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

Thank you

velterop@conceptweballiance.org