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