TypOn: The microbial typing ontology

Journal of Biomedical Semantics

Volumn 5, Issue 1, 2014, Pages

  Vaz, Cátia ^a,b   Francisco, Alexandre P ^a,c   Silva, Mickael ^d   Jolley, Keith A ^e   Bray, James E ^e   Pouseele, Hannes ^f   Rothganger, Joerg ^g   Ramirez, Mário ^d   Carriço, João A ^d  

^a INESC ID   (Portugal)

^b INSTITUTO SUPERIOR DE ENGENHARIA DE LISBOA   (Portugal)

^c INSTITUTO SUPERIOR TÉCNICO   (Portugal)

^d INSTITUTO DE MEDICINA MOLECULAR   (Portugal)

^e UNIVERSITY OF OXFORD   (United Kingdom)

^f Applied Maths NV   (Belgium)

^g Ridom GmbH   (Germany)

Author keywords

Knowledge representation; Microbial typing methods; Ontology

Indexed keywords

EID: 84927935396     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-5-43     Document Type: Article

References (37)

1. Sá-Leão R, Pinto F, Aguiar S, Nunes S, Carriço JA, Frazão N, Gonçalves-Sousa N, Melo-Cristino J, de Lencastre H, Ramirez M. Analysis of invasiveness of pneumococcal serotypes and clones circulating in portugal before widespread use of conjugate vaccines reveals heterogeneous behavior of clones expressing the same serotype. J Clin Microbiol 2011, 49(1):1369-1375. 3122870, 21270219.
2. Struelens MJ. Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems. Clin Microbiol Infect 1996, 2(1):2-11. 10.1111/j.1469-0691.1996.tb00193.x, 11866804.
3. Brueggemann AB, Griffiths DT, Meats E, Peto T, Crook DW, Spratt BG. Clonal relationships between invasive and carriageStreptococcus pneumoniae, and serotype- and clone-specific differences in invasive disease potential. J Infect Dis 2003, 187(9):1424-1432. 10.1086/374624, 12717624.
4. Allardet-Servent A, Bouziges N, Carles-Nurit MJ, Bourg G, Gouby A, Ramuz M. Use of low-frequency-cleavage restriction endonucleases for DNA analysis in epidemiological investigations of nosocomial bacterial infections. J Clin Microbiol 1989, 27(9):2057-2061. 267738, 2550517.
5. Carriço JA, Sabat AJ, Friedrich AW, Ramirez M, on behalf of the E. Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution. Euro Surveill 2013, 18(4):20382.
6. Almeida J, Tiple J, Ramirez M, Melo-Cristino J, Vaz C, Francisco AP, Carriço JA. An ontology and a rest api for sequence based microbial typing data. In JBI'2010. Lecture Notes in Computer Science, vol. 6620. Berlin Heidelberg: Springer; 2012:21-28.
7. Sabat AJ, Budimir A, Nashev D, Sa-Leao R, van Dijl J, Laurent F, Grundmann H, Friedrich AW. Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro Surveill 2013, 18(4):20380.
8. Spratt BG. Multilocus sequence typing: molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the internet. Curr Opin Microbiol 1999, 2(3):312-316. 10.1016/S1369-5274(99)80054-X, 10383857.
9. Maiden MC, Bygraves JA, Feil EJ, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 1998, 95(6):3140-3145. 10.1073/pnas.95.6.3140, 19708, 9501229.
10. MLST: Multi Locus Sequence Typing. [http://www.mlst.net], Imperial College of London.
11. PubMLST. [http://pubmlst.org/], University of Oxford (UK).
12. Institut Pasteur MLST Databases. [http://www.pasteur.fr/mlst/], Pasteur Institute.
13. Harmsen D, Claus H, Witte W, Rothgänger J, Claus H, Turnwald D,. Vogel U Typing of methicillin-resistantStaphylococcus aureus in a university hospital setting by using novel software for spa repeat determination and database management. J Clin Microbiol 2003, 41(12):5442-5448. 10.1128/JCM.41.12.5442-5448.2003, 309029, 14662923, Vogel U.
14. Boucher HW, Corey GR. Epidemiology of methicillin-resistant Staphylococcus aureus. Clin Infect Dis 2008, 46(Suppl 5):344-349.
15. Lindstedt B-A. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 2005, 26(13):2567-2582. 10.1002/elps.200500096, 15937984.
16. Jolley KA, Maiden MCJ. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010, 11:595. 10.1186/1471-2105-11-595, 3004885, 21143983.
17. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ, Maiden MCJ. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 2012, 158(Pt 4):1005-1015. 3492749,3492749, 22282518.
18. Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, von Gottberg A, Song J-H, Ko KS, Pichon B, Baker S, Parry CM, Lambertsen LM, Shahinas D, Pillai DR, Mitchell TJ, Dougan G, Tomasz A, Klugman KP, Parkhill J, Hanage WP, Bentley SD. Rapid pneumococcal evolution in response to clinical interventions. Science 2011, 331(6016):430-434. 10.1126/science.1198545, 3648787, 21273480.
19. Harris SR, Feil EJ, Quail MA, Nickerson EK, Chantratita N, Gardete S, Tavares A, Day N, Lindsay JA, Edgeworth JD, de Lencastre H, Parkhill J, Peacock SJ, Bentley SD,. Holden MT G Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010, 327(5964):469-474. 10.1126/science.1182395, 2821690, 20093474, Holden MT G.
20. Bittner T, Smith B. Normalizing medical ontologies using basic formal ontology. Kooperative Versorgung, Vernetzte Forschung, Ubiquitäre Information (Proceedings of GMDS Innsbruck, 26-30 September 2004) 2004, 199-201. Niebüll: Videel OHG.
21. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M. The sequence ontology: a tool for the unification of genome annotations. Genome Biol 2005, 6(5):44.
22. Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE,. the ENVO Consortium The environment ontology: contextualising biological and biomedical entities. J Biomed Semant 2013, 4:43. the ENVO Consortium.
23. Peters B,. the OBI Consortium Ontology for biomedical investigations. International Conference on Biomedical Ontology (ICBO 2009) 2009. Available from Nature Precedings [http://dx.doi.org/10.1038/npre.2009.3623.1], the OBI Consortium.
24. Uniprot Core Ontology. [http://purl.uniprot.org/core/].
25. The friend of a friend(foaf) project. [http://www.foaf-project.org/].
26. The DBpedia Ontology. [http://wiki.dbpedia.org/Ontology].
27. Redaschi N,. UniProt Consortium UniProt in RDF: Tackling data integration and distributed annotation with the semantic web. 3rd International Biocuration Conference 2009. Available from Nature Precedings [http://dx.doi.org/10.1038/npre.2009.3193.1], UniProt Consortium.
28. Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone S-A, Soldatova LN, Stoeckert CJ, Turner JA, Zheng J,. the OBI Consortium Modeling biomedical experimental processes with OBI. J Biomed Semant 2010, 1(Suppl 1):7. the OBI Consortium.
29. Bizer C, Lehmann J, Kobilarov G, Auer S, Becker C, Cyganiak R, Hellmann S. DBpedia - a crystallization point for the web of data. Web Semant Sci Serv Agents World Wide Web 2009, 7(3):154-165.
30. Web Access Control. [http://www.w3.org/wiki/WebAccessControl].
31. Dumbill E. Support online communities with foaf: How the friend-of-a-friend vocabulary addresses issues of accountability and privacy. 2002. IBM's XML Watch, [http://web.archive.org/web/20070226182529/http://www-128.ibm.com/developerworks/xml/library/x-foaf2.html].
32. Dumbill E. Tracking provenance of rdf data. 2003. IBM's XML Watch, [http://web.archive.org/web/20050428083208/http://www-106.ibm.com/developerworks/xml/library/x-rdfprov.html].
33. Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. Ontofox: web-based support for ontology reuse. BMC Res notes 2010, 3(1):175. 10.1186/1756-0500-3-175, 2911465, 20569493.
34. Beckett D, Berners-Lee T, Prud'hommeaux E, Carothers G. Turtle: Terse RDF Triple Language. 2012. [http://www.w3.org/TR/2012/WD-turtle-20120710/].
35. Bizer C, Seaborne A. D2RQ-treating non-RDF databases as virtual RDF graphs. Proceedings of the 3rd International Semantic Web Conference (ISWC2004) 2004, Hiroshima: Springer.
36. Bizer C, Cyganiak R, Garbers G, Maresch O, Becker C. The D2RQ Platform v0. 7-Treating Non-RDF Relational Databases as Virtual RDF Graphs. 2009. User Manual and Language Specification [http://wifo5-03.informatik.uni-mannheim.de/bizer/d2rq/spec/20090810/].
37. Maiden MCJ, van Rensburg MJJ, Bray JE, Earle SG, Ford SA, Jolley KA, McCarthy ND. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol 2013, 11(10):728-736. 10.1038/nrmicro3093, 3980634, 23979428.