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ACKnowledge            Science Publishing:       The Different Interests ofRecord Keeping and Knowledge Transfer       Jan...
Publ!hing   =knowled" transfer
Publ!hing   ≠knowled" transfer
Why $! chan" ?
A new article in PubMed   every 36 seconds        ACKnowledge
Molecular Biology Laboratory in Heidelberg, Germany,and won Elsevier’s Grand Challenge 2009 competitionfor new tools that ...
ACKnowledge
Current publishing : needle transport              ACKnowledge
What does it allmean for publ!hing ?
Why do scient!ts    publ!h ?
The record*                       “keeping the minutes of science”      1                                            of S ...
The record*                       “keeping the minutes of science”      1                                            i    ...
Credit in the ego-system; the acknowledge economy*2                    *‘Acknowledge economy’ coined by Geoffrey Bilder of...
Credit in the ego-system; the acknowledge economy*2                    *‘Acknowledge economy’ coined by Geoffrey Bilder of...
1+2=the interface with   officialdom
Transfer of    information and knowledge3
3=the interface with science
Are  requirementsfor all $ree $e same?
Are  requirementsfor all $ree $e same?
What we have maybe good for  record  and for cre(t...
What we have maybe good for  record  and for cre(t...
...but ! it sat!factory  for  transfer of     knowled" ?                   ?
)ere ! ju* too much to read
Information consumes$e a+ention of itsrecipients...
...hence a weal$ of     information creates a     pove,y of a+entionHerbert Simon
Datarrhoea ?Publicatarrh ?
Sh-ld we have to make choices ?
Can we, truly ?
How w-ld wechoose anyway?
How w-ld wechoose anyway?
Sh-ldn’t we take inALL  knowled"    in -r area?
As well as sat!fy$e academic desire to   avoid rea(ng ?
Create an overview  fir*, perhaps?
ACKnowledge
And $en home in on     detail?
ACKnowledge
What does it allmean for publ!hing ?
In the interface with publishers
Content In the interface with publishers is King
Or “was” perhaps?     ACKnowledge
Well, it’s *illcontent $at c-nts
<protein kinase> <phosphorylates> <proteins>                  ACKnowledge
<protein kinase> <phosphorylates> <proteins>      <subject>    <predicate>    <object>                  ACKnowledge
<#26277419>      <#2121378>   <#13817745><protein kinase> <phosphorylates> <proteins>      <subject>     <predicate>    <o...
<#26277419>      <#2121378>     <#13817745><protein kinase> <phosphorylates> <proteins>      <subject>     <predicate>    ...
<#26277419>      <#2121378>     <#13817745><protein kinase> <phosphorylates> <proteins>A,icles are full of $ese      <subj...
<#26277419>      <#2121378>     <#13817745><protein kinase> <phosphorylates> <proteins>A,icles are full of $ese   Let’s ca...
Nanopublications: Assertions with Attitudes                 ACKnowledge
Nanopublications: Assertions with Attributes                 ACKnowledge
Nanopublications: Assertions with AttributesExamples of attributes:assertedBy - states which entity asserted (i.e. created...
Nanopublications are asse,ions
Nanopublications    are also   references
Nanopublications: Assertions with AttributesExamples of attributes:assertedBy - states which entity asserted (i.e. created...
i.0 $ey can be cited:  good for impact&acknowled"ment
And...aren’treferences open and      free ?
<rdf:Description rdf:about=”http://www.nbic.nl/cwa/relation/#26277419#13817745"><cwa:typeRelation rdf:resource=” http://pr...
<rdf:Description rdf:about=”http://www.nbic.nl/cwa/relation/#26277419#13817745"><cwa:typeRelation rdf:resource=” http://pr...
ACKnowledge
ACKnowledge
The whole picture
Even if you don’t have all the            detail
detailACKnowledge
nanopublications (i.e. references)   can also be used to reason             ACKnowledge
nanopublications (i.e. references)       can also be used to reason‘Publications’ yield ‘data’                 ACKnowledge
nanopublications (i.e. references)   can also be used to reason             ACKnowledge
nanopublications (i.e. references)            can also be used to reasonprotein X                                         ...
nanopublications (i.e. references)            can also be used to reasonprotein X            Exposing      ‘unkno1 kno1s’ ...
Citation: van Haagen HHHBM, t Hoen PAC, Botelho Bovo A, de Morrée A, van Mulligen EM, et al.(2009) Novel Protein-Protein I...
velterop@conceptweballiancejan.velterop@acknowledgeconnect.com             ACKnowledge
Jan Velterop: Science publishing: the different interests of record keeping and knowledge transfer
Jan Velterop: Science publishing: the different interests of record keeping and knowledge transfer
Jan Velterop: Science publishing: the different interests of record keeping and knowledge transfer
Jan Velterop: Science publishing: the different interests of record keeping and knowledge transfer
Jan Velterop: Science publishing: the different interests of record keeping and knowledge transfer
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Jan Velterop: Science publishing: the different interests of record keeping and knowledge transfer

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Science publications used to have the joint function of keeping the 'Minutes of Science' as well as transferring knowledge. The sheer amounts of material published (2 new articles in PubMed every minute of every day) make comprehensive knowledge transfer via reading of articles virtually impossible. When the literature is open, though, much of the essential knowledge it contains can be distilled and the big picture obtained without having to read all the articles, so that reading can then be reserved for those key articles that give insight in the reasoning and argumentation that leads to consensus. The result is a much more efficient knowledge transfer that doesn't have to compromise on comprehensiveness.

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Jan Velterop: Science publishing: the different interests of record keeping and knowledge transfer

  1. 1. ACKnowledge Science Publishing: The Different Interests ofRecord Keeping and Knowledge Transfer Jan Velterop – “Open Access-Open Data” – Köln – December 2010
  2. 2. Publ!hing =knowled" transfer
  3. 3. Publ!hing ≠knowled" transfer
  4. 4. Why $! chan" ?
  5. 5. A new article in PubMed every 36 seconds ACKnowledge
  6. 6. Molecular Biology Laboratory in Heidelberg, Germany,and won Elsevier’s Grand Challenge 2009 competitionfor new tools that improve the communication and useof scientific information.Reflect automatically recognizes and highlights thenames of genes, proteins and small molecules in the Cellarticles. Users clicking on a highlighted term will see a pop-up box containing information related to that term, such as A new article in PubMedsequence data and molecular structures, along with links tothe sources of the data. Reflect obtains this information from every 36 secondsits dictionary of millions of proteins and small molecules.Such ‘entity recognition’ can be done fairly accuratelyby many mining tools today. But other tools take on thetougher challenge of recognizing relationships between theentities. Researchers from Leiden University and ErasmusUniversity in Rotterdam, both in the Netherlands, havedeveloped software called Peregrine, and used it to pre-dict an undocumented interaction between two proteins: ACKnowledge
  7. 7. ACKnowledge
  8. 8. Current publishing : needle transport ACKnowledge
  9. 9. What does it allmean for publ!hing ?
  10. 10. Why do scient!ts publ!h ?
  11. 11. The record* “keeping the minutes of science” 1 of S c ienc The Rec o rd e*picture inspired by Geoffrey Bilder of CrossRef
  12. 12. The record* “keeping the minutes of science” 1 i o fS c Th en e e c Re c or d*picture inspired by Geoffrey Bilder of CrossRef
  13. 13. Credit in the ego-system; the acknowledge economy*2 *‘Acknowledge economy’ coined by Geoffrey Bilder of CrossRef
  14. 14. Credit in the ego-system; the acknowledge economy*2 *‘Acknowledge economy’ coined by Geoffrey Bilder of CrossRef
  15. 15. 1+2=the interface with officialdom
  16. 16. Transfer of information and knowledge3
  17. 17. 3=the interface with science
  18. 18. Are requirementsfor all $ree $e same?
  19. 19. Are requirementsfor all $ree $e same?
  20. 20. What we have maybe good for record and for cre(t...
  21. 21. What we have maybe good for record and for cre(t...
  22. 22. ...but ! it sat!factory for transfer of knowled" ? ?
  23. 23. )ere ! ju* too much to read
  24. 24. Information consumes$e a+ention of itsrecipients...
  25. 25. ...hence a weal$ of information creates a pove,y of a+entionHerbert Simon
  26. 26. Datarrhoea ?Publicatarrh ?
  27. 27. Sh-ld we have to make choices ?
  28. 28. Can we, truly ?
  29. 29. How w-ld wechoose anyway?
  30. 30. How w-ld wechoose anyway?
  31. 31. Sh-ldn’t we take inALL knowled" in -r area?
  32. 32. As well as sat!fy$e academic desire to avoid rea(ng ?
  33. 33. Create an overview fir*, perhaps?
  34. 34. ACKnowledge
  35. 35. And $en home in on detail?
  36. 36. ACKnowledge
  37. 37. What does it allmean for publ!hing ?
  38. 38. In the interface with publishers
  39. 39. Content In the interface with publishers is King
  40. 40. Or “was” perhaps? ACKnowledge
  41. 41. Well, it’s *illcontent $at c-nts
  42. 42. <protein kinase> <phosphorylates> <proteins> ACKnowledge
  43. 43. <protein kinase> <phosphorylates> <proteins> <subject> <predicate> <object> ACKnowledge
  44. 44. <#26277419> <#2121378> <#13817745><protein kinase> <phosphorylates> <proteins> <subject> <predicate> <object> ACKnowledge
  45. 45. <#26277419> <#2121378> <#13817745><protein kinase> <phosphorylates> <proteins> <subject> <predicate> <object> ‘Asse,ion‘ a.k.a. ‘T/ple’ ACKnowledge
  46. 46. <#26277419> <#2121378> <#13817745><protein kinase> <phosphorylates> <proteins>A,icles are full of $ese <subject> <predicate> <object> ‘ asse,ions/t/ples Asse,ion‘ a.k.a. ‘T/ple’ ACKnowledge
  47. 47. <#26277419> <#2121378> <#13817745><protein kinase> <phosphorylates> <proteins>A,icles are full of $ese Let’s call $em <subject> <predicate> <object> ‘ asse,ions/t/ples ‘Nanopublications’ Asse,ion‘ a.k.a. ‘T/ple’ ACKnowledge
  48. 48. Nanopublications: Assertions with Attitudes ACKnowledge
  49. 49. Nanopublications: Assertions with Attributes ACKnowledge
  50. 50. Nanopublications: Assertions with AttributesExamples of attributes:assertedBy - states which entity asserted (i.e. created) the statementcuratedBy - states that a specified entity has curated the statementisPeerReviewed - states that this statement has been peer reviewedisPublished - states where this statement was first publishedisEvidencedBy - states that another statement, Y, should be considered evidence for thisstatement XcreatedOn - states the date/time that the statement was createdhasAuthor - states who claims authorship of the statementisApprovedBy - states who approves of the statementisDeprecatedBy - states that the statement is no longer in use by the entity in question ACKnowledge
  51. 51. Nanopublications are asse,ions
  52. 52. Nanopublications are also references
  53. 53. Nanopublications: Assertions with AttributesExamples of attributes:assertedBy - states which entity asserted (i.e. created) the statementcuratedBy - states that a specified entity has curated the statementisPeerReviewed - states that this statement has been peer reviewedisPublished - states where this statement was first publishedisEvidencedBy - states that another statement, Y, should be considered evidence for thisstatement XcreatedOn - states the date/time that the statement was createdhasAuthor - states who claims authorship of the statementisApprovedBy - states who approves of the statementisDeprecatedBy - states that the statement is no longer in use by the entity in question ACKnowledge
  54. 54. i.0 $ey can be cited: good for impact&acknowled"ment
  55. 55. And...aren’treferences open and free ?
  56. 56. <rdf:Description rdf:about=”http://www.nbic.nl/cwa/relation/#26277419#13817745"><cwa:typeRelation rdf:resource=” http://predicate.conceptwiki.org/index.php/#2121378”/><cwa:direction>1,2</cwa:direction><cwa:strength>1.0</cwa:strength><cwa:author rdf:resource=”http://people.conceptwiki.org/index.php/#85094810”/><cwa:provenance rdf:resource=”http://article.conceptwiki.org/index.php/#121646370”/><cwa:timestamp>1240641052059</cwa:timestamp><cwa:annotated_by rdf:resource=”http://people.conceptwiki.org/index.php/#43065817”/><cwa:annotation rdf resource=”http://www.virusdb.org/viruses/av/Heliothis_virescens_insect”></rdf:Description> ACKnowledge
  57. 57. <rdf:Description rdf:about=”http://www.nbic.nl/cwa/relation/#26277419#13817745"><cwa:typeRelation rdf:resource=” http://predicate.conceptwiki.org/index.php/#2121378”/><cwa:direction>1,2</cwa:direction><cwa:strength>1.0</cwa:strength><cwa:author rdf:resource=”http://people.conceptwiki.org/index.php/#85094810”/><cwa:provenance rdf:resource=”http://article.conceptwiki.org/index.php/#121646370”/><cwa:timestamp>1240641052059</cwa:timestamp><cwa:annotated_by rdf:resource=”http://people.conceptwiki.org/index.php/#43065817”/><cwa:annotation rdf resource=”http://www.virusdb.org/viruses/av/Heliothis_virescens_insect”></rdf:Description> ACKnowledge
  58. 58. ACKnowledge
  59. 59. ACKnowledge
  60. 60. The whole picture
  61. 61. Even if you don’t have all the detail
  62. 62. detailACKnowledge
  63. 63. nanopublications (i.e. references) can also be used to reason ACKnowledge
  64. 64. nanopublications (i.e. references) can also be used to reason‘Publications’ yield ‘data’ ACKnowledge
  65. 65. nanopublications (i.e. references) can also be used to reason ACKnowledge
  66. 66. nanopublications (i.e. references) can also be used to reasonprotein X protein A ACKnowledge
  67. 67. nanopublications (i.e. references) can also be used to reasonprotein X Exposing ‘unkno1 kno1s’ protein A ACKnowledge
  68. 68. Citation: van Haagen HHHBM, t Hoen PAC, Botelho Bovo A, de Morrée A, van Mulligen EM, et al.(2009) Novel Protein-Protein Interactions Inferred from Literature Context. PLoS ONE 4(11): e7894.doi:10.1371/journal.pone.0007894
  69. 69. velterop@conceptweballiancejan.velterop@acknowledgeconnect.com ACKnowledge

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