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   Science Publishing:

The Different Interests of
    Record Keeping
           and
  Knowledge Transfer
   Jan Velterop  Open Access-Open Data  K旦ln  December 2010
Why ...
... do
scient!ts
publ!h?
The record*
                       keeping the minutes of science




      1                                            of S
                                                       c
                                                     ienc
                                                            The
                                                             Rec
                                                                 o
                                                               rd
                                                      e




*picture inspired by Geoffrey Bilder of CrossRef
The record*
                       keeping the minutes of science




      1                                            i
                                                       o fS
                                                           c


                                                                 Th
                                                     en


                                                            e
                                                   e    c


                                                              Re
                                                         c or
                                                             d




*picture inspired by Geoffrey Bilder of CrossRef
Credit in the ego-system; the acknowledge economy*



2


                    *Acknowledge economy coined by Geoffrey Bilder of CrossRef
Credit in the ego-system; the acknowledge economy*



2


                    *Acknowledge economy coined by Geoffrey Bilder of CrossRef
1+2=
the interface with of鍖cialdom                     *




                    *coined by Salvatore Mele of CERN
Transfer of
    information and knowledge




3
3=
the interface with science
Are " requirements

for all $ree " same?
What we have may

be good for " record

    and cre%t...
...but ! it

 sat!factory for "

transfer of knowled&?
Isnt $ere too much

     to read?
Sh'ld we have

   to make

   choices?
Indeed can we?
ACKnowledge
Current publishing : needle transport




              ACKnowledge
In the interface with publishers
Content In the interface with publishers is King
Or was perhaps?




     ACKnowledge
How w'ld we

choose anyway?
How w'ld we

choose anyway?
Sh'ldnt we take

  in ALL "

knowled& in 'r

     area?
A new article in PubMed
   every 36 seconds




        ACKnowledge
Molecular Biology Laboratory in Heidelberg, Germany,
and won Elseviers Grand Challenge 2009 competition
for new tools that improve the communication and use
of scientific information.
Reflect automatically recognizes and highlights the
names of genes, proteins and small molecules in the Cell
articles. Users clicking on a highlighted term will see a pop-
up box containing information related to that term, such as
      A new article in PubMed
sequence data and molecular structures, along with links to
the sources of the data. Reflect obtains this information from
         every 36 seconds
its dictionary of millions of proteins and small molecules.
Such entity recognition can be done fairly accurately
by many mining tools today. But other tools take on the
tougher challenge of recognizing relationships between the
entities. Researchers from Leiden University and Erasmus
University in Rotterdam, both in the Netherlands, have
developed software called Peregrine, and used it to pre-
dict an undocumented interaction between two proteins:


                          ACKnowledge
Science publishing, record keeping, knowledge transfer
Science publishing, record keeping, knowledge transfer
Create an overview

  鍖r), perhaps?
ACKnowledge
And $en home

in on detail?
ACKnowledge
<protein kinase> <phosphorylates> <proteins>




                  ACKnowledge
<protein kinase> <phosphorylates> <proteins>

      <subject>    <predicate>    <object>




                  ACKnowledge
<#26277419>      <#2121378>   <#13817745>

<protein kinase> <phosphorylates> <proteins>

      <subject>     <predicate>    <object>




                   ACKnowledge
<#26277419>      <#2121378>     <#13817745>

<protein kinase> <phosphorylates> <proteins>

      <subject>     <predicate>      <object>


  Asse+ion        a.k.a.         T,ple




                   ACKnowledge
Nanopublications: Assertions with Attitudes




                 ACKnowledge
Nanopublications: Assertions with Attributes




                 ACKnowledge
Nanopublications: Assertions with Attributes
Examples of attributes:


assertedBy - states which entity asserted (i.e. created) the statement
curatedBy - states that a specified entity has curated the statement
isPeerReviewed - states that this statement has been peer reviewed
isEvidencedBy - states that another statement, Y, should be considered evidence for this
statement X
createdOn - states the date/time that the statement was created
hasAuthor - states who claims authorship of the statement
isApprovedBy - states who approves of the statement
isDeprecatedBy - states that the statement is no longer in use by the entity in question




                                        ACKnowledge
Nanopublications

 are asse+ions
Nanopublications

are also citations
<rdf:Description rdf:about=http://www.nbic.nl/cwa/relation/
#26277419#13817745">
<cwa:typeRelation rdf:resource= http://predicate.conceptwiki.org/index.php/
#2121378/>
<cwa:direction>1,2</cwa:direction>
<cwa:strength>1.0</cwa:strength>
<cwa:author rdf:resource=http://people.conceptwiki.org/index.php/#85094810/>
<cwa:provenance rdf:resource=http://article.conceptwiki.org/index.php/
#121646370/>
<cwa:timestamp>1240641052059</cwa:timestamp>
<cwa:annotated_by rdf:resource=http://people.conceptwiki.org/index.php/
#43065817/>
<cwa:annotation rdf resource=http://www.virusdb.org/viruses/av/
Heliothis_virescens_insect>
</rdf:Description>




                               ACKnowledge
<rdf:Description rdf:about=http://www.nbic.nl/cwa/relation/
#26277419#13817745">
<cwa:typeRelation rdf:resource= http://predicate.conceptwiki.org/index.php/
#2121378/>
<cwa:direction>1,2</cwa:direction>
<cwa:strength>1.0</cwa:strength>
<cwa:author rdf:resource=http://people.conceptwiki.org/index.php/#85094810/>
<cwa:provenance rdf:resource=http://article.conceptwiki.org/index.php/
#121646370/>
<cwa:timestamp>1240641052059</cwa:timestamp>
<cwa:annotated_by rdf:resource=http://people.conceptwiki.org/index.php/
#43065817/>
<cwa:annotation rdf resource=http://www.virusdb.org/viruses/av/
Heliothis_virescens_insect>
</rdf:Description>




                               ACKnowledge
ACKnowledge
ACKnowledge
Science publishing, record keeping, knowledge transfer
The whole picture
Science publishing, record keeping, knowledge transfer
Even if you dont have all the
            detail
Science publishing, record keeping, knowledge transfer
Science publishing, record keeping, knowledge transfer
Science publishing, record keeping, knowledge transfer
detail




ACKnowledge
nanopublications (i.e. citations)

  can also be used to reason




            ACKnowledge
nanopublications (i.e. citations)

            can also be used to reason



protein X




                                         protein A




                     ACKnowledge
Citation: van Haagen HHHBM, 't Hoen PAC, Botelho Bovo A, de Morr辿e A, van Mulligen EM, et al.
(2009) Novel Protein-Protein Interactions Inferred from Literature Context. PLoS ONE 4(11): e7894.
doi:10.1371/journal.pone.0007894
velterop@conceptweballiance
jan.velterop@acknowledgeconnect.com




             ACKnowledge

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Science publishing, record keeping, knowledge transfer

Editor's Notes