Post on 20-Sep-2014
description
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.
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
http://blogs.plos.org/plos/2012/04/bridging-the-journal-wikipedia-gap/
PLoS Computational Biology
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
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
Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure
EMTACL 2012, Trondheim, Norway, October 1 2012
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
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
• 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
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
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%)
Herbert Van de Sompel Paint-Yourself-In-The-Corner Infrastructure
EMTACL 2012, Trondheim, Norway, October 1 2012
• Content Management Systems
• Web Archives
• Transactional archives
• Search engine caches
• …
Traces of the Past Web Exist
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
Today Select Date Jun 16 1997 Jun 16 1997
From Internet Archive
Time Travel
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
• 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
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
• 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
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 …
http://alexanderponting.blogspot.com/2012/01/how-to-paint-yourself-into-corner.html
@hvdsomp