What if we could freely get to all the essential
knowledge contained in scientific articles, without
those articles necessa...
Nano-publication
in Science & Medicine



Jan Velterop – First OASPA Conference – Lund – 15 September 2009
Raw
                                  Data
                                  Now!
http://www.ted.com/talks/tim_berners_lee...
Open
 Access
Now!
Every problem has its solution
Every solution has its problem
Datarrhoea
Publicatarrh
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
S tag e -1




               from
              Term
                to
             Concept
The Ogden Triangle

                        Concept


                                  The relations between the corners:...
Terms – representing concepts




CAPN3_00265                    LGMD2A                 Jan Velterop


CAPN3:c.62G>A      ...
Stag e -2




              from
            Concept
               to
            Statement
Statements are Concept ‘Triples’
concept 1                  concept 2             concept 3


  Jan Velterop              ...
Concept ‘Triples’ are language independent
      concept 1            concept 2            concept 3




Jan Velterop     ...
Stag e -3




            Annotation
                of
            Statement
Stag e -3


        context
        strength of relation
        provenance
        condition
        directionality
     ...
<rdf:Description
rdf:about=”http://www.nbic.nl/cwa/relation/C0035820#C0060383#1240641052059">
<cwa:typeRelation rdf:resour...
Stag e -4




            treating
   Statement + Annotation
              as
       Nano-Publication
Stag e -4


        What must a publication be?

Citeable and giving appropriate credit? – yes

Valuable to scientific prog...
Stag e -4

What if nano-publications were properly credited?


     The incentive to nano-publish would increase

     Bec...
Stag e -4



author / annotator
copyright
acknowledgement
                              citeability   credits
provenance
t...
Stag e -5




              start
            Reasoning
              with
   Nano-Publications (triples)
Current knowledge transfer




                             An analogy:
                             Needle Transport
Current knowledge transfer




                             An analogy:
                             Needle Transport
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...
<needle><is><thin>
<needle><is><long>
<needle><is><rare>
<needle><is><valuable>
<valuable><is worth><finding>
<hay><is><ab...
truck                                     rare                         valuable                      is worth   finding



...
A needle is made of steel, and magnets attract steel
<needle><is made of><steel>
<magnet><attracts><steel>
truck                                     rare                         valuable                      is worth   finding



...
truck                                     rare                         valuable                                     is wor...
truck                                     rare                         valuable                                     is wor...
Triples                      Open Access

<triple><is><reference>
                                   open access triples b...
Thank you

velterop@conceptweballiance.org
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Lund Sep 15 09

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Talk on 'nano-publication' held at OAPEN conference in Lund, Sweden

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Lund Sep 15 09

  1. 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?
  2. 2. Nano-publication in Science & Medicine Jan Velterop – First OASPA Conference – Lund – 15 September 2009
  3. 3. Raw Data Now! http://www.ted.com/talks/tim_berners_lee_on_the_next_web.html
  4. 4. Open Access Now!
  5. 5. Every problem has its solution
  6. 6. Every solution has its problem
  7. 7. Datarrhoea Publicatarrh
  8. 8. Help! Information deluge! Should we stop reading? Or find different ways to take in and exchange knowledge?
  9. 9. We should learn how to reason with the essence of available knowledge
  10. 10. S tag e -1 from Term to Concept
  11. 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.
  12. 12. Terms – representing concepts CAPN3_00265 LGMD2A Jan Velterop CAPN3:c.62G>A nCL-1 Johannes Velterop CAPN3:p.(Gly21Glu) Calpain p94 JJM Velterop dbSNP:rs28364364 Calcium-activated J Velterop neutral proteinase 3 C0000053 CANP 3
  13. 13. Stag e -2 from Concept to Statement
  14. 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. 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
  16. 16. Stag e -3 Annotation of Statement
  17. 17. Stag e -3 context strength of relation provenance condition directionality time stamp annotation with comments
  18. 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. 19. Stag e -4 treating Statement + Annotation as Nano-Publication
  20. 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. 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. 22. Stag e -4 author / annotator copyright acknowledgement citeability credits provenance time stamp status (e.g. peer-reviewed)
  23. 23. Stag e -5 start Reasoning with Nano-Publications (triples)
  24. 24. Current knowledge transfer An analogy: Needle Transport
  25. 25. Current knowledge transfer An analogy: Needle Transport
  26. 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.
  27. 27. <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>
  28. 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. 29. A needle is made of steel, and magnets attract steel
  30. 30. <needle><is made of><steel> <magnet><attracts><steel>
  31. 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. 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. 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. 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>
  35. 35. Thank you velterop@conceptweballiance.org

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