The future of the science
publishing ego-system
Jan Velterop – LIBER 2013 – June 26 – München
The future of the science
publishing ego-system
Ego-system?
Advertising scientific prowess
Publish or Perish
Read or Rot
J.J.M. Velterop, “Keeping the Minutes of Science.” In: Electronic library and visual information research (Elvira
2). Edit...
Changes to the
Current Publishing System
• Increasing Open Access — new models
• Separation of Peer Review and Publishing
...
User-defined Formats
Image courtesy of
Kaveh Bazargan
Image courtesy of
Kaveh Bazargan
Image courtesy of
Kaveh Bazargan
Changes to journals or articles
are not addressing the core of
the problem
However
Scholarly Articles Growth
Last 12 months
• 989195 new abstracts in PubMed
• 525,600 minutes
• i.e. a new article every half minute
15
Datarrhoea
Publicatarrh
17
18
19
20
21
22
23
24
25
26
27
28
Not just the difficulty, mind, but the
impossibility
29
search:
‘diagnostic imaging’ AND ‘cardiovascular system’:
limited to:
human studies, core clinical journals, Medline:
1...
30
Assume you read:
5 papers/hour
8 hours/day
5 days/week
50 weeks/year
10 000 papers/year.
31
Reading all existing papers: 11 years and 124 days.
Meanwhile 82142 more papers added: another eight
years and 78 days....
32
Speed of new relevant articles appearing
Speed of being able to read articles
Read it all? — Signal to noise low!
34
The fire of
peer review?
Or of marketing?
Top journal
Bottom dweller
Filter,
Distill?
35
How are we filtering or
choosing anyway?
35
36
Lens,
Focus
38
Or maybe something more sophisticated?
39
hologramknowlogram?
40
Semantic triples
Subject Predicate Object
41
ACVR1 Fibrodisplasiais associated with
Semantic triples
Jan Velterop
Johannes Velterop
JJM Velterop
J Velterop
燕 德维尔村
presented
vertoonde
zeigte
présentait
显示
these slides
deze d...
• The entities have URIs.
• This allows for disambiguation of synonyms & homonyms,
so that the conceptual content of an as...
48
3a6c5bd1-29b0-4946-b1a4-74e909a0cdf4
41c76d76-d676-4e95-9dc0-12b10ebe9257
ceeee1f7-203b-445b-9860-e9acffd46fa6
ACVR1
is...
<rdf:Description rdf:about=”http://www.nbic.nl/cwa/relation/#26277419#13817745">
<cwa:typeRelation rdf:resource=” http://p...
51
52 52
detail
54
Fibrodysplasia Ossificans Progressiva
ACVR1
is associated with
This ‘assertion‘ – triple – can also be enhanced with
me...
Nanopublication?
Triple with attribution, provenance
• A nanopublication is a single, machine-readable, citable
scientific assertion along with associated provenance.
• Nano r...
• Publishers can extract and expose the nanopublications
contained in their publications
• They conceptually ‘link’ data a...
58
Challenge:
to convert literature to nano-publications
On-the-fly
Why nanopublications and not just triples?
60
Nanopublications come with the idea that their
authors/providers may gain credit for the use of these
assertions by oth...
• Nanopublications can be cited and thus may credit authors,
journals, databases, publishers
• And they are ‘linked’ – at ...
• Nanopublications, even very large collections of
nanopublications, do not – cannot – reflect full scientific
reality in ...
63
64
65
protein A
protein X
65
Reasoning
Triples (including nanopublications) can
also be used to reason – ‘in silico’ – and
therefore on a much larger scale
prote...
The upshot:
"Faced with information overload, we have no
alternative but pattern recognition.”
Marshall McLuhan
Example
The ‘nanopublication’ approach is being taken by the Innovative
Medicine Initiative project Open PHACTS, aimed at ...
http://www.openphacts.org/open-phacts-explorer
70
Documents
Free semantic scientific PDF viewer
http://utopiadocs.com
The semantic approach is also being taken by
this O...
Semantic
Concept Tagging
Target
Disease
Drug
Company
MicroRNA
Pathway
Context
& More
The semantic approach is being taken
...
75
Supporting scientific information with ‘infotisement’,
making annoying advertising into useful added information
Even a...
E.g. associating ATPase p97
— when mentioned in the text of an article —
with DBeQ
Scientific publications remain
important
For the record (Minutes of Science)
But perhaps not for reading
And perhaps not i...
81
Thank you!
velterop@aqnowledge.com
The future of the science publishing ego-system
The future of the science publishing ego-system
The future of the science publishing ego-system
The future of the science publishing ego-system
The future of the science publishing ego-system
The future of the science publishing ego-system
The future of the science publishing ego-system
The future of the science publishing ego-system
The future of the science publishing ego-system
The future of the science publishing ego-system
The future of the science publishing ego-system
The future of the science publishing ego-system
The future of the science publishing ego-system
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The future of the science publishing ego-system

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These are the slides from a talk given by Dr. Jan Velterop at LIBER's 2013 conference in Munich.

The amount of scientific information generated is growing exponentially. Consequently, the way this information is shared and used is changing, too. It has to, as the traditional method of reasonably comprehensively taking in new information, by reading scientific literature, is becoming woefully inadequate — in fact, impossible.

This has far-reaching consequences for the mediators in the scientific knowledge exchange environment: publishers and libraries. The only things that are not entirely clear yet are when and exactly how things will change, but not whether they will. This talk explored some likely scenarios for the near future.

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The future of the science publishing ego-system

  1. 1. The future of the science publishing ego-system Jan Velterop – LIBER 2013 – June 26 – München
  2. 2. The future of the science publishing ego-system
  3. 3. Ego-system? Advertising scientific prowess
  4. 4. Publish or Perish
  5. 5. Read or Rot
  6. 6. J.J.M. Velterop, “Keeping the Minutes of Science.” In: Electronic library and visual information research (Elvira 2). Edited by Mel Collier and Kathryn Arnold. Proceedings of the second ELVIRA conference, held in May 1995 at De Montfort University, Milton Keynes. Aslib. 1995, pp 11-17. KEEPING THE MINUTES OF SCIENCE J. J.M. Velterop Academic Press Ltd, London, UK INTRODUCTION Scientific journal publishing differs markedly from most other kinds of publishing. Born out of the exchange of letters on scientific topics and results, it has evolved into as much a service to scientists who need to publish the results of their work, as a service to those who need to be kept abreast of scientific developments elsewhere. Unlike most other publishing, scientific journal publishing has as much to do with the proper recording of scientific activity as with the conveyance of information. As far as the latter is concerned, scientists do not rely on scientific journals alone any more, in order to keep informed. Journals are only one of the variety of ways in which scientists gather scientific information. However, scientific information that comes to a scientist via a scientific journal still carries the highest degree of authority for information, as it has been peer reviewed and gone through a certification and validation process before reaching the reader.
  7. 7. Changes to the Current Publishing System • Increasing Open Access — new models • Separation of Peer Review and Publishing • Changes to Peer Review — more open • More arXiv-oids • “Extrajournaleous” articles • User-defined formats • Et cetera, et cetera
  8. 8. User-defined Formats
  9. 9. Image courtesy of Kaveh Bazargan
  10. 10. Image courtesy of Kaveh Bazargan
  11. 11. Image courtesy of Kaveh Bazargan
  12. 12. Changes to journals or articles are not addressing the core of the problem However
  13. 13. Scholarly Articles Growth
  14. 14. Last 12 months • 989195 new abstracts in PubMed • 525,600 minutes • i.e. a new article every half minute
  15. 15. 15 Datarrhoea Publicatarrh
  16. 16. 17
  17. 17. 18
  18. 18. 19
  19. 19. 20
  20. 20. 21
  21. 21. 22
  22. 22. 23
  23. 23. 24
  24. 24. 25
  25. 25. 26
  26. 26. 27
  27. 27. 28 Not just the difficulty, mind, but the impossibility
  28. 28. 29 search: ‘diagnostic imaging’ AND ‘cardiovascular system’: limited to: human studies, core clinical journals, Medline: 195 106 159 661
  29. 29. 30 Assume you read: 5 papers/hour 8 hours/day 5 days/week 50 weeks/year 10 000 papers/year.
  30. 30. 31 Reading all existing papers: 11 years and 124 days. Meanwhile 82142 more papers added: another eight years and 78 days. Before catching up, you need to read 408049 papers devoting 40 years and 295 days to it. You would finish just in time to retire. Being an expert in echocardiography
  31. 31. 32 Speed of new relevant articles appearing Speed of being able to read articles
  32. 32. Read it all? — Signal to noise low!
  33. 33. 34 The fire of peer review? Or of marketing? Top journal Bottom dweller Filter, Distill?
  34. 34. 35 How are we filtering or choosing anyway? 35
  35. 35. 36 Lens, Focus
  36. 36. 38 Or maybe something more sophisticated?
  37. 37. 39 hologramknowlogram?
  38. 38. 40 Semantic triples Subject Predicate Object
  39. 39. 41 ACVR1 Fibrodisplasiais associated with Semantic triples
  40. 40. Jan Velterop Johannes Velterop JJM Velterop J Velterop 燕 德维尔村 presented vertoonde zeigte présentait 显示 these slides deze dia’s diese Transparantien cettes diapositives 这些幻灯片 Concept ‘Triples’ are language independent
  41. 41. • The entities have URIs. • This allows for disambiguation of synonyms & homonyms, so that the conceptual content of an assertion can be reflected, irrespective of the actual words used.
  42. 42. 48 3a6c5bd1-29b0-4946-b1a4-74e909a0cdf4 41c76d76-d676-4e95-9dc0-12b10ebe9257 ceeee1f7-203b-445b-9860-e9acffd46fa6 ACVR1 is associated with Fibrodysplasia Ossificans Progressiva
  43. 43. <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>
  44. 44. 51
  45. 45. 52 52
  46. 46. detail
  47. 47. 54 Fibrodysplasia Ossificans Progressiva ACVR1 is associated with This ‘assertion‘ – triple – can also be enhanced with meta-information, such as provenance And then it becomes a ‘nanopublication’
  48. 48. Nanopublication? Triple with attribution, provenance
  49. 49. • A nanopublication is a single, machine-readable, citable scientific assertion along with associated provenance. • Nano refers just to its smallness • Publication refers to its cite-ability; a nanopublication is the smallest possible textual publication that may be scientifically meaningful Definition
  50. 50. • Publishers can extract and expose the nanopublications contained in their publications • They conceptually ‘link’ data and literature, and foster citation of the literature
  51. 51. 58 Challenge: to convert literature to nano-publications On-the-fly
  52. 52. Why nanopublications and not just triples?
  53. 53. 60 Nanopublications come with the idea that their authors/providers may gain credit for the use of these assertions by others Because we don’t just live in a knowledge economy, but also in an acknowledge economy (the ‘ego-system’)
  54. 54. • Nanopublications can be cited and thus may credit authors, journals, databases, publishers • And they are ‘linked’ – at least ‘linkable’ (URIs) – combatting the fragmentation of information that’s the bane of science http://nanopub.org
  55. 55. • Nanopublications, even very large collections of nanopublications, do not – cannot – reflect full scientific reality in all its nuances • But they help give direction, overview, hypothesis creation, etc. Caveat
  56. 56. 63
  57. 57. 64
  58. 58. 65 protein A protein X 65 Reasoning
  59. 59. Triples (including nanopublications) can also be used to reason – ‘in silico’ – and therefore on a much larger scale protein A protein X
  60. 60. The upshot: "Faced with information overload, we have no alternative but pattern recognition.” Marshall McLuhan
  61. 61. Example The ‘nanopublication’ approach is being taken by the Innovative Medicine Initiative project Open PHACTS, aimed at significantly speeding up drug discovery
  62. 62. http://www.openphacts.org/open-phacts-explorer
  63. 63. 70 Documents Free semantic scientific PDF viewer http://utopiadocs.com The semantic approach is also being taken by this Open PHACTS exemplar:
  64. 64. Semantic Concept Tagging Target Disease Drug Company MicroRNA Pathway Context & More The semantic approach is being taken by this Pharma intelligence service, too: http://scibite.com Thousands of: Patents Scientific Papers Newsfeeds Blogs Clinical Databases & More in
  65. 65. 75 Supporting scientific information with ‘infotisement’, making annoying advertising into useful added information Even advertising can use this approachEven infotising can use this approach
  66. 66. E.g. associating ATPase p97 — when mentioned in the text of an article — with DBeQ
  67. 67. Scientific publications remain important For the record (Minutes of Science) But perhaps not for reading And perhaps not in journals But to provide the raw material for knowledge pattern recognition
  68. 68. 81 Thank you! velterop@aqnowledge.com
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