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Are we finally ready for transclusion?*


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Discussing whether our current scholarly infrastructure can support the concept transclusion.

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Are we finally ready for transclusion?*

  1. 1. ARE WE FINALLY READY FOR TRANSCLUSION?* Dr. Paul Groth | @pgroth | Disruptive Technology Director Elsevier Labs | @elsevierlabs The Future of Text Symposium September 2017 Thanks Anita de Waard * AT LEAST FOR ACADEMIC TEXT
  2. 2. TRANSCLUSION Nelson, T. H. (1995). "The Heart of Connection: Hypermedia Unified by Transclusion". Communications of the ACM. 38 (8): 31-33. doi:10.1145/208344.208353
  3. 3. 3 Enabling data-centric science [[1] Bleecker, J. ‘A Manifesto for Networked Objects — Cohabiting with Pigeons, Arphids and Aibos in the Internet of Things 2] Bechhofer, S., De Roure, D., Gamble, M., Goble, C. and Buchan, I. (2010) Research Objects: Towards Exchange and Reuse of Digital Knowledge. In: The Future of the Web for Collaborative Science (FWCS 2010), April 2010, Raleigh, NC, USA. [3] Neylon, C. ‘Network Enabled Research: Maximise scale and connectivity, minimise friction’, ‘ Internet of things: (Bleecker, [1]) Interact with ‘objects that blog’ or ‘Blogjects’, that: track where they are and where they’ve been;have histories of their encounters and experienceshave agency - an assertive voice on the social web [2] Research Objects: (Bechofer et al, [2]) Create semantically rich aggregations of resources, that can possess some scientific intent or support some research objective Networked Knowledge: (Neylon, [3]) If we care about taking advantage of the web and internet for research then we must tackle the building of scholarly communication networks. These networks will have two critical characteristics: scale and a lack of friction. [3] From Anita de Waard
  4. 4. A. Changing the unit and form of the research paper 1998: Modular papers: 2000: Argumentation networks: 1987 20171997 2007 2015: Lorena Barba, GWU, teaching in Python: From Anita de Waard
  5. 5. 5 Scientific articles are stories that persuade with data The Story of Goldilocks and the Three Bears Story Grammar Paper The AXH Domain of Ataxin-1 Mediates Neurodegeneration through Its Interaction with Gfi-1/Senseless Proteins Once upon a time Time Setting Background The mechanisms mediating SCA1 pathogenesis are still not fully understood, but some general principles have emerged. a little girl named Goldilocks Characters Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract, She went for a walk in the forest. Pretty soon, she came upon a house. Location Experimental setup studied and compared in vivo effects and interactions to those of the human protein She knocked and, when no one answered, Goal Theme Research goal Gain insight into how Atx-1's function contributes to SCA1 pathogenesis. How these interactions might contribute to the disease process and how they might cause toxicity in only a subset of neurons in SCA1 is not fully understood. she walked right in. Attempt Hypothesis Atx-1 may play a role in the regulation of gene expression At the table in the kitchen, there were three bowls of porridge. Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When Overexpressed in Files Goldilocks was hungry. Subgoal Subgoal test the function of the AXH domain Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand and Perrimon, 1993) and compared its effects to those of hAtx-1. She tasted the porridge from the first bowl. Attempt This porridge is too hot! she exclaimed. Outcome Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drives expression in the differentiated R1-R6 photoreceptor cells (Mollereau et al., 2000 and O'Tousa et al., 1985), results in neurodegeneration in the eye, as does overexpression of hAtx-1[82Q]. Although at 2 days after eclosion, overexpression of either Atx-1 does not show obvious morphological changes in the photoreceptor cells So, she tasted the porridge from the second bowl. Activity Data (data not shown), This porridge is too cold, she said Outcome Results both genotypes show many large holes and loss of cell integrity at 28 days So, she tasted the last bowl of porridge. Activity Data (Figures 1B-1D). Ahhh, this porridge is just right, she said happily and Outcome Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induces eye abnormalities. The external structures of the eyes that overexpress dAtx-1 show disorganized ommatidia and loss of interommatidial bristles she ate it all up. Data (Figure 1F), Aristotle Quintilian Scientific Paper prooimion Introduction/ exordium The introduction of a speech, where one announces the subject and purpose of the discourse, and where one usually employs the persuasive appeal to ethos in order to establish credibility with the audience. Introduction: positioning prothesis Statement of Facts/narrati o The speaker here provides a narrative account of what has happened and generally explains the nature of the case. Introduction: research question Summary/ propostitio The propositio provides a brief summary of what one is about to speak on, or concisely puts forth the charges or accusation. Summary of contents pistis Proof/ confirmatio The main body of the speech where one offers logical arguments as proof. The appeal to logos is emphasized here. Results Refutation/ refutatio As the name connotes, this section of a speech was devoted to answering the counterarguments of one's opponent. Related Work epilogos peroratio Following the refutatio and concluding the classical oration, the peroratio conventionally employed appeals through pathos, and often included a summing up. Discussion: summary, implications. Anita de Waard
  9. 9. ATOMIZATION: CLAIMS & CONCEPTS nanopublications
  10. 10. TREND: PERSISTENT IDS EVERYWHERE We are adding PIDs for Funding information, Licensing, Versioning Every paper we publish has a DOI (= PID). ORCID enables every researcher to have a PID Every dataset we publish has a DOI (= PID) Knowledge components are identified through DOIs, e.g.: • Chemicals • Physical Samples • Resource Identifiers • Organisms • Materials We are helping to create Open Linked Data networks of PIDs
  11. 11. TREND: DUPLICATION “In her first revision, the author completely replaced the description of the method with a citation, as shown in Fig. ​Fig.2b.2b. This avoids the problem of self-plagiarism, but the absence of any detail makes the method section look a little thin.”
  12. 12. TREND: MACHINE WRITING Towards Automating Data Narratives. Gil, Y.; and Garijo, D. In Proceedings of the Twenty-Second ACM International Conference on Intelligent User Interfaces (IUI-17), Limassol, Cyprus, 2017.
  13. 13. AN EXISTING INFRASTRUCTURE FOR TRANSCLUSION? See also: Machine Writing PIDS w/ Metadata Background Quotation in Context Assembled w/ Jupyter Notebooks Open Annotation Rendered
  14. 14. FUTURE: CONSTRUCTING SCHOLARLY TEXT FROM DISTRIBUTED RESEARCH OBJECTS? • Transclude data, methods, background through the scholarly infrastructure • Have the machine help generate text that can be easily included • Authors can shape their narrative using blocks within notebooks • Notebooks support rendering for different consumption formats