Slides for my September 23 talk on Wikidata and WikiCite – NIH Frontiers in Data Science lecture series. Persistent URL: https://dx.doi.org/10.6084/m9.figshare.3850821

1. Wikidata: Verifiable, Linked Open
Knowledge That Anyone Can Edit
Dario Taraborelli
@readermeter
National Institutes of Health • September 23, 2016

2. Wikimedia Research
https://www.mediawiki.org/wiki/Wikimedia_Research

3. The altmetrics manifesto
http://altmetrics.org/manifesto/

5. A short history of Wikipedia
A website that anyone can edit
The largest reference work on the internet
A multi-language online encyclopedia

6. A short history of Wikipedia
A website that anyone can edit
The largest reference work on the internet
A multi-language online encyclopedia

7. A short history of Wikipedia
A website that anyone can edit
The largest reference work on the internet
A multi-language online encyclopedia

8. Wikipedia: unintended outcomes
accelerate the dissemination of scholarship
provide an infrastructure open scientific research
enable distributed fact-checking and curation of scientific knowledge

9. Outline
1. Wikipedia as the front matter to all research
2. A new kind of open knowledge
3. Wikidata: Collaboratively curated linked open data
4. WikiCite: Building the sum of all human citations
5. Applications and opportunities for open science
6. Concluding remarks

10. 1. Wikipedia as the front matter to all research

11. “Wikipedia is not the bottom
layer of authority, nor the top,
but in fact the highest layer
without formal vetting. In this
unique role, it serves as an
ideal bridge between the
validated and unvalidated
Web.”
Casper Grathwohl
Chronicle of Higher Education
http://chronicle.com/article/article-content/125899/

12. Top sources of DOI lookups
http://crosstech.crossref.org/2014/02/many-metrics-such-data-wow.html
http://blog.crossref.org/2016/05/https-and-wikipedia.html
wikipedia.org

13. World’s most accessed online medical resources
Heilman and West (2015) doi.org/10.2196/jmir.4069

14. Most visited resource on Ebola in West Africa
Heilman (2016) http://tinyurl.com/jfuyduv
Most used internet site in Liberia,
Sierra Leone and Guinea for
Ebola during 2014 outbreak
Greater than CNN, CDC and WHO

15. 2. A new kind of open knowledge

16. Schmachtenberg et al (2014)
http://lod-cloud.net [CC BY SA]

17. Challenges
Biases / errors
Coverage
Diversity and inclusiveness
Verifiability

18. Machine-readable linked open data
Editable by anyone
Supporting human + algorithmic curation
Comprehensive
Transparently verifiable

19. Machine-readable linked open data
Editable by anyone
Supporting human + algorithmic curation
Comprehensive
Transparently verifiable

20. Machine-readable linked open data
Editable by anyone
Supporting human + algorithmic curation
Comprehensive
Transparently verifiable

21. 3. Wikidata: Collaboratively curated linked open data

22. Wikidata
Free knowledge base that anyone can edit
Launched in 2012
Integrated with Wikipedia and other sister
projects
Statistics (September 2016)
Over 20M items
Over 100M statements

23. Wikidata:
Growth
http://reportcard.wmflabs.org/graphs/active_editors
English Wikipedia
Wikidata

24. Wikidata:
Growth
http://reportcard.wmflabs.org/graphs/very_active_editors
English Wikipedia
Wikidata

25. Wikidata’s anatomy
https://www.wikidata.org/wiki/Wikidata:Introduction

26. Wikidata’s anatomy
Linked data, San Francisco, Jeblad
https://commons.wikimedia.org/wiki/File:Linked_Data_-_San_Francisco.svg [CC BY SA]

27. SPARQL:
https://t.co/cDR4Lt7V6P
Birth place of people
employed by MIT
Wikidata: queries

28. SPARQL:
http://tinyurl.com/h2lqv9y
Authors with a known
location and ORCID
Wikidata: queries

29. Expert curation of scientific open data
Benjamin Good (2016) Opportunities and challenges
presented by Wikidata in the context of biocuration
http://tinyurl.com/hk9qrmz

30. Sample of current biomedical content in Wikidata
● All human, mouse genes and proteins (swissprot)
● All Gene Ontology terms
● All Human Disease Ontology terms
● All FDA approved drugs
● 109 reference microbial genomes
Mitraka et al (2015) Semantic Web Applications for the Life Sciences
Burgstaller-Muelbacher et al (2016) Database
Putman et al (2016) Database

31. Expert curation of scientific open data

32. Expert curation of scientific open data
Gene Wiki: WIkidata SPARQL examples
https://bitbucket.org/sulab/wikidatasparqlexamples/overview
Get all known drug-drug interactions for Methadone via its CHEMBL id
Get a list of all diseases known to be treated by Metformin
Get a list of all diseases that might be treated by Metformin

33. 4. WikiCite: Building the sum of all human citations
Randall Munroe, Wikipedian protester http://tinyurl.com/p3rodlb [CC BY]

34. https://twitter.com/egonwillighagen/status/718474906858582016

35. Benjamin Good (2016) Opportunities and challenges presented by Wikidata in the context of biocuration
http://tinyurl.com/hk9qrmz

37. the disappearance of provenance
http://bit.ly/SumOfAllCitations

38. the disappearance of provenance

40. a provenance-preserving answer engine
The sum of all human
knowledge
The sum of all data and
sources backing human
knowledge
+

41. https://tools.wmflabs.org/wikidata-todo/stats.php
https://www.wikidata.org/wiki/Wikidata_talk:WikiProject_Source_MetaData#Sources_used_as_references_on
_Wikidata
77%
2013 2014 2015 2016
References in Wikidata

42. The molecular origins of insulin go at least as far back as
the simplest unicellular [[eukaryotes]].<ref
name='LeRoith'>{{cite journal | vauthors = LeRoith D, Shiloach
J, Heffron R, Rubinovitz C, Tanenbaum R, Roth J | title =
Insulin-related material in microbes: similarities and
differences from mammalian insulins | journal = Can. J.
Biochem. Cell Biol. | volume = 63 | issue = 8 | pages = 839–49
| year = 1985 | pmid = 3933801 | doi = 10.1139/o85-106
}}</ref> Apart from animals, insulin-like proteins are also
known to exist in Fungi and Protista kingdoms.
References in Wikipedia

44. WikiCite: goals
Build a repository of all Wikimedia citations
and bibliographic metadata
Design data models and technology to improve the coverage,
quality, standards-compliance and machine-readability of
citations and bibliographic metadata in Wikimedia projects
@wikicite • meta.wikimedia.org/wiki/WikiCite

45. Vision
Technology
Community
Scale
Licensing
Independence

46. https://tools.wmflabs.org/sqid/#/view?id=P2860
All biomedical OA review articles of the last 5 years

47. The Zika corpus
Open citation graph layer
Bibliographic metadata layer
Expert annotation layer
Encyclopedic layer

48. The Zika corpus
Encyclopedic layer

49. The Zika corpus
Expert annotation layer
Encyclopedic layer Pathogen transmission process

50. The Zika corpus
Bibliographic metadata layer
Expert annotation layer
Encyclopedic layer

51. The Zika corpus
Open citation graph layer
Bibliographic metadata layer
Expert annotation layer
Encyclopedic layer

52. 5. Applications

53. Co-author graphs for individual researchers
SPARQL: http://tinyurl.com/zml3jox

54. Most cited authors in the Zika research corpus (+ filtering by journal, OA status, type of statement)
SPARQL: http://tinyurl.com/jb8da68

55. Semi-automated recommendation of entities, missing statements, references for unsourced statements
https://meta.wikimedia.org/wiki/Grants:IEG/StrepHit:_Wikidata_Statements_Validation_via_References
https://www.wikidata.org/wiki/Wikidata:Primary_sources_tool

56. Semi-automated recommendation of entities, missing statements, references for unsourced statements
https://meta.wikimedia.org/wiki/Grants:Project/WikiFactMine
https://twitter.com/larswillighagen/status/774614483394236416

57. Tools for crowdsourcing entity matching / disambiguation
http://www.generalist.org.uk/blog/2014/wikidata-identifiers-and-the-odnb-where-next/
http://www.generalist.org.uk/blog/2014/wikidata-and-identifiers-part-2-the-matching-process/

58. read/write interfaces for biocuration

59. all statements citing a New York Times article
the most popular scholarly journals used as citations for statements in any item that
is a subclass of economics
all statements citing the works of Joseph Stiglitz
all statements citing journal articles by physicists from Oxford University
all statements citing a journal article that was retracted
all statements citing a source that cites a journal article that was retracted
New opportunities for linked open knowledge curation and discovery
https://meta.wikimedia.org/wiki/WikiCite_2016/Report/Group_5

60. More reliable data for altmetrics services
https://www.altmetric.com/blog/new-source-alert-wikipedia/

61. 6. Concluding remarks

62. Dominant biocuration paradigm
● Cost of ad-hoc parsing of API responses or flatfile data
● Ambiguous or non-existent xrefs
● Persistence of funding
● Too much information to curate
B. Good (2016) Opportunities and challenges presented by Wikidata in the context of biocuration http://tinyurl.com/hk9qrmz

63. A new paradigm for biocuration
● Reduce API/parser proliferation
● Force up-front integration
● Facilitate coordination
● Ensure that if funding is lost, data is not
● Leverage community input
B. Good (2016) Opportunities and challenges presented by Wikidata in the context of biocuration http://tinyurl.com/hk9qrmz

64. T. Putman (2016) Centralizing content and distributing labor: a community model for curating the very long tail of
microbial genomes https://doi.org/10.6084/m9.figshare.3201796.v1

65. Accelerate the discoverability, reusability,
and societal impact of open access

66. Support new forms of open curation and distributed fact-checking
Provide long-term, sustainable infrastructure to support open science
Benefit from large-scale distribution of data in the linked data ecosystem
Wikidata: Verifiable, Linked Open
Knowledge That Anyone Can Edit

67. meta.wikimedia.org/wiki/WikiCite • @wikicite

68. Thank you
Acknowledgments
Daniel Mietchen, Jonathan Dugan, Lydia Pintscher, Cameron Neylon, James Hare, James Heilman,
Magnus Manske, Egon Willighagen, the Gene Wiki team (especially Andra Waagmeester, Tim
Putman, Benjamin Good), the ContentMine team, the University of Chicago Knowledge Lab, all
WikiCite 2016 participants and Wikidata Source Metadata project contributors.
Additional image credits
Library, National Park Service Collection thenounproject.com/term/library/191/ [CC0]
Robot, Creative Stall thenounproject.com/term/robot/132360/ [CC BY]
Open Access logo commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_transparent.svg [CC0]
dario@wikimedia.org • @readermeter • @Wikidata • @WikiCite • @WikiResearch

69. A short history of NIH and Wikimedia
● 2002: article National Institutes of Health started on English Wikipedia
● 2003: MEDLINE
● 2004: PubMed
● 2005: PubMed Central
○ along with Template:PMC
● 2007: WikiProject National Institutes of Health
○ along with Template:National Institutes of Health
● 2009: first Wikipedia Academy in the US took place at NIH
○ Susannah Fox: “Shared Kismet: Wikipedia and the NIH”
○ triggers Guidelines for Participating in Wikipedia from NIH
● 2012: bot imports multimedia from PMC into Wikimedia Commons
○ triggers formation of JATS for Reuse working group
● 2015: Template:NIH properties on Wikidata
● 2016: First papers using Wikidata queries appear in PMC