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Preprints &
scholarly
infrastructure
Webinar, 30 Jan 2017
Rachael Lammey
Member &
Community Outreach
@CrossrefOrg
Preprints & Scholarly Infrastructure
Today’s agenda!
• Introduction
• Jessica Polka, ASAPbio
• Martyn Rittman, Preprints, operated by MDPI
• Richard Sever, bioRxiv
• Q&A
Preprints & Scholarly Infrastructure
Preprints in!
• Crossref membership
• Content registration with custom metadata
• Notification of links between preprints and
publications
• ORCiD Auto-update
• Identification of funders
Preprints out!
• As with all supported content types, we make the
metadata available for machine and human access,
across multiple interfaces (e.g. REST API, OAI-PMH,
Crossref Metadata Search).
• API: 
•  http://api.crossref.org/types/posted-content/works
•  http://api.crossref.org/works/10.20944/
preprints201608.0191.v1/transform/application/
vnd.crossref.unixsd+xml 
http://blog.crossref.org/category/preprints
A preprint is a manuscript posted
online before journal-organized
peer review
Preprints & journals are compa<ble
Berg	et	al	Science	2016
arXiv:	100,000	manuscripts	per	year	
Preprint servers have existed for 25 years
In	Biology
0	
100	
200	
300	
400	
500	
600	
700	
800	
900	
1000	
Jan-03	
Jul-03	
Jan-04	
Jul-04	
Jan-05	
Jul-05	
Jan-06	
Jul-06	
Jan-07	
Jul-07	
Jan-08	
Jul-08	
Jan-09	
Jul-09	
Jan-10	
Jul-10	
Jan-11	
Jul-11	
Jan-12	
Jul-12	
Jan-13	
Jul-13	
Jan-14	
Jul-14	
Jan-15	
Jul-15	
Jan-16	
Jul-16	
figshare	(filtered	by	PrePubMed)	
Preprints.org	(arLcles/reviews	in	bio/life/med)	
Nature	Precedings	(manuscripts,	from	search	
results)	
The	Winnower	
Version	1		|		asapbio.org	
Preprints are taking off in biology
•  Immediately	openly	accessible	
•  Public	disclosure	of	recent,	“invisible”	work	for	PhD	thesis,	fellowship,	
jobs	
•  Get	more	feedback	on	your	work	
•  Control	when	work	is	made	public	(Lmestamp,	DOI)	
•  Advance	the	pace	of	science	
Major benefits of preprints
Pos<ng preprints is a good experience
392 responses. Results at asapbio.org/survey
Funders including preprints in grants
asapbio.org/funder-policies	
Jan	10,	2017	
Jan	3,	2017	
Dec	12,	2016	
Sept	29,2016	
NIH	RFI	Dec	2016	
Long-term	postdoc	fellowships	2016
“In	the	interests	of	acceleraLng	scienLfic	
discovery,	the	Biohub	will	establish	a	
publicaLon	policy	for	open	and	rapid	
disseminaLon	of	research	results:	all	
InvesLgators	will	be	required	to	post	
manuscripts	on	Arxiv	on	the	date	of	
submission	to	peer-reviewed	journals.”	
hcps://med.stanford.edu/rmg/funding/chan_zuckerberg.html	
Twicer:	#ASAPbio		@jessicapolka	 14
Twicer:	#ASAPbio		@jessicapolka	 15	
A	project	of	the	NIH	
common	fund
Journals innova<ng with preprints
October	4,	2016	
Twicer:	#ASAPbio		@jessicapolka	 16
Twicer:	#ASAPbio		@jessicapolka	 17	
Linking preprints to journals
“Now, to document and help
readers trace the complete
publication record, authors are
invited to voluntarily provide a
footnote for their BJ article
referencing their preprint in
bioRxiv or arXiv, including the
DOI number and the date the
initial manuscript was
deposited.”
AcceleraLng	Science	
and	PublicaLon	in	
biology	
•  Convening stakeholders!
•  Sharing information:
FAQ & tracking policies!
•  Raising awareness!
•  Proposing additional
preprint infrastructure!
ASAPbio.org	
Twicer:	#ASAPbio
Martyn Rittman, Ph.D.
preprints.org
Background
Preprints.org is run by MDPI, an open
access publisher
We want to support rapid dissemination
of knowledge
Preprints is run on a
not-for-profit basis
20
What is a preprint?
A preprint is any article that hasn’t yet been
peer-reviewed and published in an academic
journal. In most cases, you can think of it as a
draft or working paper. A preprint can be
updated and improved at any time.
21
“
”
•  Over 900 Preprints
online
•  12 subject
categories
•  95 advisory board
members
22
•  DOI assigned for every preprint.
•  Sign up for update alerts.
•  Comment on and rate every article.
•  Bookmark with CiteULike, BibSonomy,
Mendeley, etc.
•  See related articles.
•  Altmetrics.
23
24
How does it work?
•  Submission by authors via
Preprints.org or MDPI
submission system.
•  Internal check by Preprints
editors.
•  Refer borderline cases to the
advisory board.
•  Articles online within 24 hours.
25
How does it work?
•  Basic criteria that we check:
•  Title, abstract, keywords present
•  Document structure
•  Author affiliations and background
•  Recent citations
•  Controversial topics/junk papers
•  Use of human/animal/plant subjects
26
Working with Crossref
•  Straightforward implementation: same process as for journals.
•  Easy to cite and link to published versions.
•  Grace period for removal of preprints before DOI registration.
•  New DOI for each preprint version.
27
Outlook
•  Can preprints become standard in more
disciplines?
•  Get review/peer support into the publication
process at an earlier stage.
•  Speed up the reporting of research.
•  Support grant/job applications, especially for
ECRs.
28
29
@preprints_org
http://www.preprints.org
info@preprints.org
@
Richard Sever, PhD
Assistant Director, Cold Spring Harbor Laboratory Press
Twitter: @cshperspectives
Research at Cold Spring Harbor Lab
•  600 scientific staff
•  50 research groups
•  Molecular biology and genetics
•  Cancer
•  Neuroscience
•  Plant biology
•  Genomics and bioinformatics
•  Quantitative biology
•  Ranked #1 worldwide in
molecular biology & genetics
Science communication at Cold Spring Harbor
Conferences
•  Meetings
•  The Banbury Center
•  Cold Spring Harbor Asia, Suzhou, China
Teaching
•  Watson School of Biological Sciences
•  Residential lab and lecture courses
•  DNA Learning Center
Books & Journals
•  Cold Spring Harbor Laboratory Press
2013: CSHL launched the preprint server for biology
•  Non-profit service of CSHL
•  Submission + access free
•  Biological/medical sciences
•  Complements arXiv
Preprint (n): an unpublished manuscript yet to be certified by
peer review
Benefits
•  Rapid transmission of results
•  Pre-publication feedback/discussion
•  Visibility, especially for early-career
scientists
•  Immediate availability to grant/hiring
committees
Accelerating communication
bioRxiv
Data courtesy of Stephen Royle
Received-published
Received-accepted
Accepted-published
bioRxiv features
•  Posted manuscript date-stamped + given a DOI (citable)
•  Indexed in Google Scholar & next-generation literature-discovery tools
•  Choice of article type (New, Confirmatory, or Contradictory Results)
•  Revised version can be posted at any time
•  Choice of license (CC BY, CC BY-NC, CC BY-ND, CC BY-NC-ND, all rights reserved)
•  Article metrics
•  Commenting
•  Links to published versions
Preprints & Scholarly Infrastructure
Preprints & Scholarly Infrastructure
Preprints & Scholarly Infrastructure
Preprints & Scholarly Infrastructure
Preprints & Scholarly Infrastructure
Progress
•  ~8000 submissions (~90% approved)
•  ~30% revised (many more than once)
•  ~30,000 authors
•  >60% of papers subsequently published
•  >400 journals have published papers preprinted on bioRxiv
Progress
•  Behavior change: more biologists posting/reading preprints
•  Policy change: more journals allowing preprint posting
•  Rule change: funding bodies allow citing of preprints in grants
Posts
bioRxiv by subject
arXiv by subject
Impact
•  Citations
•  Comments
•  Blogs
•  Email
•  Social media
?
(11%)
(>>100K)
Formal
publication
Journal integration
Submission
Peer review
Yur
journal
here
B2JJ2B
Preprint
posted
BioPhysical J
Development
eLife
EMBO J
EMBO Mol Med
EMBO reports
G3
Genetics
Genome Res
J Cell Biol
J Gen Physiol
Mol Biol Cell
Mol Sys Biol
Plant J
PLOS
PNAS
& >40 more
Editorial
prospecting
Conference integration
Community integration
bioRxiv - an essential hub
Journals
Meetings Blogs
Confirmatory
results
Contradictory
results
Discussion
Reproducibility
Certification
Discovery
Crossref GoogleMeta
Questions? 
feedback@crossref.org
Thank you!

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