iExpo Paris 10 juin 2010-Velterop

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Presentation on (semantic) nanopublications (specifically in biomedicine) given at iExpo in Paris, 10 June 2010. Partially in French (but mostly with English translation).
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  • iExpo Paris 10 juin 2010-Velterop

    1. 1. ACKnowledge Les Nanopublications Jan Velterop – i-Expo – Paris – 10 juin 2010
    2. 2. Pourquoi les scientifiques publient-ils? Why do scientists publish?
    3. 3. laisser un trace – the record* “le compte-rendu de la science” – “keeping the minutes of science” 1 of S c ienc e The Rec ord *image inspirée par Geoffrey Bilder de chez CrossRef
    4. 4. laisser un trace – the record* “le compte-rendu de la science” – “keeping the minutes of science” 1 i o fS c Th en e e c Re c or d *image inspirée par Geoffrey Bilder de chez CrossRef
    5. 5. leur crédit dans un “égo-système”: une économie de la reconnaissance* 2 *”économie de la reconnaissance” néologisme créé par Geoffrey Bilder de chez CrossRef
    6. 6. leur crédit dans un “égo-système”: une économie de la reconnaissance* 2 *”économie de la reconnaissance” néologisme créé par Geoffrey Bilder de chez CrossRef
    7. 7. 1+2= l’interface avec l’officialité * the interface with officialdom * *néologisme de Salvatore Mele du CERN
    8. 8. transfert des informations et des connaissances – transfer of information and knowledge 3
    9. 9. 3= l’interface avec la science the interface with science
    10. 10. Ces exigences, sont-elles toutes les trois équivalentes? Are the requirements for all three the same?
    11. 11. Certes, tout ça permet de faire date ou d’être reconnu… What we have may be good for the record and credit...
    12. 12. ...mais quid du transfert des connaissances? ...but is it satisfactory for the transfer of knowledge?
    13. 13. Ne sommes-nous pas inondés par tout ce qu’il faudrait lire? Isn’t there too much to read?
    14. 14. Sommes-nous condamnés à choisir? Should we have to make choices?
    15. 15. Et le pouvons-nous? Indeed can we?
    16. 16. ACKnowledge
    17. 17. L’édition aujourd’hui: le transport des aguilles Current publishing : needle transport ACKnowledge
    18. 18. A l’interface avec les éditeurs
    19. 19. Le roi A l’interface avec les éditeurs c’est le contenu
    20. 20. Ou plutôt, l’était peut-être? ACKnowledge
    21. 21. Mais comment pourrions- nous choisir...?
    22. 22. Mais comment pourrions- nous choisir...?
    23. 23. Ne faudrait-il pas absorber TOUTES les connaissances de notre domaine? Shouldn’t we take in ALL the knowledge in our area?
    24. 24. PubMed: un nouvel article toutes les 36 secondes ACKnowledge
    25. 25. Molecular Biology Laboratory in Heidelberg, Germany, and won Elsevier’s 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- PubMed: un nouvel up box containing information related to that term, such as sequence data and molecular structures, along with links to article toutes les 36 the sources of the data. Reflect obtains this information from its dictionary of millions of proteins and small molecules. secondes 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
    26. 26. Avoir une vision d’ensemble pour commencer? Create an overview first?
    27. 27. ACKnowledge
    28. 28. Et puis zoomer sur les détails? And then home in on detail?
    29. 29. ACKnowledge
    30. 30. <protein kinase> <phosphorylates> <proteins> ACKnowledge
    31. 31. <protein kinase> <phosphorylates> <proteins> <sujet> <prédicat> <objet> ACKnowledge
    32. 32. <#26277419> <#2121378> <#13817745> <protein kinase> <phosphorylates> <proteins> <sujet> <prédicat> <objet> ACKnowledge
    33. 33. <#26277419> <#2121378> <#13817745> <protein kinase> <phosphorylates> <proteins> <sujet> <prédicat> <objet> Une ‘Assertion‘ (ou ‘Triplet’) ACKnowledge
    34. 34. ACKnowledge
    35. 35. Les Nanopublications: des Assertions ayant des Attributs ACKnowledge
    36. 36. Les Nanopublications: des Assertions ayant des Attributs Exemples d’attributs: assertedBy - indique quelle est l’entité à l’origine (qui l’a créée) de l’assertion curatedBy - indique qu’une entité donnée a géré l’assertion isPeerReviewed - indique que cette assertion est passée par un arbitrage entre pairs (peer review) isEvidencedBy - indique qu’une autre assertion, Y, doit être tenue comme preuve de l’assertion X en question createdOn - indique la date/heure de création de l’assertion hasAuthor - indique qui affirme être auteur de l’assertion isApprovedBy - indique qui a approuvé l’assertion isDeprecatedBy - indique que l’assertion n’est plus utilisée par l’entité en question ACKnowledge
    37. 37. une nanopublication (triplet): ACKnowledge
    38. 38. une nanopublication (triplet): <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
    39. 39. ACKnowledge
    40. 40. <#26277419> <#2121378> <#13817745> <sujet> <prédicat> <objet> <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
    41. 41. Auteur <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> http://conceptwiki.org/index.php/Concept: 85094810 ACKnowledge
    42. 42. Auteur <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> http://conceptwiki.org/index.php/Concept: 85094810 ACKnowledge
    43. 43. Auteur <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> http://conceptwiki.org/index.php/Concept: <cwa:author rdf:resource=”http://people.conceptwiki.org/index.php/#85094810”/> 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
    44. 44. http://conceptwiki.org/index.php/Concept: 85094810
    45. 45. http://conceptwiki.org/index.php/Concept: 85094810
    46. 46. Provenance <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> http://conceptwiki.org/index.php/Concept: 121646370 ACKnowledge
    47. 47. Provenance <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> http://conceptwiki.org/index.php/Concept: 121646370 ACKnowledge
    48. 48. Provenance <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”/> http://conceptwiki.org/index.php/Concept: <cwa:provenance rdf:resource=”http://article.conceptwiki.org/index.php/#121646370”/> <cwa:timestamp>1240641052059</cwa:timestamp> 121646370 <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
    49. 49. Horodatage – Timestamp <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
    50. 50. Horodatage – Timestamp <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
    51. 51. Annotations <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
    52. 52. Annotations <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
    53. 53. <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
    54. 54. <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
    55. 55. ACKnowledge
    56. 56. ACKnowledge
    57. 57. L’image...globalement The whole picture
    58. 58. Même si vous ne voyez pas tout dans les détails Even if you don’t have all the detail
    59. 59. détail ACKnowledge
    60. 60. Atteindre les informations pertinentes Connect to relevant information
    61. 61. ACKnowledge
    62. 62. ACKnowledge
    63. 63. ACKnowledge
    64. 64. ACKnowledge
    65. 65. ACKnowledge
    66. 66. ACKnowledge
    67. 67. ACKnowledge
    68. 68. Découvrir des connaissances nouvelles Discovery of new knowledge
    69. 69. Les nanopublications peuvent aussi servir à déduire Nanopublications can also be used to reason ACKnowledge
    70. 70. Les nanopublications peuvent aussi servir à déduire Nanopublications can also be used to reason protein X protein A ACKnowledge
    71. 71. 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
    72. 72. Merci! velterop@conceptweballiance jan.velterop@acknowledgeconnect.com http://bit.ly/ACKnowledgedemo1 ACKnowledge

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