Towards Machine-Actionable Scholarly Communication h"p://www.flickr.com/photos/feuilllu/3021807255/ @hvdsomp herbert van de sompel
May 08, 2015
Towards Machine-Actionable Scholarly Communication
h"p://www.flickr.com/photos/feuilllu/3021807255/
@hvdsomp
herbert van de sompel
Patterson. Re-engineering the functions of journals OAI7 Workshop presentation http://indico.cern.ch/contributionDisplay.py?sessionId=8&contribId=20&confId=103325
Patterson. Re-engineering the functions of journals OAI7 Workshop presentation http://indico.cern.ch/contributionDisplay.py?sessionId=8&contribId=20&confId=103325
http://www.flickr.com/photos/irrezolut/2974930837/
• Augmentation of the scholarly record with a machine actionable substrate • Integration of datasets into the scholarly record • Exposure of scholarly process and its integration in the scholarly record
Van de Sompel & Lagoze All Aboard: Toward a Machine-Friendly Scholarly Communication System. In: The Fourth Paradigm. h"p://research.microso=.com/en-‐us/collaboraAon/fourthparadigm/
• Unique identifiers (URI) for every Thing • Typed Links, Vocabularies, Ontologies (URI, RDF, RDFS, OWL) • Ability to publish information about a Thing • Ability for human and machine to look Things up (HTTP)
Exhibit 1: My Work in this Realm
OAI Object Reuse & Exchange
http://www.openarchives.org/ore/
Complex Objects
Open AnnotaAon
http://www.openannotation.org/
Yuma Map AnnotaAon
Haslhofer et. al. (2011) The Open Annotation Collaboration (OAC) Data Model MMWeb 2011 http://arxiv.org/abs/1106.5178
Memento: Time Travel for the Web
http://mementoweb.org
2010 Digital Preservation Coalition Digital Preservation Award
Version NavigaAon: Pic of the Day
http://www.mementoweb.org/demo/picoftheday.mov
Version NavigaAon: Time Series Analysis
Van de Sompel et. al. An HTTP-‐Based Versioning Mechanism for Linked Data LDOW 2009 h"p://arxiv.org/abs/1003.3661
Exhibit 2: Nanopublications
h"p://www.flickr.com/photos/stannate/1369623187/
The Paper Deluge
• Too much scholarly publicaAons to consume
• Too hard to make cross-‐discipline connecAons, to combine exisAng disparate findings to arrive at new insights
Palmer et. al. (2007) Weak informa<on work in scien<fic discovery Inf. Process. Manage. 43(3) 808–820 h"p://dx.doi.org/10.1016/j.ipm.2006.06.003
Ru"enberg et. al. Advancing transla<onal research with the Seman<c Web BMC Bioinf. 8(suppl. 3) S2 h"p://dx.doi.org/10.1186/1471-‐2105-‐8-‐S3-‐S2
Literature Mining
Verspoor et. al. The textual characteris<cs of tradi<onal and Open Access scien<fic journals are similar. BMC Bioinforma:cs 2009, 10:183 h"p://dx.doi.org/10.1186/1471-‐2105-‐10-‐183
Entity Identifiers & Ontologies
http://www.obofoundry.org/
Nanopublication
http://www.nanopub.org/
Nanopublication
http://www.nanopub.org/
Nanopublication
http://www.nanopub.org/
A Fix for the Nerds
Groth et. al. The Anatomy of a Nano-publication Information Services and Use 30(1), p.51-56, 2010 http://iospress.metapress.com/index/FTKH21Q50T521WM2.pdf
Publish, Merge, Search, Reason, Predict, Integrate
Clare et. al. Exploring the Genera<on and Integra<on of Publishable Scien<fic Facts Using the Concept of Nano-‐publica<ons ESWC 2011 https://svn.kwarc.info/repos/clange/conferences/eswc2011/sepublica/proceedings/999990013/999990013.pdf
Mons (2011) Nanopublications OAI7 Workshop presentation http://indico.cern.ch/contributionDisplay.py?sessionId=13&contribId=38&confId=103325
Smit & van der Graaf (2011) Journal Article Mining h"p://www.publishingresearch.net/documents/PRCSmitJAMreport20June2011VersionofRecord.pdf
Exhibit 3: Executable Papers
http://www.jeff-barr.com/?p=1446
Utopia Reader
Attwood et al. (2009) Utopia document and the Semantic Biochemical Journal. EMBnet.news , 15 (4). http://journal.embnet.org/index.php/embnetnews/article/viewArticle/45/151
h"p://www.executablepapers.com/about-‐challenge.html
Executable Paper: 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
This space intenAonally blank.
Figure 1 of
http://dx.doi.org/10.1016/j.procs.2011.04.064 goes here but is copyrighted.
Collage: Authoring and Reading
Nowakowski et al. (2011) The Collage Authoring Environment Procedia Computer Science v4 http://dx.doi.org/10.1016/j.procs.2011.04.064
This space intenAonally blank.
Figure 2 of
http://dx.doi.org/10.1016/j.procs.2011.04.064 goes here but is copyrighted.
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
This space intenAonally blank.
Figure 3 of
http://dx.doi.org/10.1016/j.procs.2011.04.064 goes here but is copyrighted.
Link Rot, CitaAon Rot, Service Rot
Sanderson et al. (2011) Analyzing the Persistence of Referenced Web Resources with Memento Open Repositories Conference Paper http://arxiv.org/abs/1105.3459
Exhibit 4: Citation
h"p://www.flickr.com/photos/themacinator/4183736814/
Citation
• Scholarly record expands: • Papers • Datasets • NanopublicaAons • Workflows • So=ware • …
• More ways to get credit
Move from Journal centric …
… to Contributor centric
Automatic Citation Graph
h"p://portal.acm.org
1. Article splash page in open access, crawl-enabled. 2. Splash page with recognizable References section 3. References that URI-link to the cited article
Open Data for Metrics
http://openurl.ac.uk/doc/data/thedata.html
Keep Your Eye On The Ball
h"p://www.flickr.com/photos/garryknight/3595141669/
Ownership
http://www.flickr.com/photos/vectorportal/5047619590/
Cost
http://www.flickr.com/photos/mammal/3455272493/
Persistence
The Long Now’s 10.000 Year Clock http://longnow.org/clock/prototype1/
Towards Machine-Actionable Scholarly Communication
h"p://www.flickr.com/photos/feuilllu/3021807255/
@hvdsomp
herbert van de sompel