{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T05:00:12Z","timestamp":1780462812157,"version":"3.54.1"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,7,15]],"date-time":"2019-07-15T00:00:00Z","timestamp":1563148800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,7,15]],"date-time":"2019-07-15T00:00:00Z","timestamp":1563148800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM089636"],"award-info":[{"award-number":["GM089636"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"published-print":{"date-parts":[[2019,12]]},"DOI":"10.1186\/s13326-019-0205-5","type":"journal-article","created":{"date-parts":[[2019,7,15]],"date-time":"2019-07-15T14:08:54Z","timestamp":1563199734000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Phenotype annotation with the ontology of microbial phenotypes (OMP)"],"prefix":"10.1186","volume":"10","author":[{"given":"Deborah A.","family":"Siegele","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra A.","family":"LaBonte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter I-Fan","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus C.","family":"Chibucos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suvarna","family":"Nandendla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle G.","family":"Giglio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9016-2684","authenticated-orcid":false,"given":"James C.","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,7,15]]},"reference":[{"issue":"3","key":"205_CR1","doi-asserted-by":"publisher","first-page":"1478","DOI":"10.1111\/brv.12405","volume":"93","author":"Marketa Zimova","year":"2018","unstructured":"Zimova M, Hackl\u00e4nder K, Good JM, Melo-Ferreira J, Alves PC, Mills LS. Function and underlying mechanisms of seasonal colour moulting in mammals and birds: what keeps them changing in a warming world? Biol Rev Camb Philos Soc. 2018;93(3):1478\u201398.","journal-title":"Biological Reviews"},{"key":"205_CR2","doi-asserted-by":"crossref","unstructured":"Kroos L. The Bacillus and Myxococcus developmental networks and their transcriptional regulators. Annu Rev Genet. 2007;41:13\u201339.","DOI":"10.1146\/annurev.genet.41.110306.130400"},{"issue":"23","key":"205_CR3","doi-asserted-by":"publisher","first-page":"3683","DOI":"10.1016\/j.jmb.2015.07.025","volume":"427","author":"RM Harshey","year":"2015","unstructured":"Harshey RM, Partridge JD. Shelter in a swarm. J Mol Biol. 2015;427(23):3683\u201394.","journal-title":"J Mol Biol"},{"issue":"1\u20132","key":"205_CR4","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1159\/000077866","volume":"7","author":"LL McCarter","year":"2004","unstructured":"McCarter LL. Dual flagellar systems enable motility under different circumstances. J Mol Microbiol Biotechnol. 2004;7(1\u20132):18\u201329.","journal-title":"J Mol Microbiol Biotechnol"},{"key":"205_CR5","doi-asserted-by":"publisher","first-page":"294","DOI":"10.1186\/s12866-014-0294-3","volume":"14","author":"MC Chibucos","year":"2014","unstructured":"Chibucos MC, Zweifel AE, Herrera JC, Meza W, Eslamfam S, Uetz P, Siegele DA, Hu JC, Giglio MG. An ontology for microbial phenotypes. BMC Microbiol. 2014;14:294.","journal-title":"BMC Microbiol"},{"issue":"6896","key":"205_CR6","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1038\/nature00935","volume":"418","author":"Guri Giaever","year":"2002","unstructured":"Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002;418(6896):387\u201391.","journal-title":"Nature"},{"issue":"1","key":"205_CR7","doi-asserted-by":"publisher","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, et al. Phenotypic landscape of a bacterial cell. Cell. 2011;144(1):143\u201356.","journal-title":"Cell"},{"issue":"6","key":"205_CR8","doi-asserted-by":"publisher","first-page":"1493","DOI":"10.1016\/j.cell.2016.05.003","volume":"165","author":"JM Peters","year":"2016","unstructured":"Peters JM, Colavin A, Shi H, Czarny TL, Larson MH, Wong S, Hawkins JS, Lu CHS, Koo BM, Marta E, et al. A comprehensive, CRISPR-based functional analysis of essential genes in Bacteria. Cell. 2016;165(6):1493\u2013506.","journal-title":"Cell"},{"issue":"1","key":"205_CR9","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1186\/2041-1480-4-43","volume":"4","author":"Pier Buttigieg","year":"2013","unstructured":"Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE, ENVO Consortium. The environment ontology: contextualising biological and biomedical entities. J Biomed Semantics. 2013;4(1):43.","journal-title":"Journal of Biomedical Semantics"},{"issue":"1","key":"205_CR10","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1186\/s13326-016-0097-6","volume":"7","author":"PL Buttigieg","year":"2016","unstructured":"Buttigieg PL, Pafilis E, Lewis SE, Schildhauer MP, Walls RL, Mungall CJ. The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. J Biomed Semantics. 2016;7(1):57.","journal-title":"J Biomed Semantics"},{"issue":"1","key":"205_CR11","doi-asserted-by":"publisher","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.","journal-title":"Genome Biol"},{"issue":"5","key":"205_CR12","doi-asserted-by":"publisher","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.","journal-title":"Genome Biol"},{"issue":"D1","key":"205_CR13","doi-asserted-by":"publisher","first-page":"D1186","DOI":"10.1093\/nar\/gky1036","volume":"47","author":"M Giglio","year":"2019","unstructured":"Giglio M, Tauber R, Nadendla S, Munro J, Olley D, Ball S, Mitraka E, Schriml LM, Gaudet P, Hobbs ET, et al. ECO, the evidence & conclusion ontology: community standard for evidence information. Nucleic Acids Res. 2019;47(D1):D1186\u201394.","journal-title":"Nucleic Acids Res"},{"key":"205_CR14","unstructured":"Ontology of Microbial Phenotypes Wiki [\n                    https:\/\/microbialphenotypes.org\n                    \n                  ]."},{"issue":"Database","key":"205_CR15","doi-asserted-by":"publisher","first-page":"D433","DOI":"10.1093\/nar\/gkp917","volume":"38","author":"S. R. Engel","year":"2009","unstructured":"Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL et al: Saccharomyces genome database provides mutant phenotype data. Nucleic Acids Res 2010, 38(Database issue):D433\u2013D436.","journal-title":"Nucleic Acids Research"},{"issue":"13","key":"205_CR16","doi-asserted-by":"publisher","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\u20138.","journal-title":"Bioinformatics"},{"issue":"8","key":"205_CR17","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1002\/dvg.22867","volume":"53","author":"S Basu","year":"2015","unstructured":"Basu S, Fey P, Jimenez-Morales D, Dodson RJ, Chisholm RL. dictyBase 2015: expanding data and annotations in a new software environment. Genesis. 2015;53(8):523\u201334.","journal-title":"Genesis"},{"key":"205_CR18","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1186\/s13326-016-0060-6","volume":"7","author":"CE Blank","year":"2016","unstructured":"Blank CE, Cui H, Moore LR, Walls RL. MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. J Biomed Semantics. 2016;7:18.","journal-title":"J Biomed Semantics"},{"issue":"1","key":"205_CR19","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1186\/s12859-016-1396-8","volume":"17","author":"J Mao","year":"2016","unstructured":"Mao J, Moore LR, Blank CE, Wu EH, Ackerman M, Ranade S, Cui H. Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources. BMC Bioinformatics. 2016;17(1):528.","journal-title":"BMC Bioinformatics"},{"issue":"7","key":"205_CR20","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1056\/NEJM198802183180706","volume":"318","author":"GR Donowitz","year":"1988","unstructured":"Donowitz GR, Mandell GL. Beta-lactam antibiotics (1). N Engl J Med. 1988;318(7):419\u201326.","journal-title":"N Engl J Med"},{"issue":"8","key":"205_CR21","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1016\/S0966-842X(98)01317-1","volume":"6","author":"J Petrosino","year":"1998","unstructured":"Petrosino J, Cantu C 3rd, Palzkill T. Beta-lactamases: protein evolution in real time. Trends Microbiol. 1998;6(8):323\u20137.","journal-title":"Trends Microbiol"},{"key":"205_CR22","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1186\/1471-2105-15-155","volume":"15","author":"RP Huntley","year":"2014","unstructured":"Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, et al. A method for increasing expressivity of gene ontology annotations using a compositional approach. BMC Bioinformatics. 2014;15:155.","journal-title":"BMC Bioinformatics"},{"key":"205_CR23","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1007\/978-1-4939-3743-1_17","volume":"1446","author":"RP Huntley","year":"2017","unstructured":"Huntley RP, Lovering RC. Annotation Extensions. Methods Mol Biol. 2017;1446:233\u201343.","journal-title":"Methods Mol Biol"},{"issue":"1","key":"205_CR24","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.jbi.2010.02.002","volume":"44","author":"CJ Mungall","year":"2011","unstructured":"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 Inform. 2011;44(1):80\u20136.","journal-title":"J Biomed Inform"},{"key":"205_CR25","doi-asserted-by":"publisher","first-page":"160018","DOI":"10.1038\/sdata.2016.18","volume":"3","author":"MD Wilkinson","year":"2016","unstructured":"Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, et al. The FAIR guiding principles for scientific data management and stewardship. Sci Data. 2016;3:160018.","journal-title":"Sci Data"},{"key":"205_CR26","unstructured":"Gene Product Association Data File Format [\n                    http:\/\/geneontology.org\/docs\/gene-product-association-data-gpad-format\/\n                    \n                  ]."},{"key":"205_CR27","unstructured":"JSON-LD 1.1: A JSON-based Serialization for Linked Data [\n                    https:\/\/www.w3.org\/TR\/json-ld11\/\n                    \n                  ]."},{"key":"205_CR28","unstructured":"MediaWiki [\n                    https:\/\/mediawiki.org\n                    \n                  ]."},{"issue":"D1","key":"205_CR29","doi-asserted-by":"publisher","first-page":"D1262","DOI":"10.1093\/nar\/gkr907","volume":"40","author":"Daniel P. Renfro","year":"2011","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\u20139.","journal-title":"Nucleic Acids Research"},{"key":"205_CR30","unstructured":"OMPwiki Github Repository [\n                    https:\/\/github.com\/microbialphenotypes\/OMPwiki\n                    \n                  ]."},{"issue":"D1","key":"205_CR31","doi-asserted-by":"publisher","first-page":"D1270","DOI":"10.1093\/nar\/gkr880","volume":"40","author":"Brenley K. McIntosh","year":"2011","unstructured":"McIntosh BK, Renfro DP, Knapp GS, Lairikyengbam CR, Liles NM, Niu L, Supak AM, Venkatraman A, Zweifel AE, Siegele DA, et al. EcoliWiki: a wiki-based community resource for Escherichia coli. Nucleic Acids Res. 2012;40(Database issue):D1270\u20137.","journal-title":"Nucleic Acids Research"}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-019-0205-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s13326-019-0205-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-019-0205-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,7,13]],"date-time":"2020-07-13T23:26:48Z","timestamp":1594682808000},"score":1,"resource":{"primary":{"URL":"https:\/\/jbiomedsem.biomedcentral.com\/articles\/10.1186\/s13326-019-0205-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,7,15]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["205"],"URL":"https:\/\/doi.org\/10.1186\/s13326-019-0205-5","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,7,15]]},"assertion":[{"value":"18 September 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 June 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 July 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"13"}}