期刊论文

【摘要】

Background

Scientific publications are documentary representations of defeasible arguments, supported by data and repeatable methods. They are the essential mediating artifacts in the ecosystem of scientific communications. The institutional “goal” of science is publishing results. The linear document publication format, dating from 1665, has survived transition to the Web.

Intractable publication volumes; the difficulty of verifying evidence; and observed problems in evidence and citation chains suggest a need for a web-friendly and machine-tractable model of scientific publications. This model should support: digital summarization, evidence examination, challenge, verification and remix, and incremental adoption. Such a model must be capable of expressing a broad spectrum of representational complexity, ranging from minimal to maximal forms.

Results

The micropublications semantic model of scientific argument and evidence provides these features. Micropublications support natural language statements; data; methods and materials specifications; discussion and commentary; challenge and disagreement; as well as allowing many kinds of statement formalization.

The minimal form of a micropublication is a statement with its attribution. The maximal form is a statement with its complete supporting argument, consisting of all relevant evidence, interpretations, discussion and challenges brought forward in support of or opposition to it. Micropublications may be formalized and serialized in multiple ways, including in RDF. They may be added to publications as stand-off metadata.

An OWL 2 vocabulary for micropublications is available at http://purl.org/mp webcite. A discussion of this vocabulary along with RDF examples from the case studies, appears as OWL Vocabulary and RDF Examples in Additional file 1.

Additional file 1. OWL Vocabulary and RDF Examples.

Format: PDFSize: 236KB Download file

This file can be viewed with: Adobe Acrobat Reader

【授权许可】

2014 Clark et al.; licensee BioMed Central Ltd.

【预览】

附件列表
Files	Size	Format	View
20151106093321192.pdf	3449KB	PDF	download
Figure 4.	65KB	Image	download
Figure 3.	46KB	Image	download
Figure 2.	123KB	Image	download
Figure 1.	45KB	Image	download

【图表】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【参考文献】

[1]Hunter L, Cohen KB: Biomedical language processing: what's beyond PubMed? Mol Cell 2006, 21(5):589-594.
[2]Krallinger M, Vazquez M, Leitner F, Valencia A: Results of the BioCreative III (Interaction) Article Classification Task. Bethesda, MD: BioCreative III Workshop; 2010:17-23.
[3]Greenberg SA: How citation distortions create unfounded authority: analysis of a citation network. Br Med J 2009, 339:b2680.
[4]Greenberg SA: Understanding belief using citation networks. J Eval Clin Pract 2011, 17(2):389-393.
[5]Lawless J: The bad science scandal: how fact-fabrication is damaging UK's global name for research. In The Independent. London: Independent Print Ltd; 2013. [http://www.independent.co.uk/news/science/the-bad-science-scandal-how-factfabrication-is-damaging-uks-global-name-for-research-8660929.html webcite]
[6]Noorden RV: Science publishing: The trouble with retractions. Nature 2011, 478:26-28.
[7]Fang FC, Steen RG, Casadevall A: Misconduct accounts for the majority of retracted scientific publications. Proc Natl Acad Sci 2012, 109(42):17028-17033.
[8]Begley CG, Ellis LM: Drug development: Raise standards for preclinical cancer research. Nature 2012, 483(7391):531-533.
[9]Marcus A, Oransky I: Bring On the Transparency Index. In The Scientist. Midland, Ontario, CA: LabX Media Group; 2012.
[10]Renear AH, Palmer CL: Strategic reading, ontologies, and the future of scientific publishing. Science 2009, 325(5942):828-832.
[11]Krallinger M, Morgan A, Smith L, Leitner F, Tanabe L, Wilbur J, Hirschman L, Valencia A: Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biol 2008, 9 Suppl 2:S1.
[12]Jelier R, Schuemie MJ, Veldhoven A, Dorssers LC, Jenster G, Kors JA: Anni 2.0: a multipurpose text-mining tool for the life sciences. Genome Biol 2008, 9(6):R96.
[13]Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, et al.: Database resources of the national center for biotechnology information. Nucleic Acids Res 2010, 38(suppl 1):D5-D16.
[14]Clark T, Kinoshita J: Alzforum and SWAN: the present and future of scientific web communities. Brief Bioinform 2007, 8(3):163-171.
[15]Buckingham Shum S, Uren V, Gangmin L, Domingue J, Motta E: Visualizing Internetworked Argumentation. In Visualizing Argumentation. Edited by Kirschner PA, Buckingham Shum S. London: Springer-Verlag; 2003.
[16]Shotton D: Semantic Publishing: the coming revolution in scientific journal publishing. Learn Publishing 2009, 22(2):85-94.
[17]Ciccarese P, Ocana M, Clark T: Open semantic annotation of scientific publications with DOMEO. J Biomed Semantics 2012, 3(Suppl 1):S1.
[18]Selventa Inc.: Biological Expression Language V1.0 Overview. [http://belframework.org/bel/overview webcite]
[19]Ciccarese P, Shotton D, Peroni S, Clark T: CiTO+SWAN: The Web Semantics of Bibliographic References, Citations, Evidence and Discourse Relationships. J Biomed Semantics 2014, 5(4):295-311.
[20]Ciccarese P, Wu E, Wong G, Ocana M, Kinoshita J, Ruttenberg A, Clark T: The SWAN biomedical discourse ontology. J Biomed Inform 2008, 41(5):739-751.
[21]SWAN/SIOC: alignment between the SWAN and SIOC ontologies. W3C interest group note 20 October 2009 [http://www.w3.org/TR/hcls-swansioc/ webcite]
[22]Mons B, van Haagen H, Chichester C, Hoen PB, den Dunnen JT, van Ommen G, van Mulligen E, Singh B, Hooft R, Roos M, Hammond J, Kiesel B, Giardine B, Velterop J, Groth P, Schultes E: The value of data. Nat Genet 2011, 43(4):281-283.
[23]Mons B, Velterop J: Nano-Publication in the e-science era. Workshop on Semantic Web Applications in Scientific Discourse (SWASD 2009) 2009; Washington DC, USA 2009. CEUR: [http://ceur-ws.org/Vol-523/Mons.pdf webcite]
[24]Groth P, Gibson A, Velterop J: The Anatomy of a Nano-publication. Inform Serv Use 2010, 30(1):51-56.
[25]Schultes E, Chichester C, Burger K, Kotoulas S, Loizou A, Tkachenko V, Waagmeester A, Askjaer S, Pettifer S, Harland L, Haupt C, Batchelor C, Vazquez M, Fernández JM, Saito J, Gibson A, Wich L: The Open PHACTS Nanopublication Guidelines V1.8. EU Innovative Medicines Initiative - Open PHACTS Project; 2012. RDF/Nanopublication Working Group; 2012 [http://www.openphacts.org/documents/publications/OpenPHACTS_Nanopublication_Guidlines_v1.8.1.pdf webcite].
[26]Williams AJ, Harland L, Groth P, Pettifer S, Chichester C, Willighagen EL, Evelo CT, Blomberg N, Ecker G, Goble C, Mons B: Open PHACTS: semantic interoperability for drug discovery. Drug Discov Today 2012, 17(21-22):1188-1198.
[27]Spilman P, Podlutskaya N, Hart MJ, Debnath J, Gorostiza O, Bredesen D, Richardson A, Strong R, Galvan V: Inhibition of mTOR by rapamycin abolishes cognitive deficits and reduces amyloid-β levels in a mouse model of Alzheimer's disease. PLoS One 2010, 5(4):e9979.
[28]Bacon F: Francis Bacon: The New Organon. Cambridge UK: Cambridge University Press; 2000.
[29]Shapin S: Pump and circumstance: Robert Boyle's literary technology. Soc Stud Sci 1984, 14(4):481-520.
[30]Cox FEG: History of human parasitology. Clin Microbiol Rev 2002, 15(2):595-612.
[31]Steup M: Epistemology. In The Stanford Encyclopedia of Philosophy (Winter 2012 Edition). Edited by Zalta EN. Palo Alto CA: Stanford University; 2012.
[32]Simkin MV, Roychowdhury VP: Stochastic modeling of citation slips. Scientometrics 2005, 62(3):367-384.
[33]Simkin MV, Roychowdhury VP: A mathematical theory of citing. J Am Soc Inf Sci Technol 2007, 58(11):1661-1673.
[34]Alsheikh-Ali AA, Qureshi W, Al-Mallah MH, Ioannidis JP: Public availability of published research data in high-impact journals. PLoS One 2011, 6(9):e24357.
[35]HYLAND K: Writing without conviction? hedging in science research articles. Appl Linguist 1996, 17(4):433-454.
[36]Gerstein M, Seringhaus M, Fields S: Structured digital abstract makes text mining easy. Nature 2007, 447(7141):142.
[37]Leitner F, Chatraryamontri A, Ceol A, Krallinger M, Licata L, Hirschman L, Cesareni G, Valencia A: Enriching Publications with Structured Digital Abstracts: the human-machine experiment. Bedford, MA: MITRE Corporation; 2012.
[38]Holmes FL: Argument and Narrative in Scientific Writing. In The Literary Structure of Scientific Argument: Historical Studies. Edited by Dear P. Philadelphia: University of Pennsylvania Press; 1991:224.
[39]Douven I: Abduction. In The Stanford Encyclopedia of Philosophy (Spring 2011 Edition). Edited by Zalta EN. Paolo Alto CA: Stanford University; 2011.
[40]Lipton P: Inference to the Best Explanation. 2nd edition. New York: Routledge; 2004.
[41]Harman GH: The inference to the best explanation. Philos Rev 1965, 74(1):88-95.
[42]Campos D: On the distinction between Peirce’s abduction and Lipton’s Inference to the best explanation. Synthese 2011, 180(3):419-442.
[43]Walton D, Reed C: Argumentation schemes and defeasible inferences. In Working Notes of the ECAI '2002 Workshop on Computational Models of Natural Argument, 15th European Conference on AI, 2002. Lyons, FR: European Coordinating Committee for Artificial Intelligence; 2002:45-55.
[44]Toulmin SE: The Uses of Argument. Cambridge UK: Cambridge University Press; 2003.
[45]Verheij B: Evaluating arguments based on Toulmin’s scheme. Argumentation 2005, 19(3):347-371.
[46]Verheij B: The Toulmin Argument Model in Artificial Intelligence. Or: how semi-formal, defeasible argumentation schemes creep into logic. In Argumentation in Artificial Intellgence. Edited by Rahwan I, Simari G. Dordrecht: Springer; 2009.
[47]Dung PM: On the acceptability of arguments and its fundamental role in nonmonotonic reasoning, logic programming and n-person games. Artif Intell 1995, 77(2):321-357.
[48]Besnard P, Hunter A: Elements of Argumentation. Cambridge MA, USA: MIT Press; 2008.
[49]Cayrol C, Lagasquie-Schiex M-C: Bipolar Abstract Argumentation Systems. In Argumentation in Artificial Intelligence. Edited by Rahwan I, Simari GR. Dordrecht: Springer; 2009.
[50]Baroni P, Cerutti F, Giacomin M, Simari GR: Computational Models of Argument. In Frontiers in Artificial Intelligence and Applications. Edited by Breuker J, Guarino N, Kok JN, Liu J, LdM R, Mizoguchi R, Musen M, Pal SK, Zhong N. Amsterdam: IOS Press; 2010.
[51]Boella G, Gabbay DM, VDT L, Villata S: Support in Abstract Argumentation. In Computational Models of Argument. Edited by Baroni P, Cerutti F, Giacomin M, Simari GR. Amsterdam: IOS Press; 2010.
[52]Reed C, Norman TJ (Eds): Argumentation Machines. Dordrecht: Kluwer Academic Publishers; 2010.
[53]Rahwan I (Ed): Argumentation in Artificial Intelligence. Dordrecht: Springer; 2009.
[54]Bench-Capon TJM, Dunne PE: Argumentation in artificial intelligence. Artif Intell 2007, 171(10–15):619-641.
[55]Alberts B, Kirschner MW, Tilghman S, Varmus H: Rescuing US biomedical research from its systemic flaws. Proc Natl Acad Sci 2014, 111(16):5773-5777.
[56]Gereffi G: The Evolution of Global Value Chains in the Internet Era. In Electronic Commerce for Development. Edited by Goldstein AE, O'Connor D. Paris FR: Organisation for Economic Co-Operation and Development; 2002.
[57]Holsapple CW, Singh M: The knowledge chain model: activities for competitiveness. Expert Syste Appl 2001, 20(1):77-98.
[58]Lee CC, Yang J: Knowledge value chain. J Manage Dev 2000, 19(9/10):783-793.
[59]Prinz F, Schlange T, Asadullah K: Believe it or not: how much can we rely on published data on potential drug targets? Nat Rev Drug Discov 2011, 10(9):712.
[60]Landis SC, Amara SG, Asadullah K, Austin CP, Blumenstein R, Bradley EW, Crystal RG, Darnell RB, Ferrante RJ, Fillit H, Finkelstein R, Fisher M, Gendelman HE, Golub RM, Goudreau JL, Gross RA, Gubitz AK, Hesterlee SE, Howells DW, Huguenard J, Kelner K, Koroshetz W, Krainc D, Lazic SE, Levine MS, Macleod MR, McCall JM, Moxley Iii RT, Narasimhan K, Noble LJ, et al.: A call for transparent reporting to optimize the predictive value of preclinical research. Nature 2012, 490(7419):187-191.
[61]Cohen KB, Hunter L: A critical review of PASBio's argument structures for biomedical verbs. BMC Bioinformatics 2006, 7 Suppl 3:S5.
[62]Ramos M, Melo J, Albuquerque U: Citation behavior in popular scientific papers: what is behind obscure citations? The case of ethnobotany. Scientometrics 2012, 92(3):711-719.
[63]Lu Z: PubMed and beyond: a survey of web tools for searching biomedical literature. Database 2011, 2011:baq036.
[64]Wan S, Paris C, Dale R: Supporting browsing-specific information needs: Introducing the Citation-Sensitive In-Browser Summariser. Web Semantics: Science, Services and Agents on the World Wide Web 2010, 8(2–3):196-202.
[65]Velterop J: Nanopublications: the future of coping with information overload. LOGOS: J World Book Commun 2010, 21(3–4):119-122.
[66]Clark T, Goble C, Ciccarese P: Discoveries and Anti-Discoveries on the Web of Argument and Data. In AAAI-14 Workshop on Discovery Informatics, July 27–31, 2014. Quebec CA: American Association for Artificial Intelligence; 2014.
[67]Clark T: Next Generation Scientific Publishing and the Web of Data. Semantic Web Jin press
[68]Arighi C, Lu Z, Krallinger M, Cohen K, Wilbur W, Valencia A, Hirschman L, Wu C: Overview of the BioCreative III Workshop. BMC Bioinformatics 2011, 12(Suppl 8):S1.
[69]Arighi C, Roberts P, Agarwal S, Bhattacharya S, Cesareni G, Chatr-aryamontri A, Clematide S, Gaudet P, Giglio M, Harrow I: BioCreative III Interactive Task: an Overview. BMC Bioinformatics 2011, 12(Suppl 8):S4.
[70]Arighi CN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE, Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, Roberts P, Matthews L, Becker K, Drabkin H, Bello S, Licata L, Chatr-aryamontri A, Schaeffer ML, Park J, Haendel M, Van Auken K, Li Y, Chan J, Muller HM, Cui H, et al.: An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database (Oxford) 2013, 2013:bas056.
[71]Arighi CN, Roberts PM, Agarwal S, Bhattacharya S, Cesareni G, Chatr-Aryamontri A, Clematide S, Gaudet P, Giglio MG, Harrow I, Huala E, Krallinger M, Leser U, Li D, Liu F, Lu Z, Maltais LJ, Okazaki N, Perfetto L, Rinaldi F, Saetre R, Salgado D, Srinivasan P, Thomas PE, Toldo L, Hirschman L, Wu CH: BioCreative III interactive task: an overview. BMC Bioinformatics 2011, 12 Suppl 8:S4.
[72]Chatr-aryamontri A, Winter A, Perfetto L, Briganti L, Licata L, Iannuccelli M, Castagnoli L, Cesareni G, Tyers M: Benchmarking of the 2010 BioCreative Challenge III Text Mining Competition by the BioGRID and MINT Interaction Databases. BMC Bioinformatics 2011, 12(Suppl 8):S8.
[73]Hirschman L, Yeh A, Blaschke C, Valencia A: Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics 2005, 6 Suppl 1:S1.
[74]Krallinger M, Vazquez M, Leitner F, Salgado D, Chatr-aryamontri A, Winter A, Perfetto L, Briganti L, Licata L, Iannuccelli M: The Protein-Protein Interaction tasks of BioCreative III: classication/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics 2011, 12(Suppl 8):S3.
[75]Lan M, Su J: Empirical investigations into full-text protein interaction Article Categorization Task (ACT) in the BioCreative II.5 Challenge. IEEE/ACM Trans Comput Biol Bioinform 2010, 7(3):421-427.
[76]Leitner F, Chatr-aryamontri A, Mardis S, Ceol A, Krallinger M, Licata L, Hirschman L, Cesareni G, Valencia A: The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. Nat Biotechnol 2009, 28:897-899.
[77]Leitner F, Chatr-aryamontri A, Mardis SA, Ceol A, Krallinger M, Licata L, Hirschman L, Cesareni G, Valencia A: The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. Nat Biotechnol 2010, 28(9):897-899.
[78]Leitner F, Mardis S, Krallinger M, Cesareni G, Hirschman L, Valencia A: An Overview of BioCreative II.5. IEEE/ACM Trans Comput Biol Bioinform 2009, 7:385-399.
[79]Lu Z, Kao H, Wei C, Huang M, Liu J, Kuo C, Hsu C, Tsai R, Dai H, Okazaki N: The gene normalization task in BioCreative III. BMC Bioinformatics 2011.
[80]Wu CH, Arighi CN, Cohen KB, Hirschman L, Krallinger M, Lu Z, Mattingly C, Valencia A, Wiegers TC, John Wilbur W: BioCreative-2012 virtual issue. Database (Oxford) 2012, 2012:bas049.
[81]Ciccarese P, Ocana M, Clark T: DOMEO: A web-based tool for semantic annotation of online documents. In Bio Ontologies 2011. Vienna, Austria; 2011. [http://bio-ontologies.knowledgeblog.org/297 webcite]
[82]Kim J, Ohta T, Tateisi Y, Tsujii J: GENIA corpus–semantically annotated corpus for bio-textmining. Bioinformatics 2003, 19(Suppl 1):i180-i182.
[83]Rebholz-Schuhmann D, Yepes A, Van Mulligen E, Kang N, Kors J, Milward D, Corbett P, Buyko E, Beisswanger E, Hahn U: CALBC silver standard corpus. J Bioinform Comput Biol 2010, 8:163-179.
[84]Comeau D, Doğan R, Ciccarese P, Cohen K, Krallinger M, Leitner F, Lu Z, Peng Y, Torii M, Valencia A, Verspoor K, Wiegers T, Wu C, Wilbur W: BioC: an interchange data format and tools for biomedical natural language processing. Database 2013, 2013:bat064.
[85]Ciccarese P, Ocana M, Das S, Clark T: AO: An open annotation ontology for science on the Web. In Bio Ontologies 2010: July 9–13, 2010. Boston MA, USA; 2010. [http://www.w3.org/wiki/images/c/c4/AO_paper_Bio-Ontologies_2010_preprint.pdf webcite]
[86]Ciccarese P, Ocana M, Garcia Castro LJ, Das S, Clark T: An open annotation ontology for science on web 3.0. J Biomed Semantics 2011, 2 Suppl 2:S4.
[87]Sanderson R, Ciccarese P, Sompel HV, Bradshaw S, Brickley D, Castro LJG, Clark T, Cole T, Desenne P, Gerber A, Isaac A, Jett J, Habing T, Haslhofer B, Hellmann S, Hunter J, Leeds R, Magliozzi A, Morris B, Morris P, Ossenbruggen J, Soiland-Reyes S, Smith J, Whaley D: W3C Open Annotation Data Model, Community Draft, 08 February 2013. W3C; 2013. [http://www.openannotation.org/spec/core/ webcite]
[88]Ciccarese P, Soiland-Reyes S, Clark T: Web annotation as a first-class object. IEEE Internet Comput 2013, Nov/Dec 2013:71-75.
[89]Schwitter R, Fuchs NE: Attempto Controlled English (ACE): A Seemingly Informal Bridgehead in Formal Territory. In JICSLP'96. Bonn, Germany: GMD STUDIEN; 1996.
[90]Fuchs NE, Höfler S, Kaljurand K, Rinaldi F, Schneider G: Attempto Controlled English: A Knowledge Representation Language Readable by Humans and Machines. In Reasoning Web, First International Summer School 2005, Msida, Malta, July 25–29, 2005, Revised Lectures, Lecture Notes in Computer Science 3564. Edited by Eisinger N, Maluszynski J. Berlin Heidelberg: Springer; 2005.
[91]Fuchs NE, Schwitter R: Attempto Controlled English (ACE). In CLAW 96, First International Workshop on Controlled Language Applications. Belgium: University of Leuven; 1996.
[92]Sanderson R, Ciccarese P, Sompel HVD, Clark T, Cole T, Hunter J, Fraistat N: Open Annotation Core Data Model Community Draft, 09 May 2012. W3C; 2012. [http://www.openannotation.org/spec/core/ webcite]
[93]de Waard A, Buckingham Shum S, Carusi A, Park J, Samwald M, Sándor Á: Hypotheses, Evidence and Relationships: The HypER Approach for Representing Scientific Knowledge Claims. In Proceedings 8th International Semantic Web Conference, Workshop on Semantic Web Applications in Scientific Discourse Volume 523. Edited by Clark T, Luciano JS, Marshall MS, Prdu'hommeaux E, Stephens S. Berlin, 26 Oct 2009, Washingon DC: Lecture Notes in Computer Science, Springer Verlag; 2009.
[94]Hunter A: Hybrid argumentation systems for structured news reports. Knowl Eng Rev 2001, 16(4):295.
[95]Aristotle: Rhetoric. Mineola NY: Dover Publications; 2004.
[96]Carroll JJ, Bizer C, Hayes P, Stickler P: Named Graphs, Provenance and Trust. In WWW '05 14th international conference on World Wide Web 2005. Chiba, Japan: ACM; 2005:613-622.
[97]Semantic Web Publishing Vocabulary (SWP) User Manual 2006. [http://wifo5-03.informatik.uni-mannheim.de/bizer/wiqa/swp/SWP-UserManual.pdf webcite]
[98]Bandrowski AE, Cachat J, Li Y, Müller HM, Sternberg PW, Ciccarese P, Clark T, Marenco L, Wang R, Astakhov V, Grethe JS, Martone ME: A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database 2012, (2012):bas005.
[99]Gardner D, Akil H, Ascoli GA, Bowden DM, Bug W, Donohue DE, Goldberg DH, Grafstein B, Grethe JS, Gupta A, Halavi M, Kennedy DN, Marenco L, Martone ME, Miller PL, Muller HM, Robert A, Shepherd GM, Sternberg PW, Van Essen DC, Williams RW: The neuroscience information framework: a data and knowledge environment for neuroscience. Neuroinformatics 2008, 6(3):149-160.
[100]Altman M, Andreev L, Diggory M, King G, Sone A, Verba S, Kiskis DL: A digital library for the dissemination and replication of quantitative social science research. Soc Sci Comput Rev 2001, 19(4):458-470.
[101]Altman M, King G: A proposed standard for the scholarly citation of quantitative data. DLib Magazine 2006., 13(3/4) march2007-altman [http://www.dlib.org/dlib/march07/altman/03altman.html webcite]
[102]Hardy J, Selkoe DJ: The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics. Science 2002, 297(5580):353-356.
[103]de Calignon A, Polydoro M, Suárez-Calvet M, William C, Adamowicz David H, Kopeikina Kathy J, Pitstick R, Sahara N, Ashe Karen H, Carlson George A, Spires-Jones Tara L, Hyman Bradley T: Propagation of Tau pathology in a model of early Alzheimer's disease. Neuron 2012, 73(4):685-697.
[104]Pimplikar SW: Reassessing the amyloid cascade hypothesis of Alzheimer's disease. Int J Biochem Cell Biol 2009, 41(6):1261-1268.
[105]Armstrong RA: The pathogenesis of Alzheimer's disease: a reevaluation of the; Amyloid cascade hypothesis. Int J Alzheimers Dis 2011., 2011
[106]Herrup K: Alzheimer's Disease - Modernizing Concept, Biological Diagnosis and Therapy. Edited by Hampel H, Carrillo MC. Basel Switzerland: S. Karger; 2012:194.
[107]Bryan KJ, Lee H-g, Perry G, Smith MA, Casadesus G: Transgenic Mouse Models of Alzheimer’s Disease: Behavioral Testing and Considerations. In Methods of Behavior Analysis in Neuroscience. 2nd edition. Edited by JJ B. Boca Raton FL, USA: CRC Press; 2009.
[108]Gao Y, Kinoshita J, Wu E, Miller E, Lee R, Seaborne A, Cayzer S, Clark T: SWAN: A distributed knowledge infrastructure for Alzheimer Disease research. Web Semantics: Science, Services and Agents on the World Wide Web 2006, 4(3):222-228.
[109]Harrison DE, Strong R, Sharp ZD, Nelson JF, Astle CM, Flurkey K, Nadon NL, Wilkinson JE, Frenkel K, Carter CS, Pahor M, Javors MA, Fernandez E, Miller RA: Rapamycin fed late in life extends lifespan in genetically heterogeneous mice. Nature 2009, 460(7253):392-395.
[110]Mucke L, Masliah E, Yu G-Q, Mallory M, Rockenstein EM, Tatsuno G, Hu K, Kholodenko D, Johnson-Wood K, McConlogue L: High-level neuronal expression of Aβ1–42 in wild-type human amyloid protein precursor transgenic mice: synaptotoxicity without plaque formation. J Neurosci 2000, 20(11):4050-4058.
[111]Hsia AY, Masliah E, McConlogue L, Yu G-Q, Tatsuno G, Hu K, Kholodenko D, Malenka RC, Nicoll RA, Mucke L: Plaque-independent disruption of neural circuits in Alzheimer’s disease mouse models. Proc Natl Acad Sci 1999, 96(6):3228-3233.
[112]D’Hooge R, De Deyn PP: Applications of the Morris water maze in the study of learning and memory. Brain Res Rev 2001, 36(1):60-90.
[113]Morris RGM: Spatial localization does not require the presence of local cues. Learn Motiv 1981, 12(2):239-260.
[114]Huang S, Houghton PJ: Mechanisms of resistance to rapamycins. Drug Resist Updat 2001, 4(6):378-391.
[115]Neuhaus P, Klupp J, Langrehr JM: mTOR inhibitors: an overview. Liver Transpl 2001, 7(6):473-484.
[116]Sabatini DM, Erdjument-Bromage H, Lui M, Tempst P, Snyder SH: RAFT1: a mammalian protein that binds to FKBP12 in a rapamycin-dependent fashion and is homologous to yeast TORs. Cell 1994, 78(1):35-43.
[117]Strawson PF: On Referring. Mind 1950, 59(235):320-344.
[118]Attwood TK, Kell DB, McDermott P, Marsh J, Pettifer SR, Thorne D: Calling International Rescue: knowledge lost in literature and data landslide! Biochem J 2009, 424(3):317-333.
[119]Attwood TK, Kell DB, McDermott P, Marsh J, Pettifer SR, Thorne D: Utopia documents: linking scholarly literature with research data. Bioinformatics 2010, 26(18):i568-i574.
[120]Clark T, Ciccarese P, Attwood T, Waard A, Pettifer S: A Round-Trip to the Annotation Store: Open, Transferable Semantic Annotation of Biomedical Publications. In Beyond the PDF: January 19–21, 2011. San Diego: University of California at San Diego; 2011.
[121]Needham M, Mastaglia FL, Garlepp MJ: Genetics of inclusion-body myositis. Muscle Nerve 2007, 35(5):549-561.
[122]Askanas V, Engel WK: New advances in the understanding of sporadic inclusion-body myositis and hereditary inclusion-body myopathies. Curr Opin Rheumatol 1995, 7(6):486-496.
[123]Askanas V, Engel WK: Sporadic inclusion-body myositis and its similarities to Alzheimer disease brain. Recent approaches to diagnosis and pathogenesis, and relation to aging. Scand J Rheumatol 1998, 27(6):389-405.
[124]Askanas V, Engel WK, Alvarez RB: Light and electron microscopic localization of beta-amyloid protein in muscle biopsies of patients with inclusion-body myositis. Am J Pathol 1992, 141(1):31-36.
[125]Askanas V, Engel WK, Alvarez RB, McFerrin J, Broccolini A: Novel immunolocalization of alpha-synuclein in human muscle of inclusion-body myositis, regenerating and necrotic muscle fibers, and at neuromuscular junctions. J Neuropathol Exp Neurol 2000, 59(7):592-598.
[126]Askanas V, Engel WK, Bilak M, Alvarez RB, Selkoe DJ: Twisted tubulofilaments of inclusion body myositis muscle resemble paired helical filaments of Alzheimer brain and contain hyperphosphorylated tau. Am J Pathol 1994, 144(1):177-187.
[127]Askanas V, McFerrin J, Alvarez RB, Baque S, Engel WK: Beta APP gene transfer into cultured human muscle induces inclusion-body myositis aspects. Neuroreport 1997, 8(9–10):2155-2158.
[128]Askanas V, McFerrin J, Baque S, Alvarez RB, Sarkozi E, Engel WK: Transfer of beta-amyloid precursor protein gene using adenovirus vector causes mitochondrial abnormalities in cultured normal human muscle. Proc Natl Acad Sci U S A 1996, 93(3):1314-1319.
[129]Needham M, Mastaglia FL: Inclusion body myositis: current pathogenetic concepts and diagnostic and therapeutic approaches. Lancet Neurol 2007, 6(7):620-631.
[130]Gupta A, Bug W, Marenco L, Qian X, Condit C, Rangarajan A, Muller HM, Miller PL, Sanders B, Grethe JS, Astakhov V, Shepherd G, Sternberg PW, Martone ME: Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF). Neuroinformatics 2008, 6(3):205-217.
[131]Quine WV: Mr. Strawson on logical theory. Mind 1953, 62(248):433-451.

Journal of Biomedical Semantics
Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications

Carole A Goble² Paolo N Ciccarese¹ Tim Clark²
[1] Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA;School of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
关键词: Nanopublications; Research reproducibility; Methods citation; Scientific evidence; Scientific discourse; Digital abstract; Data citation; Annotation; Argumentation;
Others : 1230536 DOI : 10.1186/2041-1480-5-28

received in 2013-03-12, accepted in 2014-06-16, 发布年份 2014
PDF


	文献评价指标
	下载次数：68次	浏览次数：33次

【 摘 要 】

Background

Results

【 授权许可】

【 预 览 】

【 图 表 】

【 参考文献 】

【摘要】

【授权许可】

【预览】

【图表】

【参考文献】