About

A Question

Who has an article in Lecture Notes in Computing Science?

Open Science

A broad definition would be:

Open Data
Open Source
Open Access

Some human interest

Taken from: http://en.wikipedia.org/wiki/File:Jonathan-eisen.jpg

A biologist from UC Davis.
Wanted to collect his father’s (also a biologist) life work
But couldn’t.

Story by David Dobbs Taken from: http://www.wired.com/wiredscience/2011/05/free-science-one-paper-at-a-time-2/

Harvard runs out of cash

"fiscally unsustainable"
"academically restrictive"
"online content from two providers have increased by about 145% over the past six years"
"exacerbated by […] publishers to acquire, bundle, and increase the pricing"

Taken from: http://www.guardian.co.uk/science/2012/apr/24/harvard-university-journal-publishers-prices

Taken from: http://isites.harvard.edu/icb/icb.do?keyword=k77982&tabgroupid=icb.tabgroup143448

Open Access

Pioneered by BMC — an online journal
Originally took the bottom end of the market
Followed by PLoS
Originally aimed at the top end, and grant supported

Open Access (10 years on)

BMC Bioinformatics is now high impact
PLoS has 6 main journals
And PLoS One

PLoS One

Has peer-review
Judges on scientific rigour
Not on perceived importance
Now has impact factor 4.4
In 2010 > 6000 articles
the largest journal in the world

Open Access Mandates

Many funders now mandate OA
RCUK (sort of). NIH. Wellcome.
Welcomed by all!
Research Works Act

RWA

No Federal agency may adopt, implement, maintain, continue, or otherwise engage in any policy, program, or other activity that […] causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher of such work

sponsered by senators who have recieved multiple donations from Elsevier
"private-sector research work" would include papers
Because, after all a paper is produced by the private sector

Cost of Knowledge

http://thecostofknowledge.com/
From an original post by Tim Gowers
Fields medalist
polymath, crowd sourcing maths proofs.
Not the first boycott

Arguments for Paywall Journals

Paywall promotes quality
Australasian Journal of Bone and Joint Medicine
Paid for by Merck
Positive stories about Merck products

OA is vanity publishing

Chaos, Solitons and Fractals

OA is vanity publishing

Chaos, Solitons and Fractals

OA is vanity publishing

Chaos, Solitons and Fractals

OA is vanity publishing

Chaos, Solitons and Fractals

OA is vanity publishing

Author M. S. El Naschie published >300 single author articles
A big favorite of Editor-in-Chief
M. S. El Naschie
At one point, Chaos, Solitons and Fractals was highest IF maths journal

Paywall access prevents copying

images/springer_molecule.jpg

An image of a molecule
Copyright Springer-Verlag
Actually, produced by Peter Murray-Rust
"A global resource for computational chemistry"
Journal of Molecular Modeling

A Question and an Answer

Who has an article in Lecture Notes in Computing Science?
- None of you. If it’s in LNCS, the article is Springer’s

OA or OA/2

Open Access is, however, expensive
Between 800 and 3000(!) pound
It’s "half open access"
Ultimately, do I care? It’s not my cash!
There is also a hidden cost

The Costs

The Second Biggest Scientific Publisher
250,000 articles per year
240 million Downloads
Cost: 1.5 Billion Euro
Elsevier

The Costs

The First Biggest Scientific Publisher
17 million articles
> 20 languages
365 million readers
Total Cost: 10 million dollars
Wikipedia

The process

images/800px-Herrschaftliche_Kutsche.JPG

The process

images/500px-LaTeX_cover.svg.png Taken from: http://commons.wikimedia.org/wiki/File:LaTeX_cover.svg

The process

images/500px-Adobe_PDF_Icon.svg.png Taken from: http://en.wikipedia.org/wiki/File:Adobe_PDF_Icon.svg

The process

images/500px-Adobe_PDF_Icon.svg.png

Again!

The process

images/500px-Microsoft_Word_Icon.svg.png Taken from: http://en.wikipedia.org/wiki/File:Microsoft_Word_Icon.svg

The process

images/500px-XML.svg.png Taken from: http://en.wikipedia.org/wiki/File:XML.svg

The process

images/HTML5_Logo_512.png Taken from: http://www.w3c.org/html/logo

The process

images/500px-Adobe_PDF_Icon.svg.png

Again, Again!

Hidden Cost

Compare to arXiv

The "physics" pre-print server
Cut and paste in standard metadata
Upload .tex and .bbl file (also images)
View PDF
Click "go"
Cost $7 per paper
Takes about ~7minutes (n=1) from LaTeX to published

Compare to Wordpress

Open Lab Book
Write in Word
Click "go"
Publication time measures in ms

Ontogenesis

Wanted to publish tutorial information
Writing a book is painful
Open, public peer-review
We now have around 30 articles, published over 2 years
Many articles short, discrete
We have published unpublishable material

Linked Data

Now we have a simple process
Which we have extended
Knowledgeblog
We can publish linked, semantic article

References

Academics love in text-citations (Lord, 2012)
Will describe two tools, kcite and greycite

References

Lord, P (2012) Academics love Citations. J.Unsupport.Assert

References (author)

Authors insert primary identifiers
[cite]10.100/100.1[/cite]
This is a DOI.
We also do arXiv, pubmed IDs.

images/kblog-with-edam-with-more-references.png

References (reader)

Readers can see citation or direct link
Readers can change citation style

images/kblog-with-edam-with-numeric-listing.png

References (kcite architecture)

The Problem

Inserting links is painful
Fortunately, we can use the bibliographic metadata to help
Will demonstrate this after a brief interlude

Greycite

Originally, kcite could not support URLs
As well as Publishing the Unpublishable
We want to Cite the Uncitable
We needed a source for metadata
Now we have http://greycite.knowledgeblog.org
Developed by Lindsay Marshall, Computing Science, Newcastle

Greycite

This is greycite

Greycite

Add a URL

Greycite

URL results

Greycite

Scrolling to more detail

Greycite

Provenance (coins)

Greycite

Provenance (OGP)

Greycite

And elsewhere

Greycite

And elsewhere

Greycite

Sadly, some websites have no semantics that we can find

Greycite

Preservation

Greycite

Citing Links

How does citation work?

Citing Links

We want to cite this page

Citing Links

In an article, I am writing

Citing Links

First we take the URL

Citing Links

Query Greycite

images/emacs-with-edam-url-and-mxgreycite.png

Citing Links

Get back bibtex

Citing Links

So, we search

images/emacs-and-post-ref-with-regexp.png

Citing Links

And select

images/emacs-and-post-ref-with-reftex-dialog.png

Citing Links

And insert

images/emacs-and-post-ref-with-kurl-inserted.png

Citing Links

And publish

Accessibility

This is all fairly simple
And works because the content is OA
Greycite can get to the metadata because it is open
BL can archive, because the content is open
Archive also includes metadata because it is open
Much of it works outside academic publishing
Compare DOI, CrossRef, LOCKSS and so on.

Ideas: Glossary

Short 140 word articles with a title
Word, not character!
Fully attributed
Linkble
Publish via email
Displayed inline

Ideas: Structured Knowledge

Open Disease Reports from David Shotton
Short summaries of disease information published elsewhere
Critical for third world
We want to structure the knowledge for mining.

Ideas: Enhanced Linking

Ideas: Linking

Ideas: The NearCon

Nearly a conference
Cross between a workshop and a special issue
Publish papers and then talk about them!
Like a workshop
- see papers you might miss
Asynchronous!

Publishing in Flux

eLife - modelled on PLoS one
F1000 - Cross between PLoS One and arXiv
PeerJ - $100 to register, free to publish

Dutch Tulip bulb

What can we do?

Technical Report Series

Replace with arXiv
Recognised
Stable
Standard Metadata
Supplement with Kblog
More experimental
Web First

What can we do?

Grants

Publish all our grants on the web
Successful or not!
Knowledge blog would be a good framework

What can we do?

Online thesis

We can encourage students to publish their theses online
Allyson Lister has just done this
http://themindwobbles.wordpress.com/2012/06/14/thesis-abstract/

What can we do?

Open Notebook Science

all research active staff and students
Publish as we go!

What can we do?

Cash!

Q: Can I get cash for my PhD student to conference?
A: Yes! But conference should come with publication.
All the suggested publication locations are toll access

What can we do?

Teaching

Open Education Resources
Release lecture notes online
Release all recap online
Try before you buy!

Elephant in the Room

REF
Promotion Committees
Lawyers

Acknowledments

Kblog/Ontogenesis
- Robert Stevens, Georgina Moulton (Manchester).
- Dan Swan, Simon Cockell (Newcastle)
Kcite
- Simon Cockell
Greycite
- Lindsay Marshall

Summary/Conclusion

Open Access == freely available papers
Part of the move to Open Science
Happening whether we like it or not
It should be seen as an opportunity not a risk

Is Academic Publishing a Dutch Tulip Bulb?

About

A Question

Open Science

Some human interest

Harvard runs out of cash

Open Access

Open Access (10 years on)

PLoS One

Open Access Mandates

RWA

Cost of Knowledge

Arguments for Paywall Journals

OA is vanity publishing

OA is vanity publishing

OA is vanity publishing

OA is vanity publishing

OA is vanity publishing

Paywall access prevents copying

A Question and an Answer

OA or OA/2

The Costs

The Costs

The process

The process

The process

The process

The process

The process

The process

The process

Hidden Cost

Compare to arXiv

Compare to Wordpress

Ontogenesis

Linked Data

References

References

References (author)

References (reader)

References (kcite architecture)

The Problem

Greycite

Greycite

Greycite

Greycite

Greycite

Greycite

Greycite

Greycite

Greycite

Greycite

Greycite

Greycite

Citing Links

Citing Links

Citing Links

Citing Links

Citing Links

Citing Links

Citing Links

Citing Links

Citing Links

Citing Links

Accessibility

Ideas: Glossary

Ideas: Structured Knowledge

Ideas: Enhanced Linking

Ideas: Linking

Ideas: The NearCon

Publishing in Flux

What can we do?

What can we do?

What can we do?

What can we do?

What can we do?

What can we do?

Elephant in the Room

Acknowledments

Summary/Conclusion