title: SEE: structured representation of scientific evidence in the biomedical domain using Semantic Web techniques.
abstract: BACKGROUND
  Accounts of evidence are vital to evaluate and reproduce scientific findings and integrate data on an informed basis. Currently, such accounts are often inadequate, unstandardized and inaccessible for computational knowledge engineering even though computational technologies, among them those of the semantic web, are ever more employed to represent, disseminate and integrate biomedical data and knowledge.
  
  
  RESULTS
  We present SEE (Semantic EvidencE), an RDF/OWL based approach for detailed representation of evidence in terms of the argumentative structure of the supporting background for claims even in complex settings. We derive design principles and identify minimal components for the representation of evidence. We specify the Reasoning and Discourse Ontology (RDO), an OWL representation of the model of scientific claims, their subjects, their provenance and their argumentative relations underlying the SEE approach. We demonstrate the application of SEE and illustrate its design patterns in a case study by providing an expressive account of the evidence for certain claims regarding the isolation of the enzyme glutamine synthetase.
  
  
  CONCLUSIONS
  SEE is suited to provide coherent and computationally accessible representations of evidence-related information such as the materials, methods, assumptions, reasoning and information sources used to establish a scientific finding by adopting a consistently claim-based perspective on scientific results and their evidence. SEE allows for extensible evidence representations, in which the level of detail can be adjusted and which can be extended as needed. It supports representation of arbitrary many consecutive layers of interpretation and attribution and different evaluations of the same data. SEE and its underlying model could be a valuable component in a variety of use cases that require careful representation or examination of evidence for data presented on the semantic web or in other formats.
authors.affiliation: Institute of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Bölling
authors.affiliation: Department of Computer Science, Humboldt-Universität zu Berlin, Berlin, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Weidlich
authors.affiliation: Institute of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany.
authors.forename: Hermann-Georg
authors.initials: HG
authors.lastname: Holzhütter
references.citation: Nat Biotechnol. 2007 Nov;25(11):1251-5
references.pmid: 17989687
references.citation: Brief Bioinform. 2009 Jul;10(4):392-407
references.pmid: 19457869
references.citation: J Biol Chem. 1972 Sep 10;247(17):5312-21
references.pmid: 4403443
references.citation: Stud Health Technol Inform. 2004;102:20-38
references.pmid: 15853262
references.citation: J Biomed Semantics. 2013 Apr 15;4 Suppl 1:S1
references.pmid: 23735196
references.citation: J Biomed Semantics. 2014 Mar 06;5(1):14
references.pmid: 24602174
references.citation: Mol Syst Biol. 2010 Sep 7;6:411
references.pmid: 20823849
references.citation: BMC Bioinformatics. 2007 May 09;8 Suppl 3:S2
references.pmid: 17493285
references.citation: J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S7
references.pmid: 20626927
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D1-7
references.pmid: 23203983
references.citation: J Cheminform. 2013 May 08;5(1):23
references.pmid: 23657106
references.citation: J Biomed Semantics. 2011 May 17;2 Suppl 2:S4
references.pmid: 21624159
references.citation: Nat Biotechnol. 2013 May;31(5):419-25
references.pmid: 23455439
references.citation: Nucleic Acids Res. 2015 Jul 1;43(W1):W1-2
references.pmid: 26136473
references.citation: Brief Bioinform. 2011 Nov;12(6):723-35
references.pmid: 21330331
references.citation: Brief Bioinform. 2013 Jan;14(1):109-25
references.pmid: 22492191
references.citation: J Biomed Semantics. 2013 Apr 15;4 Suppl 1:S8
references.pmid: 23734708
references.citation: Biochemistry. 1966 Mar;5(3):872-9
references.pmid: 5911299
references.citation: J Biomed Semantics. 2011 May 17;2 Suppl 2:S9
references.pmid: 21624164
references.citation: J Biomed Semantics. 2014 Jul 04;5:28
references.pmid: 26261718
references.citation: J Biomed Semantics. 2011 May 17;2 Suppl 2:S3
references.pmid: 21624158
references.citation: J Biomed Semantics. 2011 May 17;2 Suppl 2:S1
references.pmid: 21624155
references.citation: J Biomed Semantics. 2012 Apr 24;3 Suppl 1:S1
references.pmid: 22541592
references.citation: Methods Enzymol. 1985;113:185-99
references.pmid: 2868383
references.citation: J Biomed Inform. 2008 Oct;41(5):739-51
references.pmid: 18583197