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Du dépôt au partage de données

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Du dépôt au partage de données

  1. 1. Du dépôt au partage de données Antoine Blanchard, consultant en information scientifique chez Deuxième labo antoine@deuxieme-labo.fr Journée Thématique du GdR 2647 STIC-Santé CNRS/Inserm “Avantages et limites d’un dépôt national de données biologiques” 16 mars 2011 Campus des Cordeliers, Paris
  2. 2. Pourquoi déposer des données ?
  3. 3. Pour faire avancer la science http://figshare.com
  4. 4. Une responsabilité déontologique• Committee on Responsibilities of Authorship in the Biological Sciences, National Research Council. Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences (National Academy of Sciences, 2003)
  5. 5. Un mandat politique et stratégique• Commission européenne, Riding the wave – How Europe can gain from the rising tide of scientific data, octobre 2010
  6. 6. Un engagement institutionnel Inserm, janvier 2011
  7. 7. Quelles données déposer ?
  8. 8. Toronto International Data Release Workshop Authors (2009), “Prepublication data sharing”, Nature 461, 168-170
  9. 9. Quand déposer des données ?• … : lors de la publication d’un article• 1992 (États-Unis) : dans les 6 mois• 1996 (Human Genome Project) : dans les 24 h• ≠ embargo de 18 mois pour les données des brevets !
  10. 10. Les obstacles au partage et à la réutilisation
  11. 11. Le “vol” de données• “To date, many papers have been published by third parties reporting research findings enabled by data sets released before publication. The experiences shared in Toronto suggest that these have rarely affected subsequent publications authored by the data producers.”• embargo : cf. Principes des Bermudes (Human Genome Project), 1996• “the Toronto meeting participants recognized that this is an ongoing concern that is best addressed by fostering a scientific culture that encourages transparent and explicit cooperation on the part of data producers, data analysts, reviewers and journal editors” Toronto International Data Release Workshop Authors (2009), “Prepublication data sharing”, Nature 461: 168-170
  12. 12. Les licences fermées• En 1998, Celera annonce que les résultats de son initiative de séquençage seront “en accès libre”… mais est-ce suffisant ?• “any restrictions on use should be strongly resisted and we endorse explicit encouragement of open sharing, for example under the newly available CC0 public domain waiver of Creative Commons” Paul N. Schofield et al. (2009), “Post-publication sharing of data and tools”, Nature 461: 171-173
  13. 13. Les bases de données laissées en friche• 1330 bases de données en biologie moléculaire (Nucleic Acids Research online Database Collection)• il est plus facile d’obtenir un financement pour créer une nouvelle base de données que pour la maintenir en fonctionnement• quand la taille des bases de données génomiques double (tous les 18 mois), Merali Z. & J. Giles (2005), “Databases in peril”, Nature, 435: 1010-1 les coûts de maintenance augmentent de 10% OECD Megascience Forum Working Group on Biological Informatics (1999), Final Report, http:// www.gbif.org
  14. 14. La difficulté à trouver l’information • Un problème connu, cf. Altschul,sequences (1994), “Issues in searching molecular S.F. et al. databases”, Nature Genetics 6(2): 119-129 • mais accentué dans les bases de données brevets où les inventions sont décrites génériquementExemple : “A nucleic acid sequence at least90% identical to the nucleotide sequence of any of the polynucleotides of (a)–(n)…”
  15. 15. Quelques exemples de réutilisation des données
  16. 16. Dans la recherche translationnelle
  17. 17. Dans l’éducation
  18. 18. Quelques bonnes pratiques
  19. 19. Accompagner la mise enligne de ses données d’un “marker paper” citable
  20. 20. Ne pas se reposer surles “supplementary data” • une pratique courante… • …alors que ces données ne sont pas standardisées, pas cherchables, et pas pérennes (17% des SD n’étaient plus en ligne 1 an après — surtout celles stockées ailleurs que sur le site de la revue). N. Anderson et al. (2006), “On the persistence of supplementary resources in biomedical publications”, BMC Bioinformatics 7: 260
  21. 21. Avoir une politique de dépôt et d’archivage• soutenue institutionnellement• avec des moyens financiers• et des objectifs et des incitations clairs © Science
  22. 22. Etc.• Voir les autres interventions de la journée !

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