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

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

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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

1+2=the interface with officialdom

Transfer of information and knowledge3

3=the interface with science

Are requirementsfor all $ree $e same?

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?

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?

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And $en home in on detail?

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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

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The whole picture

Even if you don’t have all the detail

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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

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

by "Open Access - Open Data" conference, 13th/14th December, 2010

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