|
Atkins D., Best D., Briss P. A., Eccles M., Falck-Ytter Y., Flottorp S., Guyatt G. H., Harbour R. T., Haugh M. C., Henry D., Hill S., Jaeschke R., Leng G., Liberati A., Magrini N., Mason J., Middleton P., Mrukowicz J., O’Connell D., Oxman A. D., Phillips B., Schünemann H. J., Edejer T. T.-T., Varonen H., Vist G. E.,Williams J. W.Jr & Zaza S., GRADE Working Group2004. Grading quality of evidence and strength of recommendations. BMJ328(7454), 1490. |
|
Bairoch A.2009. The future of annotation/biocuration, Nature Precedings. |
|
Barga R. & Gannon D.2007. Scientific versus business workows. In Workows for e-Science, Taylor I. J., Deelman E., Gannon D. B. & Shields M. (eds). Springer, 9–16. |
|
Bauer-Mehren A., Furlong L. I. & Sanz F.2009. Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Molecular Systems Biology5(290). |
|
Bechhofer S., Buchan I., De Roure D., Missier P., Ainsworth J., Bhagat J., Couch P., Cruickshank D., Delderfield M., Dunlop I., Gamble M., Michaelides D., Owen S., Newman D., Sufi S. & Goble C.2013. Why linked data is not enough for scientists. Future Generation Computer Systems29(2), 599–611. |
|
Biolchini J., Mian P., Natali A. & Travassos G. H.2005. Systematic review in software engineering. Technical report No. RT-ES 679/05, Federal University of Rio de Janeiro (UFRJ/COPPE). |
|
Booth A.2011. Evidence-based practice: triumph of style over substance?Health Information & Libraries Journal28(3), 237–241. |
|
Budgen D., Turner M., Brereton P. & Kitchenham B.2008. Using mapping studies in software engineering. In Proceedings of PPIG Psychology of Programming Interest Group, 195–204. Lancaster University. |
|
Bunge M.2004. How does it work? The search for explanatory mechanisms. Philosophy of the Social Sciences34(2), 182–210. |
|
Bylander T. & Chandrasekaran B.1987. Generic tasks for knowledge-based reasoning: the ‘right’ level of abstraction for knowledge acquisition. International Journal of Man-Machine Studies26(2), 231–243. |
|
Callahan A., Dumontier M. & Shah N. H.2011. HyQue: evaluating hypotheses using semantic web technologies. Journal of Biomedical Semantics2(2), 1–17. |
|
Chua C. E. H., Storey V. C. & Chiang R. H.2012. Deriving knowledge representation guidelines by analyzing knowledge engineer behavior. Decision Support Systems54(1), 304–315. |
|
Cohen A. M. & Hersh W. R.2005. A survey of current work in biomedical text mining. Briefings in Bioinformatics6(1), 57–71. |
|
Cooper H. M., Hedges L. V. & Valentine J. C.2009. The Handbook of Research Synthesis and Meta-Analysis. Russell Sage Foundation. |
|
Craver C. F. & Darden L.2005. Introduction. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences36(2), 233–244. |
|
da Cruz S., Campos M. & Mattoso M.2009. Towards a taxonomy of provenance in scientific workow management systems. In 2009 World Conference on Services – I, 259–266. |
|
Deelman E., Gannon D., Shields M. & Taylor I.2009. Workows and e-science: an overview of workow system features and capabilities. Future Generation Computer Systems25(5), 528–540. |
|
Dennis C.2002. Biology databases: information overload. Nature417(6884), 14. |
|
Dibble D. & Bostrom R. P.1987. Managing expert systems projects: factors critical for successful implementation. In Proceedings of the Conference on the 1987 ACM SIGBDP-SIGCPR Conference, SIGCPR’ 87, 96–128. ACM. |
|
Dinakarpandian D., Lee Y., Vishwanath K. & Lingambhotla R.2006. MachineProse: an ontological framework for scientific assertions. Journal of the American Medical Informatics Association13(2), 220–232. |
|
Dixon-Woods M., Agarwal S., Jones D., Young B. & Sutton A.2005. Synthesising qualitative and quantitative evidence: a review of possible methods. Journal of Health Services Research & Policy10(1), 45–53. |
|
Dung P. M.1995. On the acceptability of arguments and its fundamental role in nonmonotonic reasoning, logic programming and n-person games. Artificial Intelligence77(2), 321–357. |
|
Dyba T., Dingsoyr T. & Hanssen G.2007. Applying systematic reviews to diverse study types: an experience report. In International Symposium on Empirical Software Engineering and Measurement, 225–234. |
|
Džeroski S., Langley P. & Todorovski L.2007. Computational discovery of scientific knowledge. In Computational Discovery of Scientific Knowledge, Džeroski S. & Todorovski L. (eds), Lecture Notes in Computer Science 4660, 1–14. Springer. |
|
Easterbrook S., Singer J., Storey M.-A. & Damian D.2008. Selecting empirical methods for software engineering research. In Guide to Advanced Empirical Software Engineering, Shull F., Singer J. & Sjøberg D. I. K. (eds). Springer, 285–311. |
|
Eriksson H.1992. A survey of knowledge acquisition techniques and tools and their relationship to software engineering. Journal of Systems and Software19(1), 97–107. |
|
Fayyad U. & Stolorz P.1997. Data mining and KDD: promise and challenges. Future Generation Computer Systems13(2–3), 99–115. |
|
Fellers J.1987. Key factors in knowledge acquisition. SIGCPR Computer Personnel11(1), 10–24. |
|
Fiore S. & Aloisio G.2011. Special section: data management for eScience. Future Generation Computer Systems27(3), 290–291. |
|
Forbus K. D. & DeKleer J.1993. Building Problem Solvers. MIT Press. |
|
Ford K. M.1993. Knowledge Acquisition as Modeling. Wiley. |
|
Freiling M., Alexande J., Messick S., Rehfuss S. & Shulman S.1985. Starting a knowledge engineering project: a step-by-step approach. AI Magazine6(3), 150. |
|
Goertz G. & Mahoney J.2012. A Tale of Two Cultures: Qualitative and Quantitative Research in the Social Sciences. Princeton University Press. |
|
Hars A.2001. Designing scientific knowledge infrastructures: the contribution of epistemology. Information Systems Frontiers3(1), 63–73. |
|
Hey T. & Trefethen A.2003. The data deluge: an e-science perspective. In Grid Computing, Berman F., Fox G. & Hey T. (eds). John Wiley & Sons Ltd, 809–824. |
|
Hunter A. & Liu W.2010. A survey of formalisms for representing and reasoning with scientific knowledge. The Knowledge Engineering Review25(2), 199–222. |
|
Hunter J.2008. Scientific publication packages—a selective approach to the communication and archival of scientific output. International Journal of Digital Curation1(1), 33–52. |
|
Ivarsson M. & Gorschek T.2012. Tool support for disseminating and improving development practices. Software Quality Journal20(1), 173–199. |
|
Khatri P., Sirota M. & Butte A. J.2012. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Computational Biology8(2), e1002375. |
|
Kiritchenko S., Bruijn B. D., Carini S., Martin J. & Sim I.2010. ExaCT: automatic extraction of clinical trial characteristics from journal publications. BMC Medical Informatics and Decision Making10(1), 56. |
|
Kitchenham B. & Charters S.2007. Guidelines for performing systematic literature reviews in software engineering. Technical Report No. EBSE 2007-001, Keele University and Durham University Joint Report. |
|
Langley P.1987. Scientific Discovery: Computational Explorations of the Creative Processes. MIT Press. |
|
Langley P., Zytkow J. M., Bradshaw G. L. & Simon H. A.1983. Three facets of scientific discovery. In Proceedings of the Eighth International Joint Conference on Artificial Intelligence – Volume 1, IJCAI’83, 465–468. Morgan Kaufmann Publishers, Inc. |
|
Lenat D. B. & Feigenbaum E. A.1991. On the thresholds of knowledge. Artificial Intelligence47(1–3), 185–250. |
|
Lewis-Beck M., Bryman A. & Liao T. F.2004. Encyclopedia of Social Science Research Methods. SAGE Publications, Inc. |
|
Lin C., Lu S., Fei X., Chebotko A., Pai D., Lai Z., Fotouhi F. & Hua J.2009. A reference architecture for scientific workflow management systems and the VIEW SOA solution. IEEE Transactions on Services Computing2(1), 79–92. |
|
Lord P., Macdonald A., Lyon L. & Giaretta D.2004. From data deluge to data curation, In Proceeding of the 3th UK e-Science All Hands Meeting, 371–375. |
|
Maccagnan A., Riva M., Feltrin E., Simionati B., Vardanega T., Valle G. & Cannata N.2010. Combining ontologies and workflows to design formal protocols for biological laboratories. Automated Experimentation2(1), 1–14. |
|
Martinez-Fernandez S., Santos P., Ayala C., Franch X. & Travassos G.2015. Aggregating Empirical Evidence about the Benefits and Drawbacks of Software Reference Architectures, 2015 ACM/IEEE. International Symposium, on Empirical Software Engineering and Measurement (ESEM), pp. 1–10. |
|
Mcdermott J.1988. Preliminary steps toward a taxonomy of problem-solving methods. In Automating Knowledge Acquisition for Expert Systems, number 57 in The Kluwer International Series in Engineering and Computer Science, Marcus S. (ed.). Springer, 225–256. |
|
Mons B.2005. Which gene did you mean?BMC Bioinformatics6(1), 142. |
|
Mons B. & Velterop J.2009. Nano-publication in the e-science era. In Workshop on Semantic Web Applications in Scientific Discourse. |
|
Moody D.2009. The ‘physics’ of notations: toward a scientific basis for constructing visual notations in software engineering. IEEE Transactions on Software Engineering35(6), 756–779. |
|
Motta E., Rajan T. & Eisenstadt M.1990. Knowledge acquisition as a process of model refinement. Knowledge Acquisition2(1), 21–49. |
|
Newman H. B., Ellisman M. H. & Orcutt J. A.2003. Data-intensive e-science frontier research. Communication of the ACM46(11), 68–77. |
|
Noblit G. W. & Hare R. D.1988. Meta-Ethnography: Synthesizing Qualitative Studies. SAGE. |
|
Novère N. L., Hucka M., Mi H., Moodie S., Schreiber F., Sorokin A., Demir E., Wegner K., Aladjem M. I., Wimalaratne S. M., Bergman F. T., Gauges R., Ghazal P., Kawaji H., Li L., Matsuoka Y., Villéger A., Boyd S. E., Calzone L., Courtot M., Dogrusoz U., Freeman T. C., Funahashi A., Ghosh S., Jouraku A., Kim S., Kolpakov F., Luna A., Sahle S., Schmidt E., Watterson S., Wu G., Goryanin I., Kell D. B., Sander C., Sauro H., Snoep J. L., Kohn K. & Kitano H.2009. The systems biology graphical notation. Nature Biotechnology27(8), 735–741. |
|
Petersen K., Feldt R., Mujtaba S. & Mattsson M.2008. Systematic mapping studies in software engineering. In Proceedings of the 12th International Conference on Evaluation and Assessment in Software Engineering, EASE’08, 68–77. British Computer Society. |
|
Plant R. T.1991. Rigorous approach to the development of knowledge-based systems. Knowledge-Based Systems4(4), 186–196. |
|
Rainer A., Jagielska D. & Hall T.2005. Software engineering practice versus evidence-based software engineering research. In Proceedings of the 2005 Workshop on Realising Evidence-Based Software Engineering, REBSE’05, 1–5. ACM. |
|
Rook F. & Croghan J.1989. The knowledge acquisition activity matrix: a systems engineering conceptual framework. IEEE Transactions on Systems, Man and Cybernetics19(3), 586–597. |
|
Rzhetsky A., Iossifov I., Koike T., Krauthammer M., Kra P., Morris M., Yu H., Duboué P. A., Weng W., Wilbur W. J., Hatzivassiloglou V. & Friedman C.2004. GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. Journal of Biomedical Informatics37(1), 43–53. |
|
Sackett D. L., Rosenberg W. M., Gray J. A., Haynes R. B. & Richardson W. S.1996. Evidence based medicine: what it is and what it isn’t. BMJ312(7023), 71–72. |
|
Sanders T. J. M., Spooren W. P. M. & Noordman L. G. M.1993. Coherence relations in a cognitive theory of discourse representation. Cognitive Linguistics4(2), 93–134. |
|
Santos P. & Travassos G.2013. On the representation and aggregation of evidence in software engineering: a theory and belief-based perspective. Electronic Notes in Theoretical Computer Science292, 95–118. |
|
Santos P. & Travassos G.2015. Aggregating empirical evidence about the benefits and drawbacks of software reference architectures. In International Symposium on Empirical Software Engineering and Measurement (in press). |
|
Santos P. S., Nascimento I. & Travassos G. H.2015. A computational infrastructure for research synthesis in software engineering. In XVIII Ibero-American Conference on Software Engineering, 309–322. URP, SPC, UCSP, UCSP. |
|
Schreiber G.2000. Knowledge Engineering and Management: The CommonKADS Methodology. MIT Press. |
|
Shafer G.1976. A Mathematical Theory of Evidence. Princeton University Press. |
|
Shotton D.2009. Semantic publishing: the coming revolution in scientific journal publishing. Learned Publishing22(2), 85–94. |
|
Shrager J.1990. Computational Models of Scientific Discovery and Theory Formation. Morgan Kaufmann Publisher. |
|
Shull F., Feldmann R. & Shaw M.2006. Building decision support in an imperfect world. In International Symposium on Empirical Software Engineering ISESE, 33–35. |
|
Shull F., Singer J. & Sjøberg D. I. K.2007. Guide to Advanced Empirical Software Engineering, 2008 edition. Springer. |
|
Simon H. A.1977. Scientific discovery and the psychology of problem solving. In Models of Discovery, Number 54 in Boston Studies in the Philosophy of Science, Simon H. A. (ed.). Springer, 286–303. |
|
Sjøberg D. I. K., Dybå T., Anda B. C. D. & Hannay J. E.2008. Building theories in software engineering. In Guide to Advanced Empirical Software Engineering, Shull F., Singer J. & Sjøberg D. I. K. (eds). Springer, 312–336. |
|
Slater T., Bouton C. & Huang E. S.2008. Beyond data integration. Drug Discovery Today13(13–14), 584–589. |
|
Stock K., Robertson A., Reitsma F., Stojanovic T., Bishr M., Medyckyj-Scott D. & Ortmann J.2009. eScience for sea science: a semantic scientific knowledge infrastructure for marine scientists. In Fifth IEEE International Conference on e-Science. e-Science’ 09, 110–117. |
|
Studer R., Benjamins V. & Fensel D.1998. Knowledge engineering: principles and methods. Data & Knowledge Engineering25(1–2), 161–197. |
|
Travassos G., Santos P., Neto P. & Biolchini J.2008. An environment to support large scale experimentation in software engineering. In 13th IEEE International Conference on Engineering of Complex Computer Systems, 2008. ICECCS 2008, 193–202. |
|
Valdés-Pérez R. E.1996. Computer science research on scientific discovery. The Knowledge Engineering Review11(1), 57–66. |
|
Vorms M.2011. Representing with imaginary models: formats matter. Studies in History and Philosophy of Science Part A42(2), 287–295. |
|
Wallace D. & Fujii R.1989. Software verification and validation: an overview. IEEE Software6(3), 10–17. |
|
Wielinga B., Schreiber A. & Breuker J.1992. KADS: a modelling approach to knowledge engineering. Knowledge Acquisition4(1), 5–53. |