The document discusses how nano-publications, which are brief statements summarizing scientific knowledge as concept triples, can increase access to and transfer of knowledge. Nano-publications treat annotated concept triples as citations, benefiting both authors through increased citations and publishers by increasing access to knowledge while respecting copyright. Reasoning can then be done with the networked concept triples to derive new insights.
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1. What if we could freely get to all the essential
knowledge contained in scientific articles, without
those articles necessarily being open access?
And what if such free access to the essential
knowledge is actually in the interest of publishers
as well?
11. The Ogden Triangle
Concept
The relations between the corners:
1. Object evokes Concept (in writer’s or speaker’s mind)
2. Writer/speaker uses Token to refer to Object
3. Token evokes Concept (in reader‘s or listener's mind)
4. Reader/listener refers Token back to Object
‘cancer’
Token or word or icon Object
‘cancer’
Malignant Neoplasms
Krebskrankheit
C0-265
Etc.
14. Statements are Concept ‘Triples’
concept 1 concept 2 concept 3
Jan Velterop presented these slides
CAPN3_00265 has pathogenicity LGMD2A
Dystrophin interacts with SNT3
Calpain-3 has GO annotation proteosome
endopeptidase
activity
15. Concept ‘Triples’ are language independent
concept 1 concept 2 concept 3
Jan Velterop presented these slides
Johannes Velterop vertoonde deze dia’s
JJM Velterop zeigte diese Transparantien
J Velterop présentait cettes diapositives
17. Stag e -3
context
strength of relation
provenance
condition
directionality
time stamp
annotation with comments
18. <rdf:Description
rdf:about=”http://www.nbic.nl/cwa/relation/C0035820#C0060383#1240641052059">
<cwa:typeRelation rdf:resource=”http://www.nbic.nl/cwa#cooccurrence”/>
<cwa:strength>0.0625</cwa:strength>
<cwa:has_query>limb girdle</cwa:has_query>
<cwa:discovered_by rdf:resource=”http://www.nbic.nl/cwa#TripleMiner”/>
<cwa:timestamp>1240641052059</cwa:timestamp>
<cwa:annotation rdf resource=”http://www.uniprot.org/uniprot/flnc_human”>
</rdf:Description>(free text?)
Triple describing the connection between two concepts as mined by a custom designed triple miner from
Uniprot.
<rdf:Description
rdf:about=”http://www.nbic.nl/cwa/relation/C0035820#C0060383#1240641052059">
<cwa:typeRelation rdf:resource=”http://www.nbic.nl/cwa#cooccurrence”/>
<cwa:strength>0.0625</cwa:strength>
<cwa:has_query>limb girdle</cwa:has_query>
<cwa:annotated_by rdf:resource=”http://people.conceptwiki.org/index.php/Concept:
85094810”/>
<cwa:timestamp>1240641052059</cwa:timestamp>
<cwa:annotation rdf resource=”http://www.uniprot.org/uniprot/flnc_human”>
</rdf:Description>(free text?)
The same triple, but now also annotated by a person referred to as concept 85094810. When following this URL,
it leads to Prof. Johan den Dunnen, a top expert in the two concepts referred to in the triple, as the annotator.
19. Stag e -4
treating
Statement + Annotation
as
Nano-Publication
20. Stag e -4
What must a publication be?
Citeable and giving appropriate credit? – yes
Valuable to scientific progress and understanding? – yes
Conveying knowledge? – yes
Full-length? – no
21. Stag e -4
What if nano-publications were properly credited?
The incentive to nano-publish would increase
Because they are brief and machine-readable,
the intake capacity of knowledge would
increase
22. Stag e -4
author / annotator
copyright
acknowledgement
citeability credits
provenance
time stamp
status (e.g. peer-reviewed)
23. Stag e -5
start
Reasoning
with
Nano-Publications (triples)
26. A needle is long and a needle is thin, very much like a dry blade of
grass, known as hay. Hay is long and hay is thin also. A haystack
is a large quantity of hay, and if we have a needle in the haystack
it is difficult to distinguish. Needles are rare, but hay is abundant.
Hay is cheap and a needle is valuable. Valuables are worth
finding.
We have a haystack on a truck, and the truck is used to transport
it.
28. truck rare valuable is worth finding
used for
abundant
is situated on
has property
has property
transport
cheap haystack is situated in needle
has property
has property
Consists of
has property
has property
has property long
hay has property
thin
29. A needle is made of steel, and magnets attract steel
31. truck rare valuable is worth finding
used for
abundant
is situated on
has property
has property
transport
cheap haystack is situated in needle
has property
has property
Consists of
has property
has property
has property long
hay has property
thin
32. truck rare valuable is worth finding
used for
abundant
is situated on
has property
has property
transport
cheap haystack is situated in needle has property steel
has property
has property
attracts
Consists of
has property
has property
magnet
has property long
hay has property
thin
33. truck rare valuable is worth finding
used for
abundant
is situated on
has property
has property
transport
cheap haystack is situated in needle has property steel
has property
has property
attracts
Consists of
has property
has property
magnet
has property long
hay has property
thin
34. Triples Open Access
<triple><is><reference>
open access triples benefit
<reference><is><open access>
authors and publishers,
<reference><may be><cited>
including traditional
<citation><benefits><author>
publishers
<citation><benefits><publisher>
