Scott Edmunds slides for class 8 from the HKU Data Curation (module MLIM7350 from the Faculty of Education) course covering open science and data publishing

1. Class 10…open science
'if I have seen further it is by
standing on the shoulders of
giants'.
Scott Edmunds, HKU Data Curation MLIM7350

2. Communicating in-class
• Chat channel:
• http://backchannelchat.com/chat/dw131
• Feel free to ask questions, requests to speed
up/slow down
Also feel free to email: scott@gigasciencejournal.com

3. Reflection: how fair is FAIR?
Read the FAIR principles paper.
Do you think they are applicable and
feasible for HK? If it is feasible, what is
needed to implement them?
http://www.nature.com/articles/sdata201618

4. Reflection: how fair is FAIR?
• Lots of summarizing the principles, with stress on
importance of “machine-actionability” (important)
• Not everybody mentioned HK context, but a few said
more on this, including:
– Meifeng Chen looked at how FAIR data.gov.hk was (not very)
– Tak Hei Lam thought scholarhub could be a good testbed (more
accessible formats & experiment with RDF)
– Jiafeng Zhou thinks government (?) & ODHK (yes) can help advocate
for implementation
http://www.nature.com/articles/sdata201618

5. HKU Repeatability in HK
Research Experiment
What have we found?
Emailed all controlled access examples for access.
Only 2 responses so far. One bounced. One postal address only.
Data available (by standards of the field) 20 (39.2%)
Data sort of available (raw would have been better) 12 (23.5%)
Need to request access (ethics) 17 (33.3%)
Data not accessible 2 (4%)
Googledoc:https://docs.google.com/spreadsheets/d/15BszEhUodygyu4eGckR2b5p153nyeYmB3Uh4U
23HX-o/edit?usp=sharing
CSV Archive: http://publicdatahk.com/dataset/hku-repeatability-in-hk-research-experiment
Figshare: https://figshare.com/s/0e0906894fc934f8c7b2

6. Final Project
• Presentation Time – 5 mins inc. feedback
• Who has slides to give me?
Ernest Tak-Hei
Lamhttps://docs.google.com/presentation/d/1lYDxCCtumuUBbMwcd5XfgqER
2z9yfU_uTo6DGD3sdpw/edit?usp=sharing
Mika Qiao Zihttps://drive.google.com/file/d/0B-
If8LKUjDK6eVdOaWNVeHdEMTg/view?usp=sharing

7. Questions? | 15 minute break

8. What is open science? 5 flavours:
Benedikt Fecher and Sascha Friesike: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2272036

9. Democratic:

10. Biggest Challenge: Closed Access
WWW.RIGHTTORESEARCH.ORG

11. Biggest Challenge: Closed Access
Handful of closed access STM publishers control market
Force libraries to buy “bundles”
Revenue >$9B
Average cost /article >$5000 USD
Publishers retain copyright
Prevent data mining of content
Withold information from 99.9% who need it!

12. Publishing: better than a gold mine
See: http://alexholcombe.wordpress.com/2013/01/09/scholarly-publishers-and-their-high-profits/

13. Increasing strain on library budgets
-50%
0%
50%
100%
150%
200%
250%
300%
350%
400%
1986 1988 1990 1992 1994 1996 1998 2000 2002 2004
PercentageChange
Year
MIT library purchases v inflation 1986-2006
Consumer Price Index % + Serial Expenditures % + # Serials Purchased % +
# Books Purchased % + Book Expenditures % +
Journal expenditure
Inflation

14. Too expensive for Harvard…

15. The good news: the fightback has started…
http://thecostofknowledge.com/

16. The Solution: Open Access
“By “open access” to [peer-reviewed research literature], we mean its
free availability on the public internet, permitting any users to read,
download, copy, distribute, print, search, or link to the full texts of
these articles, crawl them for indexing, pass them as data to
software, or use them for any other lawful purpose, without financial,
legal, or technical barriers other than those inseparable from gaining
access to the internet itself. The only constraint on reproduction and
distribution, and the only role for copyright in this domain, should be
to give authors control over the integrity of their work and the right to
be properly acknowledged and cited.”
Budapest Open Access Initiative:
• Maximizes reuse and access
• Gives authors control over the integrity of their work and the right
to be properly acknowledged and cited.
• “Real” OA asks for no restrictions/limitations = CC-BY

17. The Solution: Pre-prints
Greatly speeds up research

18. The Solution: Pre-prints
Finally taking off across the globe
http://ec.europa.eu/research/openscience/index.cfm?section=monitor&pg=access#3
>50K pre-prints in China
Now has ChinaXiv:
http://chinaxiv.org/

19. The Solution: OER
Open Education Resources: democratising education
https://www.oercommons.org/

20. The Solution: OER
Open Education Resources: democratising education
https://www.oercommons.org/
(Hint, can be useful for one of the project options…)

21. Pragmatic:
Infrastructure:

22. Data platforms: easy to build
https://ckan.org/
Open source, from OKI. Used by Governments (inc. HK),
Universities (Bristol), even hospital registries.

23. Pragmatic/Infrastructure:
Wiki science:
• 10,000 distinct gene pages.
• 2.07 million words and 82MB data.
• 50 million views & 15,000 edits per year.
Crowdsourcing, wisdom of the masses
GeneWiki
GitHub science:
A hypothetical Git workflow for a scientific collaboration involving 3 authors.
Karthik Ram: http://www.scfbm.org/content/8/1/7
http://en.wikipedia.org/wiki/Portal:Gene_Wiki

24. Open Lab Notebooks

25. http://www.gov.hk/en/theme/psi/contest/contest_events.htm
Pragmatic/Infrastructure:
Open Innovation Challenges
http://www.scientificamerican.com/openinnovation/

26. Public:

27. Utilizing students: iGEM
iGEM:
http://2011.igem.org/Team:UC_Davis

28. Indie Science
Biohacker spaces
CoResearch labs
Crowdfunding
DIYbio
Open hardware
http://www.perlsteinlab.com/

29. Now in Hong Kong…
http://www.scmp.com/lifestyle/article/2017906/biohackers-diy-biologists-out-barcode-all-hong-kongs-plants-insects-and

30. Biggest crowdfunding successes

31. http://bauhiniagenome.hk/

32. Public: Citizen Science
Galaxy Zoo:
Zoonoverse:
1M> “Zooites” and counting
https://www.zooniverse.org/

33. Public: Citizen Science
1987-1997
http://sabap2.adu.org.za/
http://www.hkbws.org.hk/

34. Easy to get started…
http://crowdcrafting.org/

35. Public: Games with a Purpose
http://fold.it/
http://www.sciencegamecenter.org/

36. https://apps.facebook.com/fraxinusgame/

37. http://dx.doi.org/10.6084/m9.figshare.1286826
Putting in context…

38. Explosion in number of platforms
http://dashboard101innovations.silk.co/

39. http://101innovations.silk.co/page/workflows
Lots of potential workflows…

40. Things surveyed (>20K respondents)

41. Things surveyed (>20K respondents)

42. Things surveyed (>20K respondents)
Alerts: Do any of you use these?

43. Things surveyed (>20K respondents)
Read/annotate: Do any of you use these?

44. Things surveyed (>20K respondents)
Referencing: Do any of you use these?

45. Things surveyed (>20K respondents)
Pre/post-print publication sharing: Do any of you use these?

46. http://dashboard101innovations.silk.co/page/Archive-share-data-%26-code
Things surveyed (>20K respondents)

47. Things surveyed (>20K respondents)
Poster/presentation sharing: Do any of you use these?
(Hint hint: useful for final project)

48. Things surveyed (>20K respondents)
Measuring impact: Do any of you use these?

49. Things surveyed (>20K respondents)
Journal types: Do any of you use these? Inc. Data journals?

50. Publishing Open Data

51. Specific things we should be rewarding:

52. • Review
• Data
• Software
• Models
• Pipelines
• Re-use…
= Credit
}
Credit where credit is overdue:
“One option would be to provide researchers who release data to public repositories with
a means of accreditation.”
“An ability to search the literature for all online papers that used a particular data set
would enable appropriate attribution for those who share. “
Nature Biotechnology 27, 579 (2009)
New incentives/credit

53. Step 1: Archived data
Step 2: Landing Page
Step 3: Persistent Identifier
Step 4: Clear metadata
Step 5: Advertisement (cite our data like this…)
Data Citation Principles
https://www.force11.org/group/joint-declaration-data-citation-principles-final

54. https://peerj.com/articles/cs-86/
Software: how to credit?

55. Software: how to credit?

56. Not just carrots…
“The data discovery index (DDI) enabled through
bioCADDIE is to do for data what PubMed (and
PubMed Central) did for the literature.”
https://datamed.org/

57. How do we find datasets?
Commercial products: Data Citation Index
http://wokinfo.com/products_tools/multidisciplinary/dci/

58. How do we publish datasets?
http://dashboard101innovations.silk.co/page/Archive-share-data-%26-code

59. How do we publish datasets?
http://dashboard101innovations.silk.co/page/Archive-share-data-%26-code
6156 respondents to survey answered (preset answers or “other”):

60. How do we publish datasets?
http://dashboard101innovations.silk.co/page/Archive-share-data-%26-code
6156 respondents to survey answered (preset answers or “other”):

61. Federated approach: DataVerse
https://data.mendeley.com/

62. Inc Hong Kong: DataSpace@HKUST
https://dataspace.ust.hk/

63. How do we find datasets?
https://search.datacite.org/
https://datamed.org/

64. How do we find dataset citations?
Workarounds in Europe PMC & GoogleScholar & Europe (DOI string)

65. Exercise: find the data citations
How many citations does the Darwin (ground) finch genome data
in this paper have?
Can find it by searching through the comparative genomic datasets.
Should be in https://search.datacite.org/ or https://datamed.org/
http://science.sciencemag.org/content/346/6215/1311

66. Data Publishing: nothing new…
Data & Metadata Collection/Experiments
Analysis/Hypothesis/Analysis
Conclusions
+ Area of Interest/Question
1839
1859
20 Yrs.

67. Rewarding open data
http://gigasciencejournal.com/
Launched July 2012. Publishes “Data Notes” for CC0 data. Uses ISA-Tab.

68. Rewarding open data
APC covers 1TB of storage in GigaDB

69. Rewarding open data
https://www.nature.com/sdata/
Launched May 2014. Publishes “Data Descriptors” for CC0 data. Uses ISA-Tab.

70. Rewarding open data
APC covers 100 GB of storage in figshare

71. Rewarding open data
https://www.journals.elsevier.com/data-in-brief
Launched December 2014. Publishes “Data Articles” for data.

72. Rewarding open data
https://data.mendeley.com/
Initially promoted Data In Brief Dataverse. Now also has Mendeley Data.

73. Rewarding open data
http://www.csdata.org/
Launched March 2016. Publishes “Data Articles”.

74. Rewarding open data
http://www.sciencedb.cn/
Associated CAS database, publishes CC-BY data.

75. Submitting to CKAN: basic version
Need to install
Very Basic Metadata:
Title,
Description,
Source,
Organisation,
Maintainer & Author
(names and emails),
Source (URL),
License
& custom tags.

76. Submitting to OSF
Very Very Basic Metadata (all optional):
Title, Authors, Keywords, Description, License (CC0,
CCBY). Free.
https://osf.io/8zfty/

77. Submitting to Mendeley data
Basic Metadata:
Contributors,
Institutions (optional),
Categories,
Description,
Steps to reproduce (optional),
Related Links (optional)
Lots of license options (inc NC).
Free.
https://data.mendeley.com/

78. Submitting to figshare
Very Basic Metadata:
Title,
Authors,
Catagories/File Type,
Keywords,
Description.
License (CC0, CCBY, OSI).
Free if <5GB.
https://figshare.com/s/0e0906894fc934f8c7b2

79. Looking ahead…
• Final project due 15th May
• Any interest in summer project – writing up
Reproducibility Exercise into a short paper let
me know…
• Questionnaire to fill out for Dr Chu (we’ll hand
this out)…