Dealing with scientific information 'overwhelm'. This slide set has been converted to ppt from Apple Keynote, and looks different from the original, especially the animations.
6. • maximal usefulness of scientific
research results
efficient, fast, and effective new
knowledge creation & discovery
efficient, fast, and effective new
knowledge creation & discovery
Optimal dissemination for
7. There’s too much and it’s
impossible to read everything,
even if you have access!
There’s too much and it’s
impossible to read everything,
even if you have access!
There’s too much and it’s
impossible to read everything,
even if you have access!
9. Looking merely at the literature that
one can read – which is not
necessarily all the literature that is
potentially important to one’s research
Lamp post research:
25. Possible strategies:
1.Publish a smaller number of papers
2.Accept that an ever smaller proportion of the
available papers is actually being read
3.Capture the knowledge contained in all papers
and map it in such a way that you can navigate
that knowledge
26. Possible strategies:
1.Publish a smaller number of papers
Maybe, but if it means less information, it’s
ludicrous
2.Accept that an ever smaller proportion of the
available papers is actually being read
3.Capture the knowledge contained in all papers and
map it in such a way that you can navigate that
knowledge
27. Possible strategies:
1.Publish a smaller number of papers
2.Accept that an ever smaller proportion of the
available papers is actually being read
How to choose, though?
3.Capture the knowledge contained in all papers
and map it in such a way that you can navigate
that knowledge
31. Possible strategies:
1.Publish a smaller number of papers
2.Accept that an ever smaller proportion of the
available papers is actually being read
3.Capture the knowledge contained in all papers
and map it in such a way that you can navigate
that knowledge
Yes! Helps to see trends and what to
choose!
35. “As the rate of publishing accelerates,
the need for computational support to
work out which articles to read, and
how to interpret, reproduce and validate
the claims they contain is growing.”
Quote from ‘Lazarus’:
http://www.bbsrc.ac.uk/pa/grants/AwardDetails.aspx?FundingReference=BB/L005298/1
37. Imagine you had a paper that concluded:
“On hot days, it turns out that aspirin
decreases the chances of blot clots, but
increases the chances of heart attack in
humans; the effect wasn't observed in rats
at all; simulations of dogs seem to
suggest that the effect is present but
independent of temperature unless the dog
is accompanied by a human”
38. Imagine you had a paper that concluded:
“On hot dayshot days, it turns out that aspirinaspirin
decreasesdecreases the chances of blot clotsblot clots, but
increasesincreases the chances of heart attackheart attack in
humanshumans; the effect wasn't observed in ratsrats
at all; simulations of dogsdogs seem to
suggest that the effect is present but
independent of temperaturetemperature unless the dogdog
is accompanied by a humanhuman”
39. Significant concepts:
[CHEMBL25] (aspirin)
[EFO_0001702] ('temperature' from the
experimental factors ontology)
[Canis lupus familiaris]
[Homo sapiens]
[Mus musculus]
Headline Interactions (in the form of Triples):
[ASPIRIN] [DECREASES] [THROMBOSIS]
[ASPIRIN] [INCREASES] [MYOCARDIAL INFARCTION]
Significant concepts:
[CHEMBL25] (aspirin)
[EFO_0001702] ('temperature' from the
experimental factors ontology)
[Canis lupus familiaris]
[Homo sapiens]
[Mus musculus]
Headline Interactions (in the form of Triples):
[ASPIRIN] [DECREASES] [THROMBOSIS]
[ASPIRIN] [INCREASES] [MYOCARDIAL INFARCTION]
Add this to the article’s abstract
(after it’s been validated by the author):
40. Most efficient:
If publishers were to do this
(doesn’t cost much, and makes articles far more useful)
In case publishers don’t, alternative
ways are being developed outside
publishers’ control
42. ocuments
Via Utopia Documents, LAZARUS ‘resurrects’
knowledge from being buried in articles:
• entities (‘concepts’, incl. synonyms, e.g. proteins)
• phrases, statements, assertions (e.g. triples)
• molecules (incl. Markush structure groups)
• graphs
• tables http://utopiadocs.com
43. • entities (‘concepts’, incl. synonyms, e.g. proteins)
• phrases, statements, assertions (e.g. triples)
• molecules (incl. Markush structure groups)
• graphs
• tables
These are captured – with their provenance, e.g.
DOI – in a ‘Knowledge Graph’ of their relationships
When assertions are captured, they are compared
to the Knowledge Graph and labelled as ‘new’ (to
the Graph) or ‘already found earlier’
should beshould be
interesting forinteresting for
the peerthe peer
reviewer of areviewer of a
newlynewly
submittedsubmitted
articlearticle
should beshould be
interesting forinteresting for
the peerthe peer
reviewer of areviewer of a
newlynewly
submittedsubmitted
articlearticle
44. “Lazarus to harness the crowd reading life-
science articles to resurrect the swathes of
legacy data buried in charts, tables, diagrams
and free-text, to liberate processable data into a
shared resource that benefits the community.”
45. “Lazarus to harness the crowd reading life-
science articles to resurrect the swathes of
legacy data buried in charts, tables, diagrams
and free-text, to liberate processable data into a
shared resource that benefits the community.”
“…activities currently carried out anyway by
individuals for their own purposes (annotating,
cross-referencing articles with databases,
organising collections of articles).”
46. “Lazarus to harness the crowd reading life-
science articles to resurrect the swathes of
legacy data buried in charts, tables, diagrams
and free-text, to liberate processable data into a
shared resource that benefits the community.”Works on any pdf, from paywalled
Works on any pdf, from paywalled
and open sources alike
and open sources alike
Works on any pdf, from paywalled
Works on any pdf, from paywalled
and open sources alike
and open sources alike
“…activities currently carried out anyway by
individuals for their own purposes (annotating,
cross-referencing articles with databases,
organising collections of articles).”
47.
48. VHL protein binds to HIF-α which is ubiquitinated and tagged for degradation in the proteasome.
49.
50.
51. ‘Assertions’ and ‘significant concepts’ extracted
from articles (either by the publisher or by others,
like Utopia’s LAZARUS), are added to a growing
‘knowledge graph’ which can be analysed for
trends, clusters, areas of intensive activity, etc.
81. What ResearchPad can do for publishers who
want it, at no extra cost*, is to integrate a
publisher’s content with anything from
elsewhere that’s freely available with open
access, so that this open access material can
be accessed from within the publisher’s platform
* personal communication
Project Definition
Collect sample article files
Understanding publisher’s business needs
Costing / Negotiation
Sample article evaluation
Branding
Demonstrate the app with publisher content
Develop a customer branding / skin / features both for the app and EPUB
Develop a specific version of ResearchPad using the branding assets
Create specific cloud repositories and web service accounts/developer accounts
Publishing
Develop a process that ties into front list development to publish simultaneously
Understand and integrate with your user / subscription management system
Estimate journal catalog archive size and establish a plan and cost to convert to EPUB
Go Live
Push to the stores/launch web app
Align with marketing programs to be run from the publisher
