Paint-Yourself-In-The-Corner Infrastructure

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Presentation given at the EMTACL12 conference in Trondheim, Norway, on October 1 2012. Discusses the evolution towards a highly dynamic scholarly record (assets don't have the sense of fixity they used to have; assets are highly interdependent) and how the archiving infrastructure used for scholarly communication can not adequately deal with this dynamism.

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Paint-Yourself-In-The-Corner Infrastructure

  1. @hvdsomp http://alexanderponting.blogspot.com/2012/01/how-to-paint-yourself-into-corner.html
  2. Consideration 1 - A Dynamic Scholarly Record•  The scholarly record is extending with a wide range of non- traditional assets emerging from eScience and eHumanities endeavors. •  e.g. datasets, software, ontologies, workflows, online debate, slides, blogs, videos, collaborative environments, etc.•  Many of these non-traditional assets: •  Do not have the sense of fixity that traditional assets such as journal articles or books have. •  Have a wide range of dependencies on other assets.•  Even traditional assets are becoming increasingly dynamic and dependent on other assets, which may themselves be dynamic. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  3. PeerJ Dynamic Contenthttp://peerj.com - http://www.publishersweekly.com/pw/by-topic/digital/content-and-e-books/article/ 52512-scholarly-publishing-2012-meet-peerj.html Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  4. Article Wikipedia BridgePLoS Computational Biology http://blogs.plos.org/plos/2012/04/bridging-the-journal-wikipedia-gap/ Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  5. Research ObjectsBechhofer, S. et al. (2010) http://precedings.nature.com/documents/4626/version/1 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  6. Executable Paper – Collage - Conceptual ViewNowakowski et al. (2011) The Collage Authoring Environment Procedia Computer Science v4 http:// dx.doi.org/10.1016/j.procs.2011.04.064 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  7. Executable Paper – Collage – Rendering a PaperNowakowski et al. (2011) The Collage Authoring Environment Procedia Computer Science v4 http:// dx.doi.org/10.1016/j.procs.2011.04.064 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  8. Scientific Workflows, Services, Data, Workflow EnginesCarole Goble, JCDL 2012 Keynote https://dl.dropbox.com/u/617206/JCDL2012keynoteGoble.ppt Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  9. What is the Scholarly Record? •  It becomes challenging to define what the scholarly record is: where does it start and where does it end? •  Transforming from a stack of journals or a bunch of PDF files into a dynamic network of interconnected assets and actors.“An article about computational science in a scientific publication is not the scholarship itself, it is merely advertising of the scholarship. The actual scholarship is the complete software development environment, [the complete data] and the complete set of instructions which generated the figures.” David Donoho, “Wavelab and Reproducible Research,” 1995 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  10. Fixity is Challenged …•  The ever-evolving nature of some assets challenges the notion of fixity as “forever frozen” and begs considering the notion of the “state of the scholarly record at a specific moment in time”. •  Evolution from the version of record to a version of the record.•  Whatever the boundaries of the scholarly record are, it will be essential to be able to look back at certain assets in order to understand how findings came about. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  11. Consideration 2 – The Web as the Infrastructure•  For quite some time, the Web has been the conduit for scholarlyinformation. But, the scholarly endeavor is increasingly embedded into,native to, the Web. •  From PDF to HTML. •  Social component: Contributors taking a central role. •  Machine component: Semantic, Linked Data technologies.•  The Web is becoming the infrastructure for the Scholarly Record. •  Long Term Sustainability: Reuse of infrastructure (network, software, platforms, standards, etc.) that the entire world depends on. •  Integration of scholarly discourse with other Web-based discourse.•  The special requirements of Scholarly Communication (certification,archiving, persistence, trust, annotation, metrics, …) must be addressed inan interoperable manner within the Web infrastructure, not in some parallelscholarly universe. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  12. The Web as the Infrastructure: alt-metrics http://altmetrics.org/manifesto/ Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  13. http://impactstory.it/ Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  14. The HTTP URI is the Identifier•  At the core of the Web are HTTP URIs.•  The Web-based scholarly record works because of HTTP URIs.•  Even when persistent identifiers are assigned to assets, contributors,and institutions they need to be instantiated as HTTP URIs in order to doanything useful with them on the Web. •  cf. http://dx.doi.org/… •  same for ORCID, I2, pmid, etc.•  Many non-traditional assets are born with an HTTP URI and neverobtain a persistent identifier. •  cf. presentations on SlideShare, software, ontologies, workflows, etc. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  15. Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  16. Existing Archival Infrastructure Assumes Fixity and Boundary Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  17. The Web Exists in the Perpetual Now Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  18. The Web Exists in the Perpetual NowThe lack of temporal capabilities of the Web has shaped ourexpectations.•  We don’t object to prior versions not being available. We tolerate 404s.•  Reviewer of Memento paper at WWW 2010: •  Is there (sic) any statistics to show that many or a good number of Web users should like to get obsolete data or resources•  Web archives are destinations, not integrated in the Web browsing experience. Nelson, M.L. (2012) http://arxiv.org/abs/1209.2664 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  19. Not Accessible From cnn.com Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  20. Paper Era: Publication Context Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  21. Paper Era: Publication Context Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  22. Web Era: Publication Context Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  23. Web Era: Publication Context Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  24. Several Challenges•  Archival approach and infrastructure to deal with dynamic, interdependent content•  Referencing scholarly assets•  Recreating a version of the scholarly record Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  25. Recreating a Version of the Scholarly Record•  Is it possible to reconstruct the Web-based scholarly record as it was ata certain point in time?•  For example, given a paper can one see the referenced/linked assetsas they were at the time of publication of the paper?•  The ability to reconstruct a version of the scholarly record willbecome increasingly important as the scholarly endeavor anddiscourse becomes increasingly dynamic and Web-based. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  26. To Be Expected Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  27. Time-dependent decay of URLs published in MEDLINE abstractsMost common types dead links were for computer programs (43%), followed byscholarly content (38%) and databases (19%) Wren J D, Bioinformatics, 2008;24:1381-1385 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  28. Traces of the Past Web Exist •  Content Management Systems •  Web Archives •  Transactional archives •  Search engine caches •  … Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  29. If Only It Would Be Possible to Follow a URI in Time Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  30. It is with Memento Digital Preservation Award 2010 http://www.mementoweb.org/ Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  31. Time Travel Select DateToday Jun 16 1997 Jun 16 1997 From Internet Archive Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  32. June 16 1997 http://www.ntnu.no/ @ June 16 1997 Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  33. Original Resources and Mementos Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  34. Bridge from Present to Past Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  35. Bridge from Past to Present Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  36. Memento Framework Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  37. Also with 404, etc. Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  38. Memento & IIPC http://netpreserve.org/projects/memento Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  39. Memento & Wikipedia, Mediawikihttp://en.wikipedia.org/wiki/Wikipedia:Requests_for_comment/Memento Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  40. Memento & DBpedia http://mementoweb.org/depot/native/dbpedia/ Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  41. To Be ExpectedNOT IN ARCHIVE Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  42. Recreating a Version of the Scholarly Record•  Is it possible to reconstruct the Web-based scholarly record as it was ata certain point in time?•  For example, given a paper can one see the referenced materials asthey were at the time of publication of the paper?•  Example: Van de Sompel, H., Payette, S., Erickson, J., Lagoze, C., and Warner, S.(2004) Rethinking scholarly communication: Building the System thatScholars Deserve. D-Lib Magazine, 10(9). doi:10.1045/september2004-vandesompel ; http://dx.doi.org/10.1045/september2004-vandesompel Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  43. Published September 15 2004 Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  44. Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  45. Domain Gone Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  46. Archived copy December 5 2003 Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  47. Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  48. Current version Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  49. Archived copy December 11 2004 Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  50. Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  51. Resource gone Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  52. Archived copy December 5 2003 Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  53. Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  54. Resource gone Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  55. Archived copy unavailable Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  56. Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  57. Current version Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  58. Archived copy August 26 2003 Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  59. Citation Rot Studies at Scale with Memento •  Pilot study: •  Papers from arXiv: 400,000 papers => 144,000 unique URIs •  Thesis from UNT ETD repository: 3,600 papers => 18,000 URIs •  URIs of established scholarly repositories removed (e.g. http:// dx.doi.org), i.e. focusing in on the periphery of the scholarly record.Sanderson, R., Phillips, M., and Van de Sompel, H. (2011) Analyzing the Persistence of Referenced WebResources with Memento. Open Repositories 2011; Arxiv preprint. arXiv:1105.3459 ; http://arxiv.org/abs/1105.3459 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  60. UNT Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  61. arXiv Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  62. UNT Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  63. arXiv Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  64. Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  65. DOI Redirects to R1 Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  66. Later, DOI Redirects to R2, then R3 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  67. R1, R2, R3 Have Mementos Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  68. Looking for Memento of DOI with t in [t2,t3[ Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  69. End Up at Wrong Memento Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  70. Introduce Temporal Awareness for DOI Resolver Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  71. End Up at Correct Memento Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  72. But … the DOI Resolver Exists in the Perpetual Now•  The latest information indicates that the DOI redirection history is currently not maintained•  The situation is aggravated by multiple consecutive redirects at publisher’s end (which are likely not archived because of strict robots.txt rules)•  While HTTP DOIs help achieve long-term workable links, they exist in the Perpetual Now like the rest of the Web’s URIs Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  73. Several Challenges•  Archival approach and infrastructure to deal with dynamic, interdependent content•  Referencing scholarly assets•  Recreating a version of the scholarly record Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  74. Referencing Scholarly Assets•  With Memento, the same HTTP URI can function as the reference to temporally evolving resources•  But in order to reference the appropriate temporal version, both the HTTP URI and the desired time are needed. •  Essential for referencing resources in annotations•  A few possibilities: •  Express URI and time as is currently done in citations – human readable, not machine actionable •  Turn the reference into a tuple: URI and machine-actionable annotation of the URI – allows expressing fragments of resources too •  Use DURI scheme Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  75. DURI http://tools.ietf.org/html/draft-masinter-dated-uri Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  76. duri:1997-06-17:http://www.ntnu.no http://www.ntnu.no/ @ June 16 1997 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  77. HTML5 Custom Protocol Handlerhttp://dev.opera.com/articles/view/html5-custom-protocol-and-content-handlers/ Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  78. HTML5 Custom Protocol Handlerhttp://dev.opera.com/articles/view/html5-custom-protocol-and-content-handlers/ Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  79. HTML5 Custom Protocol Handlerhttp://dev.opera.com/articles/view/html5-custom-protocol-and-content-handlers/ Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  80. Referencing Scholarly Assets Herbert Van de Sompel Paint-Yourself-In-The-Corner InfrastructureEMTACL 2012, Trondheim, Norway, October 1 2012
  81. Several Challenges•  Archival approach and infrastructure to deal with dynamic, interdependent content•  Referencing scholarly assets•  Recreating a version of the scholarly record Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  82. Archival Approach•  Archiving via a combination of “curated”, “at point of interaction”, and “in the wild” approaches: o  CMS, wikis, datawikis with solid versioning mechanisms can play a significant role as archival hubs o  Archiving the linked context at the time of publication (cf. WebCite), when submitted into institutional repository, etc. o  Archiving at the moment of interaction with assets: reading, commenting, annotating, liking, tweeting, executing, etc. o  Web archives come to the rescue for “in the wild” materials. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  83. SiteStory Transactional Archiving http://mementoweb.github.com/SiteStory/ Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  84. SiteStory Transactional Archiving http://mementoweb.github.com/SiteStory/ Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  85. Conclusions•  Scholarly assets are increasingly dynamic and interdependent•  The existing scholarly archiving infrastructure is about fixity and boundary•  Scholarly communication, and, as a matter of fact, the entire scholarly endeavor is increasingly Web-native•  The Web exists in the perpetual now•  This brings along significant challenges … Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  86. @hvdsomp http://alexanderponting.blogspot.com/2012/01/how-to-paint-yourself-into-corner.html

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