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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?
Nano-publicationin Science & Medicine
Jan Velterop – First OASPA Conference – Lund – 15 September 2009
RawDataNow!
http://www.ted.com/talks/tim_berners_lee_on_the_next_web.html
Open AccessNow!
problemEvery has its solution
problemEvery has itssolution
DatarrhoeaPublicatarrh
Help! Information deluge!
Should we stop reading?
Or find different ways to take in and exchange knowledge?
We should learn how to reason with the essence of available knowledge
from Term
to Concept
S t a g e - 1
‘cancer’
The relations between the corners:
1. Object evokes Concept (in writer’s or speaker’s mind)2. Writer/speaker uses Token to refer to Object3. Token evokes Concept (in reader‘s or listener's mind)4. Reader/listener refers Token back to Object
The Ogden Triangle
Token or word or icon Object
Concept
‘cancer’Malignant NeoplasmsKrebskrankheitC0-265Etc.
CAPN3_00265
CAPN3:c.62G>A
CAPN3:p.(Gly21Glu)
dbSNP:rs28364364
C0000053
LGMD2A
nCL-1
Calpain p94
Calcium-activated neutral proteinase 3
CANP 3
Jan Velterop
Johannes Velterop
JJM Velterop
J Velterop
燕 德维尔村
Terms – representing concepts
from Concept
to Statement
S t a g e - 2
Statements are Concept ‘Triples’
presented
has pathogenicity
interacts with
has GO annotation
these slides
LGMD2A
SNT3
proteosome endopeptidase activity
Jan Velterop
CAPN3_00265
Dystrophin
Calpain-3
concept 1 concept 2 concept 3
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
concept 1 concept 2 concept 3
Annotationof
Statement
S t a g e - 3
context
strength of relation
provenance
condition
directionality
time stamp
annotation with comments
S t a g e - 3
<rdf:Descriptionrdf: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?)
<rdf:Descriptionrdf: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.
Triple describing the connection between two concepts as mined by a custom designed triple miner from Uniprot.
treating Statement + Annotation
as Nano-Publication
S t a g e - 4
Citeable and giving appropriate credit? – yes
Valuable to scientific progress and understanding? – yes
Conveying knowledge? – yes
Full-length? – no
What must a publication be?
S t a g e - 4
The incentive to nano-publish would increase
Because they are brief and machine-readable, the intake capacity of knowledge would increase
What if nano-publications were properly credited?
S t a g e - 4
author / annotator
copyright
acknowledgement
provenance
time stamp
status (e.g. peer-reviewed)
S t a g e - 4
citeability credits
start Reasoning
with Nano-Publications (triples)
S t a g e - 5
An analogy:
Needle Transport
Current knowledge transfer
An analogy:
Needle Transport
Current knowledge transfer
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.
<needle><is><thin>
<needle><is><long><needle><is><rare><needle><is><valuable><valuable><is worth><finding><hay><is><abundant>
<hay><is><thin><hay><is><long><hay><is><cheap><haystack><consists of><hay><haystack><is on><truck>
<truck><is for><transport><needle><is in><haystack>
needle
has property
valuable
is situated inhaystack
is worth finding
Consists of
has property
long
has property
thinhay
has
prop
erty
has
prop
erty
abundantrare
has
prop
erty
has property
has
prop
erty
cheap
is s
itua
ted
on
truck
used for
transport
A needle is made of steel, and magnets attract steel
<needle><is made of><steel><magnet><attracts><steel>
needle
has property
valuable
is situated inhaystack
is worth finding
Consists of
has property
long
has property
thinhay
has
prop
erty
has
prop
erty
abundantrare
has
prop
erty
has property
has
prop
erty
cheap
is s
itua
ted
on
truck
used for
transport
needle
has property
valuable
is situated inhaystack
is worth finding
Consists of
has property
long
has property
thinhay
has
prop
erty
has
prop
erty
abundantrare
has
prop
erty
has property
has
prop
erty
cheap
is s
itua
ted
on
truck
used for
transport
attracts
magnet
steelneedle has property
needle
has property
valuable
is situated inhaystack
is worth finding
Consists of
has property
long
has property
thinhay
has
prop
erty
has
prop
erty
abundantrare
has
prop
erty
has property
has
prop
erty
cheap
is s
itua
ted
on
truck
used for
transport
attracts
magnet
steelneedle has property
Triples Open Access
<triple><is><reference>
<reference><is><open access><reference><may be><cited><citation><benefits><author><citation><benefits><publisher>
open access triples benefit
authors and publishers, including traditional publishers