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.

1. ACKnowledge
Science Publishing:
The Different Interests of
Record Keeping and Knowledge Transfer
Jan Velterop – “Open Access-Open Data” – Köln – December 2010

2. Publ!hing =
knowled" transfer

3. Publ!hing ≠
knowled" transfer

4. Why $! chan" ?

5. A new article in PubMed
every 36 seconds
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6. Molecular Biology Laboratory in Heidelberg, Germany,
and won Elsevier’s Grand Challenge 2009 competition
for new tools that improve the communication and use
of scientific information.
Reflect automatically recognizes and highlights the
names of genes, proteins and small molecules in the Cell
articles. Users clicking on a highlighted term will see a pop-
up box containing information related to that term, such as
A new article in PubMed
sequence data and molecular structures, along with links to
the sources of the data. Reflect obtains this information from
every 36 seconds
its dictionary of millions of proteins and small molecules.
Such ‘entity recognition’ can be done fairly accurately
by many mining tools today. But other tools take on the
tougher challenge of recognizing relationships between the
entities. Researchers from Leiden University and Erasmus
University in Rotterdam, both in the Netherlands, have
developed software called Peregrine, and used it to pre-
dict an undocumented interaction between two proteins:
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7. ACKnowledge

8. Current publishing : needle transport
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9. What does it all
mean for publ!hing ?

10. Why do scient!ts
publ!h ?

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. 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. Credit in the ego-system; the acknowledge economy*
2
*‘Acknowledge economy’ coined by Geoffrey Bilder of CrossRef

14. Credit in the ego-system; the acknowledge economy*
2
*‘Acknowledge economy’ coined by Geoffrey Bilder of CrossRef

15. 1+2=
the interface with
officialdom

16. Transfer of
information and knowledge
3

17. 3=
the interface with science

18. Are ' requirements
for all $ree $e same?

19. Are ' requirements
for all $ree $e same?

20. What we have may
be good for ' record
and for cre(t...

21. What we have may
be good for ' record
and for cre(t...

22. ...but ! it sat!factory
for ' transfer of
knowled" ?
?

23. )ere ! ju* too
much to read

24. Information consumes
$e a+ention of its
recipients...

25. ...hence a weal$ of
information creates a
pove,y of a+ention
Herbert Simon

26. Datarrhoea ?
Publicatarrh ?

27. Sh-ld we have to
make choices ?

28. Can we, truly ?

29. How w-ld we
choose anyway?

30. How w-ld we
choose anyway?

31. Sh-ldn’t we take in
ALL ' knowled"
in -r area?

32. As well as sat!fy
$e academic desire to
avoid rea(ng ?

33. Create an overview
fir*, perhaps?

34. ACKnowledge

35. And $en home in on
detail?

36. ACKnowledge

37. What does it all
mean for publ!hing ?

38. In the interface with publishers

39. Content In the interface with publishers is King

40. Or “was” perhaps?
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41. Well, it’s *ill
content $at c-nts

42. <protein kinase> <phosphorylates> <proteins>
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43. <protein kinase> <phosphorylates> <proteins>
<subject> <predicate> <object>
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44. <#26277419> <#2121378> <#13817745>
<protein kinase> <phosphorylates> <proteins>
<subject> <predicate> <object>
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45. <#26277419> <#2121378> <#13817745>
<protein kinase> <phosphorylates> <proteins>
<subject> <predicate> <object>
‘Asse,ion‘ a.k.a. ‘T/ple’
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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’
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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’
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48. Nanopublications: Assertions with Attitudes
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49. Nanopublications: Assertions with Attributes
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50. Nanopublications: Assertions with Attributes
Examples of attributes:
assertedBy - states which entity asserted (i.e. created) the statement
curatedBy - states that a specified entity has curated the statement
isPeerReviewed - states that this statement has been peer reviewed
isPublished - states where this statement was first published
isEvidencedBy - states that another statement, Y, should be considered evidence for this
statement X
createdOn - states the date/time that the statement was created
hasAuthor - states who claims authorship of the statement
isApprovedBy - states who approves of the statement
isDeprecatedBy - states that the statement is no longer in use by the entity in question
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51. Nanopublications
are asse,ions

52. Nanopublications
are also
references

53. Nanopublications: Assertions with Attributes
Examples of attributes:
assertedBy - states which entity asserted (i.e. created) the statement
curatedBy - states that a specified entity has curated the statement
isPeerReviewed - states that this statement has been peer reviewed
isPublished - states where this statement was first published
isEvidencedBy - states that another statement, Y, should be considered evidence for this
statement X
createdOn - states the date/time that the statement was created
hasAuthor - states who claims authorship of the statement
isApprovedBy - states who approves of the statement
isDeprecatedBy - states that the statement is no longer in use by the entity in question
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54. i.0
$ey can be cited:
good for impact
&acknowled"ment

55. And...aren’t
references open and
free ?

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>
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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>
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58. ACKnowledge

59. ACKnowledge

61. The whole picture

63. Even if you don’t have all the
detail

67. detail
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68. nanopublications (i.e. references)
can also be used to reason
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69. nanopublications (i.e. references)
can also be used to reason
‘Publications’ yield ‘data’
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70. nanopublications (i.e. references)
can also be used to reason
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71. nanopublications (i.e. references)
can also be used to reason
protein X
protein A
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72. nanopublications (i.e. references)
can also be used to reason
protein X
Exposing '
‘unkno1 kno1s’
protein A
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73. 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

74. velterop@conceptweballiance
jan.velterop@acknowledgeconnect.com
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