How	  to	  Execute	  	            A	  Research	  Paper	                Anita	  de	  Waard	  	    Disrup8ve	  Technologies	...
Outline	  •  Ten	  people/ideas	  who/that	  are	  changing	     scholarly	  publishing:	      –  New	  forms	      –  Wor...
Theme	  1:	  New	  forms	  of	  publica8on	  •  Main	  issue:	  the	  format	  of	  the	  scien8fic	  paper	  comes	     fr...
Steve	  PeTfer,	  U	  Manchester	  •  Utopia:	  ‘Everything	  you	  always	  wanted	  to	  do	     with	  a	  PDF….’:	  in...
Gully	  Burns,	  USC	  ISI	  •  KEfED:	  model	  of	  research	  as	  an	     ac8vity	  •  Map	  out	  dependent/   indepe...
Tim	  Clark,	  Harvard/MGH	  •  DOMEO:	  automated	  en8ty	  markup	  +	  manual	     mark	  up	  of	  claim/evidence	  ne...
Theme	  2:	  data	  and	  workflow	  integra8on	  •  Issues:	  	       –  Format	  of	  the	  research	  paper	  hard	  to	...
Dave	  DeRoure,	  Oxford	  e-­‐Research	  Centre	  •  Research	  objects:	  consist	  of	  all	  	                        ...
Phil	  Bourne,	  UCSD	  •  Big	  need:	  keep	  track	  of	  the	  data	  in	  my	  lab!	  •  Other	  need:	  know	  what	...
Deborah	  McGuinness,	  RPI	  •  Future	  Web:	  	    •  ‘if	  everything	  is	  everywhere,	  how	  do	  we	  find	       ...
Theme	  3:	  New	  Models	  for	  Access/AHribu8on	  •  Issues:	  	      –  User-­‐created	  content,	  crowdsourcing	  me...
Paul	  Groth,	  VU	  Amsterdam	  Altmetrics:	  “the	  crea8on	  and	  study	  of	  	  new	  metrics	  based	  on	  the	  S...
Leslie	  Chan,	  U.	  Toronto	  Scarborough	   •  ElPub	  conference	  series	  that	  focus	  	      on	  globally	  conn...
John	  Wilbanks,	  Kauffman/CC	  •  As	  data	  becomes	  more	  accessible,	  need:	  	    •  raw	  metadata	  	    •  sta...
Cameron	  Neylon,	  Cambridge	  •  Main	  arguments	  for	  Open	  Access:	  	    •  Ci8zen	  science	  is	  becoming	  mo...
In	  summary,	  scien8sts	  are	  working	  on:	                                                           	  •  Tools	  f...
So	  do	  we	  s8ll	  need	  publishers?	  	                                    Or libraries?•  Technically,	  there	  is	...
“Publishers	  have	  been	  thinking	  we’re	  going	  out	  of	  business	  for	  20	  years,	  what	  has	  suddenly	  c...
What	  do	  we	  need?	    Internet of things: (Bleecker, [1])  Interact with ‘objects that blog’ or ‘Blogjects’, that:  t...
Some	  examples	  of	  networked	  science:	                                                 	  •  Mathoverflow:	  virtual	...
Some	  further	  parts	  of	  a	  solu8on:                                                  	  •  Iden8fying	  the	  key	 ...
DOMEO:	  Annota8ng	  claims                                 	  22                                      22
Finding	  ‘Claimed	  Knowledge	  Updates’                                                	  23                            ...
Executable	  Papers                                    	  •  E.g.:	  hHp://  ...
Wrapping	  a	  story	  around	  your	  data:                                                	                             ...
FORCE11	  Community	  of	  Prac8ce	  •  Workshop	  in	  August	  of	  2011:	  35	  invited	  aHendees	  from	  different	  ...
Summary:	                                  	  •  Ten	  people	  who	  are	  changing	  scholarly	     publishing:	      – ...
….	  but	  I	  am	  sure	  you	  can	  come	  up	  with	  beHer	  ideas!	                                                 ...
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How to Execute A Research Paper


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Talk on changes in scholarly publishing, University of Lethbridge Dept of e-Humanities

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How to Execute A Research Paper

  1. 1. How  to  Execute     A  Research  Paper   Anita  de  Waard     Disrup8ve  Technologies  Director   Elsevier  Labs  University  of  Lethbridge,  April  3,  2012  
  2. 2. Outline  •  Ten  people/ideas  who/that  are  changing   scholarly  publishing:   –  New  forms   –  Workflow/data  integra8on   –  New  models  of  business/aHribu8on  •  So  what  does  this  mean?  •  Some  projects  to  help  us  move  towards  these   new  models   2
  3. 3. Theme  1:  New  forms  of  publica8on  •  Main  issue:  the  format  of  the  scien8fic  paper  comes   from  a  8me  when  our  communica8on  was  paper-­‐ centric  •  Solu8on:  Rethink  the  unit  and  form  of  the  scholarly   publica8on  from  the  ground  (i.e.,  the  experiment)  up  •  Three  projects  doing  that:   3
  4. 4. Steve  PeTfer,  U  Manchester  •  Utopia:  ‘Everything  you  always  wanted  to  do   with  a  PDF….’:  interac8ve,  sharable  •  Working  on  integra8on  with  DOMEO  to  add/ share  annota8ons  •  Final  goal:  don’t  ‘reconstruct  the  cow  from  a   hamburger’:  include  workflows  and  models   4
  5. 5. Gully  Burns,  USC  ISI  •  KEfED:  model  of  research  as  an   ac8vity  •  Map  out  dependent/ independent  variables     within  an  experiment  and   model  them  •  Start:  appendix  to  paper;  later:   precede  paper,  gra`  paper  on   top  of  model.   5
  6. 6. Tim  Clark,  Harvard/MGH  •  DOMEO:  automated  en8ty  markup  +  manual   mark  up  of  claim/evidence  networks  •  Working  on  plagorm  for  workflow  integra8on   rdf:type <hHp://>   swande:Claim   dct:title Intramembranous  Aβ  behaves  as  chaperones  of   other  membrane  proteins   G1 swanrel:referencesAsSupportiveEvidence <hHp://>   G5 pav:contributedBy <hHp://>   G6
  7. 7. Theme  2:  data  and  workflow  integra8on  •  Issues:     –  Format  of  the  research  paper  hard  to  integrate  within  a   scien8fic/clinical  workflow     –  Hard  to  reproduce/deduce:  what  methods  were  used  and   what  data  was  created  for  a  piece  of  research,  making   reproduc8on  or  even  review  difficult  •  Some  solu8ons  for  sharing  workflows  and  data:     7
  8. 8. Dave  DeRoure,  Oxford  e-­‐Research  Centre  •  Research  objects:  consist  of  all     Workflow  16   academic  output,  including:     Results   produc Q es   T L   -  Papers   Include d  in   Published   -  Workflows   Included   in   Feeds   in   into   -  Logs   Data   produc es   Include d  in   Included   in   -  Talks,  lectures   Metadata   Slides   Paper   -  Blogs   produce s   Published   in   Common   pathways     Workflow  13•  Move  towards  executable  work:   Results   -  Execute  periodically  to  validate   -  Run  automa8cally  when  data  updates  –  by  self  or  others!   -  No8fy  researchers  of  new  results   8
  9. 9. Phil  Bourne,  UCSD  •  Big  need:  keep  track  of  the  data  in  my  lab!  •  Other  need:  know  what  I  did/what  other  people   did  –  Yolanda  Gil  made  workflow  representa8on,   was  hard  to  remember  what  we  did…  •  Need:  beHer  ways  to  record,  share,  archive  what   we  did.    •  New  role  for  the  publisher  >     9
  10. 10. Deborah  McGuinness,  RPI  •  Future  Web:     •  ‘if  everything  is  everywhere,  how  do  we  find   it/know  what  we  want?’   •  Internet,  Web,  Grid,  Cloud,  Seman8c  Grid   Middleware  •  Xinforma8cs:   •  Where  X  =  geo,  eco,  econo…   •  Linked  Data  to  Seman8cs    •  Seman8c  Founda8ons:     •  Pushing  the  boundaries  of     Seman8c  Web  standards   •  Ontology  evolu8on   10
  11. 11. Theme  3:  New  Models  for  Access/AHribu8on  •  Issues:     –  User-­‐created  content,  crowdsourcing  means  (scien8fic)   impact  is  measured  very  differently  from  the  past   –  Need  new  models  for  copyright/IP   –  Ci8zen  scien8sts  par8cipate  as  well  •  Some  efforts  to  address  this:   11
  12. 12. Paul  Groth,  VU  Amsterdam  Altmetrics:  “the  crea8on  and  study  of    new  metrics  based  on  the  Social  Web    for  analyzing  and  informing  scholarship.”  Including:     - Downloads   - Where  readers  read   - Data  cita8on   - Social  network  diffusion   - Slide  reuse   - Peer  review  contribu8ons     - Youtube  views   12
  13. 13. Leslie  Chan,  U.  Toronto  Scarborough   •  ElPub  conference  series  that  focus     on  globally  connec8ng  informa8on  scien8sts   •  Bioline  Interna8onal  system  “a  not-­‐for-­‐profit   scholarly  publishing  coopera8ve  commiHed  to   providing  open  access  to  quality  research  journals   published  in  developing  countries”:     13
  14. 14. John  Wilbanks,  Kauffman/CC  •  As  data  becomes  more  accessible,  need:     •  raw  metadata     •  standards  processes   •  consensus  processes   •  document  submission  standards   •  data  archives  •  Ways  of  governing  access:     •  Privacy  vs.  IP  vs.  policies   •  Technology  only  helps  so  much…     •  This  is  mostly  a  social/policy  issue   14
  15. 15. Cameron  Neylon,  Cambridge  •  Main  arguments  for  Open  Access:     •  Ci8zen  science  is  becoming  more  important   •  Science  changes  when  it  is  crowdsourced:   Tim  Gowers:  ‘ This  is  to  normal  research  as   driving  is  to  pushing  a  car’  •  Three  principles:   •  Scale  and  connec8vity   •  Reduced  fric8on  to  access   •  Demand-­‐side  filters   15
  16. 16. In  summary,  scien8sts  are  working  on:    •  Tools  for  knowledge…   –  Visualisa8on  (Steve  PeTfer)   –  Modeling  (Gully  Burns)   –  Annota8on  (Tim  Clark)  •  Ways  to  link  to   –  Workflows  (Dave  De  Roure)   –  Lab  data  (Phil  Bourne)   –  Linked  research  data  (Deborah  McGuinness)  •  And  models  for   –  AHribu8on/credit  (Paul  Groth)   –  Allowing  new  players  to  par8cipate  (Leslie  Chan)   –  Copyright/IP  rights  (John  Wilbanks)   –  Networked  science  (Cameron  Neylon).   16
  17. 17. So  do  we  s8ll  need  publishers?     Or libraries?•  Technically,  there  is  no  reason  to  publish  in  a   journal–  or  even,  for  that  maHer,  to  publish  a  paper   at  all!  •  A  few  good  blog  posts  linked  to  workflows  and  data   with  some  valida8on  from  peers  and  good   download  sta8s8cs  might  serve  you  just  as  well  –   or,  in  fact,  much  beHer….    •  Is  publishing  in  journals  mostly  a  habit?         17
  18. 18. “Publishers  have  been  thinking  we’re  going  out  of  business  for  20  years,  what  has  suddenly  changed?”  The  internet!  Not  the  technical  web,  but  the  social  web….  ‘The  value  of  a  […]  network  is  propor8onal  to  the  square   of  the  number  of  users  of  the  system  (n²)’   1990’s: 2000’s: 2015: Big Player Medium Participant Irrelevant!18
  19. 19. What  do  we  need?   Internet of things: (Bleecker, [1]) Interact with ‘objects that blog’ or ‘Blogjects’, that: track where they are and where they’ve been;have histories of their encounters and experienceshave agency - an assertive voice on the social web [2] Research Objects: (Bechofer et al, [2]) Create semantically rich aggregations of resources, that can possess some scientific intent or support some research objective Networked Knowledge: (Neylon, [3]) If we care about taking advantage of the web and internet for research then we must tackle the building of scholarly communication networks. These networks will have two critical characteristics: scale and a lack of friction. [3][[1] Bleecker, J. ‘A Manifesto for Networked Objects — Cohabiting with Pigeons, Arphids and Aibos in the Internet of Things] Bechhofer, S., De Roure, D., Gamble, M., Goble, C. and Buchan, I. (2010) Research Objects: Towards Exchange andReuse of Digital Knowledge. In: The Future of the Web for Collaborative Science (FWCS 2010), April 2010, Raleigh, NC, USA.[3] Neylon, C. ‘Network Enabled Research: Maximise scale and connectivity, minimise friction’, 19 19network-enabled-research/ ‘
  20. 20. Some  examples  of  networked  science:    •  Mathoverflow:  virtual  network  of   mathemagicians  working  collec8vely  to  answer   big,  small,  clear  and  fuzzy  ques8ons  •  Galaxy  Zoo:  ci8zen  science:  classify  galaxies  in   the  comfort  of  your  own  home  –  like  Hanny!  •  Tim  Gowers,  Polymath:     “…the  real  contributors  will  be  the  process  owners  and   project  leaders  that  are  able  to  provide  horizontal   leadership.  To  support  this  shi`,  organiza8ons  will  need  to   reward  and  recognize  horizontal  contribu8ons  as  much,  if   not  more,  than  hierarchical  posi8ons.”   20
  21. 21. Some  further  parts  of  a  solu8on:  •  Iden8fying  the  key  claims  the  authors  make  and   linking  them  to  their  suppor8ng  evidence  both   within  and  across  papers    •  Develop  ‘executable  papers’  that  contain   computable  and  ‘living’  components  •  BeHer  integra8ng  papers  with  research   workflows  and  data      •  New  models  for  business,  aHribu8on  and   copyright  in  scholarly  publishing   21
  22. 22. DOMEO:  Annota8ng  claims  22 22
  23. 23. Finding  ‘Claimed  Knowledge  Updates’  23 23
  24. 24. Executable  Papers  •  E.g.:  hHp:// Levels2and3     24
  25. 25. Wrapping  a  story  around  your  data:   metadata 1. Research: Each item in the system has metadata (including metadata provenance) and relations to other data items added to it. 2. Workflow: All data items created in the lab are added to a metadata (lab-owned) workflow system. 3. Authoring: A paper is written in an authoring tool which can pull data with provenance from the workflow tool in the appropriate representation into the document. metadata 4. Editing and review: Once the co-authors agree, the paper is ‘exposed’ to the editors, who in turn expose it to reviewers. metadata Reports are stored in the authoring/editing system, the paper gets updated, until it is validated. 5. Publishing and distribution: When a paper is published, a collection of validated information is exposed to the world. It remains connected to its related data item, and its heritage can Rats were subjected to two be traced. grueling tests (click on fig 2 to see underlying 6. User applications: distributed applications run on this data). These results suggest that ‘exposed data’ universe. the neurological pain pro- Some other publisher Review Revise Edit Concept developed with Ed Hovy, Phil Bourne, 25 Gully Burns and Cartic Ramakrishnan
  26. 26. FORCE11  Community  of  Prac8ce  •  Workshop  in  August  of  2011:  35  invited  aHendees  from  different   parts  of  science,  industry,  funding  agencies,  data  centers  •  Goal:  map  main  obstacles  preven8ng  new  models  of  science   publishing  and  develop  ways  to  overcome  them  •  Just  received  funding  from   Sloan  founda8on  to:   •  Start  online  community   •  Hold  next  workshop   •  Look  at  new  efforts     26
  27. 27. Summary:    •  Ten  people  who  are  changing  scholarly   publishing:   –  New  forms   –  Workflow/data  integra8on   –  New  models  of  business/aHribu8on   –  Networked  science!  •  We  (publishers,  editors,  libraries,  etc)need  to   revisit  if  and  how  we  are  needed    •  Some  projects  are  underway  to  help  us  move   towards  these  new  models…   27
  28. 28. ….  but  I  am  sure  you  can  come  up  with  beHer  ideas!     hHp://     28