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Publishing data and code openly

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Written and presented by Tom Ingraham (F1000), at the Reproducible and Citable Data and Model Workshop, in Warnemünde, Germany. September 14th -16th 2015.

Published in: Science
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Publishing data and code openly

  1. 1. Thomas Ingraham Publishing Editor, F1000Research thomas.ingraham@f1000.com
  2. 2. Conventional publishing Model
  3. 3. F1000research publishing Model
  4. 4. Enabling early access to results Pre-print server OA Journal Early access to results & data Editorial input Precedence for authors Peer review & indexing Multiple versions Publication ethics No Editor in Chief Perfected paper OA
  5. 5. Open peer review Decision based on scientific soundness
  6. 6. Versioning
  7. 7. Versioning
  8. 8. Publishing data & code
  9. 9. publishing raw data and source code Uses •Exploratory analyses, LOD, reproducibility checks (data, reanalyses + software) Linking with Research Articles •Better metadata/documentation •Quality control Software Tool Articles & Data Articles •Big/small datasets – no analyses •Software packages/web tools •Even better metadata/documentation •Versioning – updates & point releases •High visibility •More credit (quantity and quality)
  10. 10. Requirements for data and code Interoperable formats Metadata All?
  11. 11. Workflow & repositories Submission Pre-Pub Check Publish Peer review Repository Crosslink Further requests F1000Research curates approved repo list
  12. 12. Credit for data and software Data availability: Repository: Data entry title, PID [Ref] [Ref] Author Names. Data entry title [v]. Repository. Year. PID Cite the data or the Data Article? Clear accessibility info and actively encourage data/software citation Software availability: Software access (opt): URL Latest source code (opt): VCS URL Archived entry: Repository: Software title, PID [Ref] Licence: OSI [Ref] Author Names. Software title [v]. Repository. Year. PID
  13. 13. INTERGRATION, VISUALIZATION & ANALYSIS OF DATA
  14. 14. Living figures: Data + Code Colomb & Brembs: http://f1000research.com/articles/3-176/v1
  15. 15. Challenges Sensitive data •Protected repositories •HIPPA-compliant (safe harbour) •DataSHIELD Other challenges •Rawness & granularity
  16. 16. Jisc Bodleian 1-click data submission Project Reducing the friction data sharing
  17. 17. SUMMARY: F1000RESEARCH’S APPROACH TO OPEN SCIENCE • Near-immediate publication Open, invited peer review conducted after publication • Transparent peer-review Signed referee reports and author responses published alongside each article • No editorial bias Publication of all findings, including null results, software tools and data notes. • Data included All research articles accompanied by the data on which they are based
  18. 18. ANNOTATOR PLUGIN
  19. 19. PREDICTS CITATIONS
  20. 20. COLLABORATE

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