Robert David Stevens

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Robert Stevens
DrRobertDavidStevens.jpg
Robert Stevens
Born Robert David Stevens
(1965-02-11) 11 February 1965 (age 52)
Nationality British
Fields
Institutions University of Manchester
Alma mater
Thesis Principles for the design of auditory interfaces to present complex information to blind people (1996)
Doctoral advisor Alistair Edwards[5]
Doctoral students
Known for TAMBIS[24][25][26]
Website
www.cs.man.ac.uk/~stevensr
robertdavidstevens.wordpress.com
manchester.ac.uk/research/robert.d.stevens/

Robert David Stevens (born 1965) is a Professor of Bio-Health Informatics in the School of Computer Science at the University of Manchester.[27][28]

Education[edit]

Stevens gained his Bachelor of Science degree in Biochemistry from the University of Bristol in 1986,[29] a Master of Science degree in bioinformatics in 1991 and a DPhil in Computer Science in 1996, both from the University of York.[5]

Research[edit]

Stevens current research interests[4][30][31][32][33] are the construction of biological ontologies,[34][35] such as the Gene Ontology,[36][37][38][39] and the reconciliation of semantic heterogeneity[40] in bioinformatics.[41][42] This research has been funded by the Engineering and Physical Sciences Research Counci (EPSRC),[43][44] Biotechnology and Biological Sciences Research Council (BBSRC)[45] and the European Union.[12] Stevens has been Principal investigator for a range of research projects including Ondex,[46][47] ComparaGrid,[48] SWAT (Semantic Web Authoring Tool)[43] and the Ontogenesis Network.[43]

Career[edit]

Stevens served as Program Chair and co-organiser for the International Conference on Biomedical Ontology (ICBO) 2012[49] and co-founded the UK Ontology Network.[50] He has also participated in the Health care and Life Sciences Interest Group (HCLSIG) of the World Wide Web Consortium (W3C).[51] Stevens is currently on the editorial board of the Journal of Biomedical Semantics.[52] Stevens started as a lecturer, then became a senior lecturer, Reader and became a Professor in August 2013.

Teaching[edit]

Stevens teaches on several undergraduate and postgraduate courses on software engineering, databases, bioinformatics and runs introductory and advanced courses on the Web Ontology Language. He has also been the main doctoral advisor to five successful PhD students[6][9][11][13][16] and co-supervised two others.[21][22]

References[edit]

  1. ^ Field, D.; Garrity, G.; Gray, T.; Morrison, N.; Selengut, J.; Sterk, P.; Tatusova, T.; Thomson, N.; Allen, M. J.; Angiuoli, S. V.; Ashburner, M.; Axelrod, N.; Baldauf, S.; Ballard, S.; Boore, J.; Cochrane, G.; Cole, J.; Dawyndt, P.; De Vos, P.; Depamphilis, C.; Edwards, R.; Faruque, N.; Feldman, R.; Gilbert, J.; Gilna, P.; Glöckner, F. O.; Goldstein, P.; Guralnick, R.; Haft, D.; et al. (2008). "The minimum information about a genome sequence (MIGS) specification". Nature Biotechnology. 26 (5): 541–7. doi:10.1038/nbt1360. PMC 2409278Freely accessible. PMID 18464787. 
  2. ^ Goble, C.; Harper, S.; Stevens, R. (2000). "The travails of visually impaired web travellers". Proceedings of the eleventh ACM on Hypertext and hypermedia - HYPERTEXT '00 (PDF). p. 1. doi:10.1145/336296.336304. ISBN 1581132271. 
  3. ^ Stevens, Robert (2007). "Day in the life of a disabled(?) scientist: Sightless in Science" (PDF). The Biochemist. Retrieved 20 June 2013. 
  4. ^ a b Robert David Stevens's publications indexed by Google Scholar
  5. ^ a b Stevens, Robert David (1996). Principles for the design of auditory interfaces to present complex information to blind people (Ph.D. thesis). University of York. 
  6. ^ a b Egaña Aranguren, Mikel (2009). Role and application of ontology design patterns in bio-ontologies (PhD thesis). University of Manchester. 
  7. ^ Aranguren, M. E. A.; Antezana, E.; Kuiper, M.; Stevens, R. (2008). "Ontology Design Patterns for bio-ontologies: A case study on the Cell Cycle Ontology". BMC Bioinformatics. 9: S1. doi:10.1186/1471-2105-9-S5-S1. PMC 2367624Freely accessible. PMID 18460183. 
  8. ^ Aranguren, M.; Bechhofer, S.; Lord, P.; Sattler, U.; Stevens, R. (2007). "Understanding and using the meaning of statements in a bio-ontology: Recasting the Gene Ontology in OWL". BMC Bioinformatics. 8: 57. doi:10.1186/1471-2105-8-57. PMC 1819394Freely accessible. PMID 17311682. 
  9. ^ a b Brenchley, Rachel (2009). Towards automated annotation of protein phosphatases (PhD thesis). University of Manchester. 
  10. ^ Brenchley, R.; Tariq, H.; McElhinney, H.; Szoor, B.; Huxley-Jones, J.; Stevens, R.; Matthews, K.; Tabernero, L. (2007). "The TriTryp Phosphatome: Analysis of the protein phosphatase catalytic domains". BMC Genomics. 8: 434. doi:10.1186/1471-2164-8-434. PMC 2175518Freely accessible. PMID 18039372. 
  11. ^ a b Brown, Andrew J. (2007). Non-visual interaction with graphs (PhD thesis). University of Manchester. 
  12. ^ a b Duck, G.; Nenadic, G.; Brass, A.; Robertson, D. L.; Stevens, R. (2013). "BioNerDS: Exploring bioinformatics' database and software use through literature mining". BMC Bioinformatics. 14: 194. doi:10.1186/1471-2105-14-194. PMC 3693927Freely accessible. PMID 23768135. 
  13. ^ a b Fisher, Paul Ryan (2009). Towards a systematic approach to the large-scale analysis of genotype-phenotype correlations (PhD thesis). University of Manchester. 
  14. ^ Fisher, P.; Noyes, H.; Kemp, S.; Stevens, R.; Brass, A. (2009). "A Systematic Strategy for the Discovery of Candidate Genes Responsible for Phenotypic Variation". Cardiovascular Genomics. Methods in Molecular Biology. 573. pp. 329–345. doi:10.1007/978-1-60761-247-6_18. ISBN 978-1-60761-246-9. PMID 19763936. 
  15. ^ Fisher, P.; Hedeler, C.; Wolstencroft, K.; Hulme, H.; Noyes, H.; Kemp, S.; Stevens, R.; Brass, A. (2007). "A systematic strategy for large-scale analysis of genotype phenotype correlations: Identification of candidate genes involved in African trypanosomiasis". Nucleic Acids Research. 35 (16): 5625–5633. doi:10.1093/nar/gkm623. PMC 2018629Freely accessible. PMID 17709344. 
  16. ^ a b Hull, Duncan (2008). Semantic matching of bioinformatic web services (PhD thesis). University of Manchester. 
  17. ^ Hull, D.; Wolstencroft, K.; Stevens, R.; Goble, C. A.; Pocock, M. R.; Li, P.; Oinn, T. (2006). "Taverna: A tool for building and running workflows of services". Nucleic Acids Research. 34 (Web Server issue): W729–W732. doi:10.1093/nar/gkl320. PMC 1538887Freely accessible. PMID 16845108.  open access publication – free to read
  18. ^ Mikroyannidi, E.; Iannone, L.; Stevens, R.; Rector, A. (2011). "Inspecting Regularities in Ontology Design Using Clustering". The Semantic Web – ISWC 2011. Lecture Notes in Computer Science. 7031. p. 438. doi:10.1007/978-3-642-25073-6_28. ISBN 978-3-642-25072-9. 
  19. ^ Mikroyannidi, Eleni (2013). Detection of Syntactic and Semantic Detection of Syntactic and Semantic Regularities in Ontologies (PhD thesis). University of Manchester. 
  20. ^ Mikroyannidi, E.; Quesada-Martínez, M.; Tsarkov, D.; Fernández Breis, J. T. S.; Stevens, R.; Palmisano, I. (2014). "A Quality Assurance Workflow for Ontologies Based on Semantic Regularities". Knowledge Engineering and Knowledge Management. Lecture Notes in Computer Science. 8876. p. 288. doi:10.1007/978-3-319-13704-9_23. ISBN 978-3-319-13703-2. 
  21. ^ a b Yesilada, Yeliz (2005). Annotation and transformation of web pages to improve mobility for visually impaired users (Ph.D. thesis). University of Manchester. [dead link]
  22. ^ a b Zhao, Jun (2007). Conceptual model for e-science provenance (PDF) (PhD thesis). University of Manchester. Archived from the original (PDF) on October 6, 2012. 
  23. ^ Stevens, R.; Zhao, J.; Goble, C. (2007). "Using provenance to manage knowledge of in Silico experiments". Briefings in Bioinformatics. 8 (3): 183–194. doi:10.1093/bib/bbm015. PMID 17502335. 
  24. ^ Goble, C. A.; Stevens, R.; Ng, G.; Bechhofer, S.; Paton, N. W.; Baker, P. G.; Peim, M.; Brass, A. (2001). "Transparent access to multiple bioinformatics information sources" (PDF). IBM Systems Journal. 40 (2): 532–551. doi:10.1147/sj.402.0532. 
  25. ^ Stevens, R.; Baker, P.; Bechhofer, S.; Ng, G.; Jacoby, A.; Paton, N. W.; Goble, C. A.; Brass, A. (2000). "TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources". Bioinformatics. 16 (2): 184–185. doi:10.1093/bioinformatics/16.2.184. PMID 10842744. 
  26. ^ Baker, P. G.; Brass, A.; Bechhofer, S.; Goble, C.; Paton, N.; Stevens, R. (1998). "TAMBIS--Transparent Access to Multiple Bioinformatics Information Sources". Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology. 6: 25–34. PMID 9783206. 
  27. ^ "Professor Robert Stevens, research profile - personal details (The University of Manchester)". Retrieved 2012-06-10. 
  28. ^ Klein, J.; Eales, J.; Zürbig, P.; Vlahou, A.; Mischak, H.; Stevens, R. (2013). "Proteasix: A tool for automated and large-scale prediction of proteases involved in naturally occurring peptide generation". Proteomics. 13 (7): 1077–1082. doi:10.1002/pmic.201200493. PMID 23348921. 
  29. ^ Meng, Y. B.; Stevens, R. D.; China, W.; McGill, S.; Ashburner, M. (1988). "Five glycyl tRNA genes within the noc gene complex of Drosophila melanogaster". Nucleic Acids Research. 16 (14): 7189. doi:10.1093/nar/16.14.7189. PMC 338370Freely accessible. PMID 3136440. 
  30. ^ Robert Stevens at DBLP Bibliography Server
  31. ^ List of publications from Microsoft Academic Search
  32. ^ Robert David Stevens's publications indexed by the Scopus bibliographic database, a service provided by Elsevier. (subscription required)
  33. ^ Robert David Stevens author profile page at the ACM Digital Library
  34. ^ Malone, J.; Brown, A.; Lister, A. L.; Ison, J.; Hull, D.; Parkinson, H.; Stevens, R. (2014). "The Software Ontology (SWO): A resource for reproducibility in biomedical data analysis, curation and digital preservation". Journal of Biomedical Semantics. 5: 25. doi:10.1186/2041-1480-5-25. 
  35. ^ Lord, P.; Stevens, R. (2010). Friedberg, Iddo, ed. "Adding a Little Reality to Building Ontologies for Biology". PLoS ONE. 5 (9): e12258. doi:10.1371/journal.pone.0012258. PMC 2933225Freely accessible. PMID 20838431. 
  36. ^ Jupp, S.; Stevens, R.; Hoehndorf, R. (2012). "Logical Gene Ontology Annotations (GOAL): Exploring gene ontology annotations with OWL". Journal of biomedical semantics. 3 Suppl 1 (Suppl 1): S3. doi:10.1186/2041-1480-3-S1-S3. PMC 3337258Freely accessible. PMID 22541594. 
  37. ^ Kalankesh, L. R.; Stevens, R.; Brass, A. (2012). "The language of gene ontology: A Zipf's law analysis". BMC Bioinformatics. 13: 127. doi:10.1186/1471-2105-13-127. PMC 3473240Freely accessible. PMID 22676436. 
  38. ^ Lord, P. W.; Stevens, R. D.; Brass, A.; Goble, C. A. (2003). "Semantic similarity measures as tools for exploring the gene ontology". Pacific Symposium on Biocomputing: 601–612. PMID 12603061. 
  39. ^ Wroe, C. J.; Stevens, R.; Goble, C. A.; Ashburner, M. (2003). "A methodology to migrate the gene ontology to a description logic environment using DAML+OIL". Pacific Symposium on Biocomputing: 624–635. PMID 12603063. 
  40. ^ Semantic Heterogeneity in Bioinformatics Resources
  41. ^ Lord, P. W.; Stevens, R. D.; Brass, A.; Goble, C. A. (2003). "Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation". Bioinformatics. 19 (10): 1275–1283. doi:10.1093/bioinformatics/btg153. PMID 12835272. 
  42. ^ Hastings, J.; Magka, D.; Batchelor, C.; Duan, L.; Stevens, R.; Ennis, M.; Steinbeck, C. (2012). "Structure-based classification and ontology in chemistry". Journal of Cheminformatics. 4: 8. doi:10.1186/1758-2946-4-8. PMC 3361486Freely accessible. PMID 22480202. 
  43. ^ a b c "Grants awarded to Robert Stevens by the EPRSC". Retrieved 2012-06-21. 
  44. ^ UK Government Grants awarded to Robert Stevens, via Research Councils UK
  45. ^ "Investigator / Supervisor details - Robert Stevens @ BBSRC". Retrieved 2012-06-21. 
  46. ^ Kohler, J.; Baumbach, J.; Taubert, J.; Specht, M.; Skusa, A.; Rüegg, A.; Rawlings, C.; Verrier, P.; Philippi, S. (2006). "Graph-based analysis and visualization of experimental results with ONDEX". Bioinformatics. 22 (11): 1383–1390. doi:10.1093/bioinformatics/btl081. PMID 16533819. 
  47. ^ "BBSRC Award details BB/F006012/1: Ondex". 
  48. ^ "BBSRC Award details BBS/B/17131: ComparaGrid - enabling GRID technologies for comparative genomics". 
  49. ^ "ICBO FOIS 2012". Retrieved 2012-06-19. 
  50. ^ UK Ontology Network http://www.ukontology.org/
  51. ^ Robert Stevens introduction on public-semweb-lifesci mailing list
  52. ^ http://www.jbiomedsem.com/about/edboard Editorial Board jbiomedsem.com