Jan Velterop: Science publishing: the different interests of record keeping and knowledge transfer
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Jan Velterop: Science publishing: the different interests of record keeping and knowledge transfer

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Science publications used to have the joint function of keeping the 'Minutes of Science' as well as transferring knowledge. The sheer amounts of material published (2 new articles in PubMed every ...

Science publications used to have the joint function of keeping the 'Minutes of Science' as well as transferring knowledge. The sheer amounts of material published (2 new articles in PubMed every minute of every day) make comprehensive knowledge transfer via reading of articles virtually impossible. When the literature is open, though, much of the essential knowledge it contains can be distilled and the big picture obtained without having to read all the articles, so that reading can then be reserved for those key articles that give insight in the reasoning and argumentation that leads to consensus. The result is a much more efficient knowledge transfer that doesn't have to compromise on comprehensiveness.

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Jan Velterop: Science publishing: the different interests of record keeping and knowledge transfer Jan Velterop: Science publishing: the different interests of record keeping and knowledge transfer Presentation Transcript

  • ACKnowledge Science Publishing: The Different Interests ofRecord Keeping and Knowledge Transfer Jan Velterop – “Open Access-Open Data” – Köln – December 2010
  • Publ!hing =knowled" transfer
  • Publ!hing ≠knowled" transfer
  • Why $! chan" ?
  • A new article in PubMed every 36 seconds ACKnowledge
  • Molecular Biology Laboratory in Heidelberg, Germany,and won Elsevier’s Grand Challenge 2009 competitionfor new tools that improve the communication and useof scientific information.Reflect automatically recognizes and highlights thenames of genes, proteins and small molecules in the Cellarticles. Users clicking on a highlighted term will see a pop-up box containing information related to that term, such as A new article in PubMedsequence data and molecular structures, along with links tothe sources of the data. Reflect obtains this information from every 36 secondsits dictionary of millions of proteins and small molecules.Such ‘entity recognition’ can be done fairly accuratelyby many mining tools today. But other tools take on thetougher challenge of recognizing relationships between theentities. Researchers from Leiden University and ErasmusUniversity in Rotterdam, both in the Netherlands, havedeveloped software called Peregrine, and used it to pre-dict an undocumented interaction between two proteins: ACKnowledge
  • ACKnowledge
  • Current publishing : needle transport ACKnowledge
  • What does it allmean for publ!hing ?
  • 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 officialdom
  • Transfer of information and knowledge3
  • 3=the interface with science
  • Are requirementsfor all $ree $e same?
  • Are requirementsfor all $ree $e same?
  • What we have maybe good for record and for cre(t...
  • What we have maybe good for record and for cre(t...
  • ...but ! it sat!factory for transfer of knowled" ? ?
  • )ere ! ju* too much to read
  • Information consumes$e a+ention of itsrecipients...
  • ...hence a weal$ of information creates a pove,y of a+entionHerbert Simon
  • Datarrhoea ?Publicatarrh ?
  • Sh-ld we have to make choices ?
  • Can we, truly ?
  • How w-ld wechoose anyway?
  • How w-ld wechoose anyway?
  • Sh-ldn’t we take inALL knowled" in -r area?
  • As well as sat!fy$e academic desire to avoid rea(ng ?
  • Create an overview fir*, perhaps?
  • ACKnowledge
  • And $en home in on detail?
  • ACKnowledge
  • What does it allmean for publ!hing ?
  • In the interface with publishers
  • Content In the interface with publishers is King
  • Or “was” perhaps? ACKnowledge
  • Well, it’s *illcontent $at c-nts
  • <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
  • <#26277419> <#2121378> <#13817745><protein kinase> <phosphorylates> <proteins>A,icles are full of $ese <subject> <predicate> <object> ‘ asse,ions/t/ples Asse,ion‘ a.k.a. ‘T/ple’ ACKnowledge
  • <#26277419> <#2121378> <#13817745><protein kinase> <phosphorylates> <proteins>A,icles are full of $ese Let’s call $em <subject> <predicate> <object> ‘ asse,ions/t/ples ‘Nanopublications’ Asse,ion‘ a.k.a. ‘T/ple’ ACKnowledge
  • Nanopublications: Assertions with Attitudes ACKnowledge
  • Nanopublications: Assertions with Attributes ACKnowledge
  • Nanopublications: Assertions with AttributesExamples of attributes:assertedBy - states which entity asserted (i.e. created) the statementcuratedBy - states that a specified entity has curated the statementisPeerReviewed - states that this statement has been peer reviewedisPublished - states where this statement was first publishedisEvidencedBy - states that another statement, Y, should be considered evidence for thisstatement XcreatedOn - states the date/time that the statement was createdhasAuthor - states who claims authorship of the statementisApprovedBy - states who approves of the statementisDeprecatedBy - states that the statement is no longer in use by the entity in question ACKnowledge
  • Nanopublications are asse,ions
  • Nanopublications are also references
  • Nanopublications: Assertions with AttributesExamples of attributes:assertedBy - states which entity asserted (i.e. created) the statementcuratedBy - states that a specified entity has curated the statementisPeerReviewed - states that this statement has been peer reviewedisPublished - states where this statement was first publishedisEvidencedBy - states that another statement, Y, should be considered evidence for thisstatement XcreatedOn - states the date/time that the statement was createdhasAuthor - states who claims authorship of the statementisApprovedBy - states who approves of the statementisDeprecatedBy - states that the statement is no longer in use by the entity in question ACKnowledge
  • i.0 $ey can be cited: good for impact&acknowled"ment
  • And...aren’treferences open and free ?
  • <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
  • The whole picture
  • Even if you don’t have all the detail
  • detailACKnowledge
  • nanopublications (i.e. references) can also be used to reason ACKnowledge
  • nanopublications (i.e. references) can also be used to reason‘Publications’ yield ‘data’ ACKnowledge
  • nanopublications (i.e. references) can also be used to reason ACKnowledge
  • nanopublications (i.e. references) can also be used to reasonprotein X protein A ACKnowledge
  • nanopublications (i.e. references) can also be used to reasonprotein X Exposing ‘unkno1 kno1s’ protein A ACKnowledge
  • Citation: van Haagen HHHBM, t Hoen PAC, Botelho Bovo A, de Morrée 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@conceptweballiancejan.velterop@acknowledgeconnect.com ACKnowledge