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Paint-Yourself-In-The-Corner Infrastructure

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Herbert Van de Sompel
Herbert Van de Sompel

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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@hvdsomp http://alexanderponting.blogspot.com/2012/01/how-to-paint-yourself-into-corner.html
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
PeerJ Dynamic Content http://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
Article Wikipedia Bridge PLoS 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
Research Objects Bechhofer, 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
Executable Paper – Collage - Conceptual View Nowakowski 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
Executable Paper – Collage – Rendering a Paper Nowakowski 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
Scientific Workflows, Services, Data, Workflow Engines Carole 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
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
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
Consideration 2 – The Web as the Infrastructure •  For quite some time, the Web has been the conduit for scholarly information. 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 in an interoperable manner within the Web infrastructure, not in some parallel scholarly universe. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
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
http://impactstory.it/ Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
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 do anything 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 never obtain 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
Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Existing Archival Infrastructure Assumes Fixity and Boundary Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
The Web Exists in the Perpetual Now Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
The Web Exists in the Perpetual Now The lack of temporal capabilities of the Web has shaped our expectations. •  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
Not Accessible From cnn.com Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Paper Era: Publication Context Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Paper Era: Publication Context Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Web Era: Publication Context Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Web Era: Publication Context Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
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
Recreating a Version of the Scholarly Record •  Is it possible to reconstruct the Web-based scholarly record as it was at a certain point in time? •  For example, given a paper can one see the referenced/linked assets as they were at the time of publication of the paper? •  The ability to reconstruct a version of the scholarly record will become increasingly important as the scholarly endeavor and discourse becomes increasingly dynamic and Web-based. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
To Be Expected Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Time-dependent decay of URLs published in MEDLINE abstracts Most common types dead links were for computer programs (43%), followed by scholarly 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
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 Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
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
It is with Memento Digital Preservation Award 2010 http://www.mementoweb.org/ Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Time Travel Select Date Today 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
June 16 1997 http://www.ntnu.no/ @ June 16 1997 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Original Resources and Mementos Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Bridge from Present to Past Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Bridge from Past to Present Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Memento Framework Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Also with 404, etc. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Memento & IIPC http://netpreserve.org/projects/memento Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Memento & Wikipedia, Mediawiki http://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
Memento & DBpedia http://mementoweb.org/depot/native/dbpedia/ Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
To Be Expected NOT IN ARCHIVE Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Recreating a Version of the Scholarly Record •  Is it possible to reconstruct the Web-based scholarly record as it was at a certain point in time? •  For example, given a paper can one see the referenced materials as they 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 that Scholars 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
Published September 15 2004 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Domain Gone Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Archived copy December 5 2003 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Current version Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Archived copy December 11 2004 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Resource gone Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Archived copy December 5 2003 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Resource gone Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Archived copy unavailable Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Current version Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Archived copy August 26 2003 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
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 Web Resources 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
UNT Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
arXiv Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
UNT Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
arXiv Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
DOI Redirects to R1 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Later, DOI Redirects to R2, then R3 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
R1, R2, R3 Have Mementos Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
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
End Up at Wrong Memento Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
Introduce Temporal Awareness for DOI Resolver Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
End Up at Correct Memento Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
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
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
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
DURI http://tools.ietf.org/html/draft-masinter-dated-uri Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
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
HTML5 Custom Protocol Handler http://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
HTML5 Custom Protocol Handler http://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
HTML5 Custom Protocol Handler http://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
Referencing Scholarly Assets Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
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
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
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
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
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
@hvdsomp http://alexanderponting.blogspot.com/2012/01/how-to-paint-yourself-into-corner.html

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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 Content http://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 Bridge PLoS 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 Objects Bechhofer, 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 View Nowakowski 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 Paper Nowakowski 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 Engines Carole 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 scholarly information. 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 in an interoperable manner within the Web infrastructure, not in some parallel scholarly 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 Infrastructure EMTACL 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 do anything 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 never obtain 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 Infrastructure EMTACL 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 Now The lack of temporal capabilities of the Web has shaped our expectations. •  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 Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 20. Paper Era: Publication Context Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 21. Paper Era: Publication Context Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 22. Web Era: Publication Context Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 23. Web Era: Publication Context Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 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 at a certain point in time? •  For example, given a paper can one see the referenced/linked assets as they were at the time of publication of the paper? •  The ability to reconstruct a version of the scholarly record will become increasingly important as the scholarly endeavor and discourse 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 Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 27. Time-dependent decay of URLs published in MEDLINE abstracts Most common types dead links were for computer programs (43%), followed by scholarly 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 Infrastructure EMTACL 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 Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 31. Time Travel Select Date Today 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 Infrastructure EMTACL 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 Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 35. Bridge from Past to Present Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 36. Memento Framework Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 37. Also with 404, etc. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 38. Memento & IIPC http://netpreserve.org/projects/memento Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 39. Memento & Wikipedia, Mediawiki http://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 Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 41. To Be Expected NOT 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 at a certain point in time? •  For example, given a paper can one see the referenced materials as they 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 that Scholars 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 Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 44. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 45. Domain Gone Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 46. Archived copy December 5 2003 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 47. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 48. Current version Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 49. Archived copy December 11 2004 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 50. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 51. Resource gone Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 52. Archived copy December 5 2003 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 53. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 54. Resource gone Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 55. Archived copy unavailable Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 56. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 57. Current version Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 58. Archived copy August 26 2003 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 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 Web Resources 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 Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 61. arXiv Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 62. UNT Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 63. arXiv Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 64. Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 2012, Trondheim, Norway, October 1 2012
  • 65. DOI Redirects to R1 Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure EMTACL 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 Infrastructure EMTACL 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 Infrastructure EMTACL 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 Infrastructure EMTACL 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 Infrastructure EMTACL 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 Handler http://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 Handler http://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 Handler http://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 Infrastructure EMTACL 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