paint-yourself-in-the-corner infrastructure

http://alexanderponting.blogspot.com/2012/01/how-to-paint-yourself-into-corner.html

@hvdsomp

Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure

EMTACL 2012, Trondheim, Norway, October 1 2012

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.



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



Article Wikipedia Bridge

http://blogs.plos.org/plos/2012/04/bridging-the-journal-wikipedia-gap/

PLoS Computational Biology



Research Objects

Bechhofer, S. et al. (2010) http://precedings.nature.com/documents/4626/version/1



Nowakowski et al. (2011) The Collage Authoring Environment Procedia Computer Science v4 http://dx.doi.org/10.1016/j.procs.2011.04.064

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

Executable Paper – Collage – Rendering a Paper



Scientific Workflows, Services, Data, Workflow Engines

Carole Goble, JCDL 2012 Keynote https://dl.dropbox.com/u/617206/JCDL2012keynoteGoble.ppt



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



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.



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.



The Web as the Infrastructure: alt-metrics

http://altmetrics.org/manifesto/



http://impactstory.it/



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.



Existing Archival Infrastructure Assumes Fixity and Boundary



The Web Exists in the Perpetual Now



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



Not Accessible From cnn.com



Paper Era: Publication Context



Web Era: Publication Context



Several Challenges

•  Archival approach and infrastructure to deal with dynamic, interdependent content

•  Referencing scholarly assets

•  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.

Recreating a Version of the Scholarly Record



To Be Expected



Time-dependent decay of URLs published in MEDLINE abstracts

Wren J D, Bioinformatics, 2008;24:1381-1385

Most common types dead links were for computer programs (43%), followed by scholarly content (38%) and databases (19%)



•  Content Management Systems

•  Web Archives

•  Transactional archives

•  Search engine caches

•  …

Traces of the Past Web Exist



If Only It Would Be Possible to Follow a URI in Time



It is with Memento

Digital Preservation Award 2010

http://www.mementoweb.org/



Today Select Date Jun 16 1997 Jun 16 1997

From Internet Archive

Time Travel



June 16 1997

http://www.ntnu.no/ @ June 16 1997



Original Resources and Mementos



Bridge from Present to Past



Bridge from Past to Present



Memento Framework



Also with 404, etc.



Memento & IIPC

http://netpreserve.org/projects/memento



Memento & Wikipedia, Mediawiki

http://en.wikipedia.org/wiki/Wikipedia:Requests_for_comment/Memento



Memento & DBpedia

http://mementoweb.org/depot/native/dbpedia/



To Be Expected

NOT IN ARCHIVE



•  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

Recreating a Version of the Scholarly Record



Published September 15 2004



Domain Gone



Archived copy December 5 2003



Current version



Resource gone



Archived copy unavailable



Current version



Archived copy August 26 2003



•  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.

Citation Rot Studies at Scale with Memento

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



UNT



arXiv



UNT



arXiv



DOI Redirects to R1



Later, DOI Redirects to R2, then R3



R1, R2, R3 Have Mementos



Looking for Memento of DOI with t in [t2,t3[



End Up at Wrong Memento



Introduce Temporal Awareness for DOI Resolver



End Up at Correct Memento



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



Several Challenges






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



DURI

http://tools.ietf.org/html/draft-masinter-dated-uri



duri:1997-06-17:http://www.ntnu.no

http://www.ntnu.no/ @ June 16 1997



HTML5 Custom Protocol Handler

http://dev.opera.com/articles/view/html5-custom-protocol-and-content-handlers/



Referencing Scholarly Assets



Several Challenges






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.



SiteStory Transactional Archiving

http://mementoweb.github.com/SiteStory/



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 …

http://alexanderponting.blogspot.com/2012/01/how-to-paint-yourself-into-corner.html

@hvdsomp

paint-yourself-in-the-corner infrastructure

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