SD, Hanley-Way S, Silhavy TJ: Suppressor mutations that restore export of a protein with a defective signal sequence. Cell. 1981, 23 (1): 79-88. 10.1016\/0092-8674(81)90272-5.","journal-title":"Cell"},{"issue":"3","key":"294_CR19","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1128\/MCB.11.3.1295","volume":"11","author":"A Bender","year":"1991","unstructured":"Bender A, Pringle JR: Use of a screen for synthetic lethal and multicopy suppressee mutants to identify two new genes involved in morphogenesis in Saccharomyces cerevisiae. Mol Cell Biol. 1991, 11 (3): 1295-1305.","journal-title":"Mol Cell Biol"},{"issue":"7137","key":"294_CR20","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1038\/nature05649","volume":"446","author":"SR Collins","year":"2007","unstructured":"Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ: Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature. 2007, 446 (7137): 806-810. 10.1038\/nature05649.","journal-title":"Nature"},{"issue":"9","key":"294_CR21","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1038\/nmeth.1240","volume":"5","author":"A Typas","year":"2008","unstructured":"Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, Lim B, Braberg H, Yamamoto N, Takeuchi R, Wanner BL, Mori H, Weissman JS, Krogan NJ, Gross CA: High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods. 2008, 5 (9): 781-787. 10.1038\/nmeth.1240.","journal-title":"Nat Methods"},{"issue":"9","key":"294_CR22","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1038\/nmeth.1239","volume":"5","author":"G Butland","year":"2008","unstructured":"Butland G, Babu M, Diaz-Mejia JJ, Bohdana F, Phanse S, Gold B, Yang W, Li J, Gagarinova AG, Pogoutse O, Mori H, Wanner BL, Lo H, Wasniewski J, Christopolous C, Ali M, Venn P, Safavi-Naini A, Sourour N, Caron S, Choi JY, Laigle L, Nazarians-Armavil A, Deshpande A, Joe S, Datsenko KA, Yamamoto N, Andrews BJ, Boone C, Ding H: eSGA: Ec coli synthetic genetic array analysis. Nat Methods. 2008, 5 (9): 789-795. 10.1038\/nmeth.1239.","journal-title":"Nat Methods"},{"issue":"3\u20134","key":"294_CR23","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1016\/j.ijmedinf.2005.07.015","volume":"75","author":"J Simon","year":"2006","unstructured":"Simon J, Dos Santos M, Fielding J, Smith B: Formal ontology for natural language processing and the integration of biomedical databases. Int J Med Inform. 2006, 75 (3\u20134): 224-231. 10.1016\/j.ijmedinf.2005.07.015.","journal-title":"Int J Med Inform"},{"issue":"1","key":"294_CR24","doi-asserted-by":"crossref","first-page":"R8","DOI":"10.1186\/gb-2004-6-1-r8","volume":"6","author":"GV Gkoutos","year":"2005","unstructured":"Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Using ontologies to describe mouse phenotypes. Genome Biol. 2005, 6 (1): R8-10.1186\/gb-2004-6-1-r8.","journal-title":"Genome Biol"},{"key":"294_CR25","first-page":"20","volume":"102","author":"P Grenon","year":"2004","unstructured":"Grenon P, Smith B, Goldberg L: Biodynamic ontology: applying BFO in the biomedical domain. Stud Health Technol Inform. 2004, 102: 20-38.","journal-title":"Stud Health Technol Inform"},{"key":"294_CR26","doi-asserted-by":"crossref","first-page":"D530","DOI":"10.1093\/nar\/gks1050","volume":"41","author":"JA Blake","year":"2013","unstructured":"Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Gene Ontology Consortium: Gene Ontology annotations and resources. Nucleic Acids Res. 2013, 41 (Database issue): D530-D535.","journal-title":"Nucleic Acids Res"},{"key":"294_CR27","unstructured":"AmiGO2 - GO:0044464 cell part. [ http:\/\/amigo.geneontology.org\/amigo\/term\/GO:0044464 ]"},{"issue":"19","key":"294_CR28","doi-asserted-by":"crossref","first-page":"12585","DOI":"10.1074\/jbc.X800017200","volume":"284","author":"J Beckwith","year":"2009","unstructured":"Beckwith J: Genetic suppressors and recovery of repressed biochemical memory. J Biol Chem. 2009, 284 (19): 12585-12592. 10.1074\/jbc.X800017200.","journal-title":"J Biol Chem"},{"key":"294_CR29","unstructured":"Introduction to Cross Products. [ http:\/\/oboedit.org\/docs\/html\/Introduction_to_Cross_Products.htm ]"},{"issue":"5","key":"294_CR30","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1186\/gb-2005-6-5-r46","volume":"6","author":"B Smith","year":"2005","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 (5): R46-10.1186\/gb-2005-6-5-r46.","journal-title":"Genome Biol"},{"issue":"1","key":"294_CR31","doi-asserted-by":"crossref","first-page":"R2","DOI":"10.1186\/gb-2010-11-1-r2","volume":"11","author":"CJ Mungall","year":"2010","unstructured":"Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M: Integrating phenotype ontologies across multiple species. Genome Biol. 2010, 11 (1): R2-10.1186\/gb-2010-11-1-r2.","journal-title":"Genome Biol"},{"key":"294_CR32","doi-asserted-by":"crossref","first-page":"103","DOI":"10.3389\/fmicb.2013.00103","volume":"4","author":"J Olivares","year":"2013","unstructured":"Olivares J, Bernardini A, Garcia-Leon G, Corona F, B Sanchez M, Martinez JL: The intrinsic resistome of bacterial pathogens. Front Microbiol. 2013, 4: 103-10.3389\/fmicb.2013.00103.","journal-title":"Front Microbiol"},{"key":"294_CR33","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.copbio.2014.02.006","volume":"28C","author":"CP Long","year":"2014","unstructured":"Long CP, Antoniewicz MR: Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook. Curr Opin Biotechnol. 2014, 28C: 127-133. 10.1016\/j.copbio.2014.02.006.","journal-title":"Curr Opin Biotechnol"},{"issue":"Web Server issu","key":"294_CR34","doi-asserted-by":"crossref","first-page":"W170","DOI":"10.1093\/nar\/gkp440","volume":"37","author":"NF Noy","year":"2009","unstructured":"Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA: BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009, 37 (Web Server issue): W170-W173. 10.1093\/nar\/gkp440.","journal-title":"Nucleic Acids Res"},{"key":"294_CR35","unstructured":"Ontology of Microbial Phenotypes issue tracker. [ http:\/\/purl.obolibrary.org\/obo\/omp\/devel\/omp-term-request ]"},{"issue":"16","key":"294_CR36","doi-asserted-by":"crossref","first-page":"2198","DOI":"10.1093\/bioinformatics\/btm112","volume":"23","author":"J Day-Richter","year":"2007","unstructured":"Day-Richter J, Harris MA, Haendel M, Working Group Gene Ontology OBO-Edit, Lewis S: OBO-Edit\u2013an ontology editor for biologists. Bioinformatics. 2007, 23 (16): 2198-2200. 10.1093\/bioinformatics\/btm112.","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"294_CR37","doi-asserted-by":"crossref","first-page":"D1262","DOI":"10.1093\/nar\/gkr907","volume":"40","author":"DP Renfro","year":"2012","unstructured":"Renfro DP, McIntosh BK, Venkatraman A, Siegele DA, Hu JC: GONUTS: the gene ontology normal usage tracking system. Nucleic Acids Res. 2012, 40 (Database issue): D1262-D1269. 10.1093\/nar\/gkr907.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"294_CR38","doi-asserted-by":"crossref","first-page":"D700","DOI":"10.1093\/nar\/gkr1029","volume":"40","author":"JM Cherry","year":"2012","unstructured":"Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED:Saccharomyces genome database: the genomics resource of budding yeast. Nucleic Acids Res. 2012, 40 (Database issue): D700-D705. 10.1093\/nar\/gkr1029.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"294_CR39","doi-asserted-by":"crossref","first-page":"D695","DOI":"10.1093\/nar\/gkr853","volume":"40","author":"V Wood","year":"2012","unstructured":"Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bahler J, Kersey PJ, Oliver SG: PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res. 2012, 40 (Database issue): D695-D699. 10.1093\/nar\/gkr853.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"294_CR40","doi-asserted-by":"crossref","first-page":"1300","DOI":"10.1073\/pnas.64.4.1300","volume":"64","author":"GL Hazelbauer","year":"1969","unstructured":"Hazelbauer GL, Mesibov RE, Adler J:Escherichia coli mutants defective in chemotaxis toward specific chemicals. Proc Natl Acad Sci USA. 1969, 64 (4): 1300-1307. 10.1073\/pnas.64.4.1300.","journal-title":"Proc Natl Acad Sci USA"}],"container-title":["BMC Microbiology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12866-014-0294-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-014-0294-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-014-0294-3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,2,26]],"date-time":"2019-02-26T12:43:26Z","timestamp":1551185006000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcmicrobiol.biomedcentral.com\/articles\/10.1186\/s12866-014-0294-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,30]]},"references-count":40,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["294"],"URL":"https:\/\/doi.org\/10.1186\/s12866-014-0294-3","relation":{},"ISSN":["1471-2180"],"issn-type":[{"value":"1471-2180","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,30]]},"article-number":"294"}}