1. What is Open Access?

Day 1 – am
1.
2.
3.
4.
5.
6.
7.
8.
What is Open Access?
Open Access at University of Zurich
Licenses of Open Access
Examples of Open Access Journals
Open Access Repositories
DOI: Digital Object Identifier
Open Access Search Engines
Publishing in high-impact journals:
• Impact Factors
• Debate
9. Open Access Publication Strategies
10. Open Access and Web 2.0
Day 1 – pm
1.
2.
3.
4.
5.
6.
7.
What is a Weblog?
Types of Blogs
The Structure of Blogs and some Technical Terms
Some Examples of Science Blogs
Why should Academics use or publish Blogs?
Credibility
Science Blogs with some Influence – could we calculate an impact factor for
weblogs?
8. Familiarize yourself with the Wordpress Technology
• Build your own Blog
• Choose a Design for your Blog
• Navigation of your new Blog
• Write and edit a Post
• Publish a Post
• Comment on a Post
• Links and Images
LEARNING OBJECTIVES
Research Management
C3. Identify and access appropriate bibliographical resources, archives, and other sources of relevant
information
C4. Use information technology appropriately for database management, recording and presenting
information
Communicate
E1. Write clearly and in a style appropriate to purpose, e.g. progress reports, published documents, thesis
E2. Construct coherent arguments and articulate ideas clearly to a range of audiences, formally and
informally through a variety of techniques
E4. Contribute to promoting the public understanding of one’s research field
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
1
Networking
F1. Develop and maintain co-operative networks and working relationships with supervisors, colleagues and
peers, within the institution and the wider research community
F2. Understand one’s behaviours and impact on others when working in and contributing to the success of
formal and informal teams
F3. Listen, give and receive feedback and respond perceptively to others
Career Management
G4. Present one’s skills, personal attributes and experiences through effective CVs, applications and
interviews
Training and Development Needs Analysis
http://www.leeds.ac.uk/rtd/downloads.htm
Open Access Journals
Open Access Journals are freely accessible via the Internet for immediate,
worldwide, open access to full articles at no cost:
•
•
•
•
No subscription fees for Open Access Journals
Open Access publication costs are usually covered by the authors institution
or research funds
Authors retain the copyrights of their articles
Open Access Journals are peer-reviewed journals
Open Access Jat University of Zurich and ETH Zurich
•
•
•
•
The University of Zurich (UZH) encourages and supports their authors to
publish their research articles in open access journals.
The SNSF requires Open Access for all publications by its sponsored
researchers, starting Sept. 1, 2007. Deposition in a freely accessible server is
mandatory. Researchers of the UZH fulfill this duty by depositing their
publications in ZORA (http://www.zora.uzh.ch/);
For ETHZ it is ETH e-collection (http://ecollection.ethbib.ethz.ch/index.php?lang=en)
The UZH and ETHZ are member of Biomed Central (authors do not pay any
publication costs): http://www.biomedcentral.com
License Models of Open Access
Creative Commons Attribution License (CCAL)
•
•
Authors retain ownership of the copyright for their article
Authors allow anyone to download, reuse, reprint, modify, distribute and/or
copy articles, so long as the authors and source are cited. No permission is
required from the author ort he publisher.
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
2
•
Reuse of parts of a work, e.g. an illustration: indicate the origination of the
work, and the volumes, issue of the journal. You must also make clear the
license terms under which the work was published
Other Licences: Creative Commons http://creativecommons.org/affiliates/ch/
Restrictions of Open Access (OA)
•
Some OA allow reuse or distribution only after 6 month after publication
Examples of Open Access Publishers
Public Library of Science (PLoS): http://www.plos.org/
Public Library of Science was the first open access publisher. PLoS is a nonprofit
organization Top journal: PLoS Biology, the most successful open access journal at
present, featuring an impact facture of 14.1 (2006).
BioMed Central (BMC): http://www.biomedcentral.com/
BioMed Central is the largest independent open access publisher, featuring more
than 180 peer-reviewed biomedical research journals. Top journals: Journal of
Biology, Genome Biology.
Bentham Science: http://www.bentham.org/
Bentham Publishers are launching more than 200 peer-reviewed open access
journals during 2007, under the banner of "Bentham OPEN".
(More open access journals:
http://www.oai.uzh.ch/index.php?option=content&task=view&id=378&Itemid=258)
The Concept of Open Access Repositories
An increasing number of universities worldwide deposit their academic publications
in freely accessible repositories.
Open Access
Journal
Metadata*
Open Access
Repository
Abstract*
DOI*
PDF
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
License* mandatory
Terms
3
Some Examples of Open Access Repositories
•
ZORA – Open Access repository of University of Zurich:
http://www.oai.uzh.ch
o Only refereed publications and postprint is accepted
o What is postprint: After publication!
o What is refereed: see
http://www.oai.uzh.ch/index.php?option=content&task=view&id=418&It
emid=294
•
e-collection – ETHZ: http://e-collection.ethbib.ethz.ch/index.php?lang=en
•
•
Postprints, Preprints
What is preprint? manuscripts that have not been peer-reviewed but
have been submitted
•
Pubmed – free digital archive of biomedical and life sciences:
http://www.ncbi.nlm.nih.gov/pubmed/
•
For a list see: http://www.oai.uzh.ch/ -> OA worldwide
•
Preprint archives: http://www.lib.uts.edu.au/students/findinginformation/research-links/preprint-archives
DOI: Digital Object Identifier
•
•
•
•
A digital object identifier (abbreviated DOI) is a permanent identifier given to
an electronic document that, in contrast to a URL, is not dependent upon the
electronic document's location.
DOI follow a namespace convention and are unique to each document
DOI are listed in an „address book“ – resolving of DOI to document and
current location is done by a resolve server/service: The DOI System
(http://doi.org/)
It is like an electronic ISBN.
Exercise - Search for the document: doi:10.1371/journal.pbio.0020175 at
http//doi.org
Open Access Search Engines
International search engines allow data mining for key words, authors, journals that
are published under open access licenses.
Metasearch in all freely accessible document archives that meet metadata standard
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
4
OAIster is a project of Michigan University, U.S., and allows access to document
servers worldwide - at present almost 9 million publications from nearly 700
repositories.
OASE: Open Access to Scientific Literature
OASE allows searching the bibliographical data of the most important document
servers in Germany and abroad. It uses Karlsruhe virtual catalog technology
developed by the university library. OASE - the former KVVK (Karlsruher Virtueller
Volltextkatalog) - is a free service of the university library Karlsruhe set up to
demonstrate the benefits of open access for scientists.
OPUS Meta search: Using Opus Meta search in Germany, digital documents can be
found from 34 universities, 12 technical universities and 4 library networks.
(Source: http://www.oai.uzh.ch/ -> Search Engines)
Citation of Open Access Articles
Halpin DR, Lee JA, Wrenn SJ, Harbury PB (2004). DNA Display III. Solid-Phase
Organic Synthesis on Unprotected DNA. PLoS Biol 2(7): e175
doi:10.1371/journal.pbio.0020175
Note, always prefer DOI to URL!
Publish in High-Impact Open-Access Journals: Bibliometric Measurements
Definition Impact Factor (IF)
Average number of citations of a journal - calculated on a three-year period
Proxy of the importance of a journal to its field
A = number of times articles published in 2005 – 2006 were cited in other journals in
2007
B = number of articles published 2005 – 2006
IF = A/B
Exercise: 1 citation per each article published: IF = ?
Exercise: Search for IF of well-known journals in ISI Web of Knowledge
Exercise
IF at ISI Web of Knowledge (http://isiwebofknowledge.com) for
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
5
Journal
Nature
Science
Conservation Biology
IF based on 3-year period
The Impact Factor of Open Access Journals
ISI covers several OA journals following the same quality guidelines for inclusion
than non-open access journals
OA Journal*
BMC Genetics
BMC Genomics
BMC Microbiology
BMC Plant Biology
BMC Structural Biology
IF
1.46
4.03
2.90
3.23
1.98
(*2009)
Some Debate
•
•
•
•
•
•
Different citation practices decide about how quickly citations appear, i.e. in
ecology three-year is to low for determining IF
Compare a journal in the category of its peers (and not between disciplines)
Bias of IF towards English journals
Book citations are not included into the IF
No correction for self-citations (better: Eigenfactor, www.eigenfactor.org)
IF often misused to predict the importance of an individual publication
based on where it is published. However Nature (2006) showed that 30%
of their articles generate 90% of all citations.
Better: Walther GR, Post E, Convey P, Menzel A, Parmesan C, Beebee TJC,
Fromentin JM, Hoegh-Guldberg O, Bairlein F (2002) ECOLOGICAL RESPONSES
TO RECENT CLIMATE CHANGE. Nature 416: 389 – 395. Times cited: 1499
(28.01.2011, WoS Cited References)
How is a Journal Getting an Impact Factor?
Basic Journal Standards for Inclusion in ISI Web of Knowledge
Timeliness of publication: A journal must be publishing according to its stated
frequency
(However, when an e-journal publishes articles one at a time rather than collecting
articles for release as an 'issue' we take a slightly different approach to measuring
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
6
timeliness. In these cases the editors look for a steady flow of articles over several
months time.)
International editorial conventions:
• Informative journal titles
• Fully descriptive article titles and abstracts
• Complete bibliographic information for all cited references
• Full address information for every author
English:
• Publish full text in English
• Or at very least, their bibliographic information in English.
Application of the peer review process
From ISI WEB OF KNOWLEDGE:
http://scientific.thomson.com/free/essays/selectionofmaterial/journalselection/
Publishing and WEB 2.0
Definition of WEB 2.0
Refers to a supposed second-generation of Internet-based services - such as social
networking sites, wikis, communication tools, and folksonomies - that let people
collaborate and share information online in ways previously unavailable.
Cited after: thehatchergroup.wordpress.com/2008/05/08/glossary-of-new-mediaterminology/ (May 2009)
Share INFORMATION
The PLoS Example
•
•
•
http://www.plosbiology.org/home.action -> Featured Discussions (Tab) ->
Learn how to add comments and start discussions on articles.
Rate this Article
Share this Article
Examples how to share information an create a network of peers:
•
•
•
Mendeley is a free reference manager and academic social network http://www.mendeley.com/
Connotea: http://www.connotea.org/
Cite You Like: http://www.citeulike.org
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
7
Science is …
Collaborative:
• Critiquing, suggesting, sharing ideas and data with peers—this
communication is the heart of science. (Example of Web 2.0 approaches:
Blog, Wiki, Collaborative Platforms)
• As a researcher you have a responsibility to communicate your research
beyond science (i.e. to the public). (Web 2.0 approach: e.g. Research Blog)
What is a Weblog?



A blog (also called a weblog) is a user-generated website where entries are
made in journal style and displayed in a reverse chronological order.
Many blogs provide commentary or news on a particular subject; others
function as more personal online diaries
As of December 2007, blog search engine Technorati was tracking more than
112 million blogs.
(Source: en.wikipedia.org/wiki/Weblog)
Types of Blogs
There are many different types of blogs, differing not only in the type of content, but
also in the way that content is delivered or written.
 Personal blogs
 Corporate blogs
 By media type, e.g.
o Vlog: A blog comprising videos
o Linklog: A blog comprising links
o Podcast: Audioblog
 By device, e.g.
o Moblog: A blog written by a mobile device like a
 By genre
o Some blogs focus on a particular subject, such as political blogs, travel
blogs, fashion blogs, project blogs, education blogs.
(Source: en.wikipedia.org/wiki/Weblog)
The Structure of Blogs and Some Technical Terms
e.g. www.netzlernen.ch



Post: Entries displayed in reverse chronically order
Navigation: categories (of posts), last posts, archive (by month, year...),
blogroll (list of favorite blogs of author)
Comments: all registered Readers can leave a comment
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
8

Permalink: this is the permanent URL of a post, e.g.
http://netzlernen.kaywa.ch/lernen/google-apps-in-der-schule.html
Why should Academics use Blogs?
In his post Mark Trodden asked how academic should use blogs (Permalink:
http://cosmicvariance.com/2007/02/11/how-can-we-best-use-blogs-help-please/,
February 11th, 2007, Last Access in May 2009):


“Academics could form a presence for themselves on the web” (see the
section about research portfolios)
“Academics can disseminate and discuss their research interests and new
ideas with peers”
In the comments on the discussion Suresh Venkat explained how different types of
blogs may be helpful in this context (also including some good examples):
“A private research blog: I maintain a notepad of thoughts on a research blog.
Wordpress allows me easy categorization, and bookmarklets allow me to post links
to papers that I want to read. Cosma Shalizi
(http://www.cscs.umich.edu/~crshalizi/weblog/ ) has the best example of this.
A private research blog among collaborators: again, a good place to share and
exchange ideas easily, especially at long distance
A public research blog, like the n-category cafe. Apart from being an interesting
experiment in opening up the innards of research, it provides a somewhat more
realistic sense of how ideas develop.
Disseminating blogs, like Cosmic Variance: spread the latest new results in a field
out to the community, and to the public at large.
Real outreach blogs, like Good Math, Bad Math, and RealClimate
(http://www.realclimate.org/): dispelling myths in the press, trying to be a one-stop
source for media to reference to get good science”
Some more food of thoughts for private research blogs:
Research Blogs used for Personal Knowledge Blogging:
http://radio.weblogs.com/0110772/stories/2002/10/03/personalKnowledgePubli
shingAndItsUsesInResearch.html#pkp
Some Examples of Science Blogs/Researcch Blogs
•
•
•
•
•
http://cabiblog.typepad.com/hand_picked/plant_sciences/index.html
Genomics, Evolution, and Pseudoscience: http://genome.fieldofscience.com/
Cosmic Variance: http://blogs.discovermagazine.com/cosmicvariance/
Blog collection: http://scienceblogs.com/ (with channels about lifescience/molecular biology/ecology/evolution …)
ETH Klimablog: http://blogs.ethz.ch/klimablog/feed/atom/
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
9
•
Not Exactly Rocket Science:
http://blogs.discovermagazine.com/notrocketscience/
Credibility of Science Blogs/Research Blogs
Your perspective: Being a researcher who uses weblogs as source of information for
daily work.
•
•
Can you trust the information on a research blog?
Can you cite the information on a research blog as source of your ideas?
o Is a research blog a primary, a secondary or a tertiary resource?
o Please read http://crookedtimber.org/2008/04/07/citing-blogs/
Bring your point of view to the audience!
What makes Science Blogs Credible?
The 'Stanford Guidelines for Web Credibility' published by the Stanford Persuasive
Technology Lab serve as guideline for building the credibility of a science blog. The
guidelines are based on three years of research that included over 4,500 people
asking them for their opinion what makes a website credible.
(http://www.webcredibility.org/guidelines/)
Guideline
Additional Comments
1. Make it easy to
verify the accuracy
of the information
on your site.
You can build web site credibility by
providing third-party support (citations,
references, source material) for
information you present, especially if you
link to this evidence. Even if people don't
follow these links, you've shown
confidence in your material.
2. Show that there's a
real organization
behind your site.
Showing that your web site is for a
legitimate organization will boost the site's
credibility. The easiest way to do this is
by listing a physical address. Other
features can also help, such as posting a
photo of your offices or listing a
membership with the chamber of
commerce.
3. Highlight the
expertise in your
organization and in
the content and
services you
Do you have experts on your team? Are
your contributors or service providers
authorities? Be sure to give their
credentials. Are you affiliated with a
respected organization? Make that clear.
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
10
provide.
Conversely, don't link to outside sites that
are not credible. Your site becomes less
credible by association.
4. Show that honest
and trustworthy
people stand behind
your site.
The first part of this guideline is to show
there are real people behind the site and
in the organization. Next, find a way to
convey their trustworthiness through
images or text. For example, some sites
post employee bios that tell about family
or hobbies.
5. Make it easy to
contact you.
A simple way to boost your site's
credibility is by making your contact
information clear: phone number, physical
address, and email address.
6. Design your site so
it looks professional
(or is appropriate for
your purpose).
We find that people quickly evaluate a
site by visual design alone. When
designing your site, pay attention to
layout, typography, images, consistency
issues, and more. Of course, not all sites
gain credibility by looking like IBM.com.
The visual design should match the site's
purpose.
7. Make your site easy We're squeezing two guidelines into one
to use -- and useful. here. Our research shows that sites win
credibility points by being both easy to
use and useful. Some site operators
forget about users when they cater to
their own company's ego or try to show
the dazzling things they can do with web
technology.
8. Update your site's
People assign more credibility to sites
content often (at
that show they have been recently
least show it's been updated or reviewed.
reviewed recently).
9. Use restraint with
any promotional
content (e.g., ads,
offers).
If possible, avoid having ads on your site.
If you must have ads, clearly distinguish
the sponsored content from your own.
Avoid pop-up ads, unless you don't mind
annoying users and losing credibility. As
for writing style, try to be clear, direct, and
sincere.
10.Avoid errors of all
types, no matter
how small they
seem.
Typographical errors and broken links
hurt a site's credibility more than most
people imagine. It's also important to
keep your site up and running.
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
11
Science Blogs with some Influence – Could we calculate an IF for Weblogs?
Examples to work with:
• Pharyngula (http://scienceblogs.com/pharyngula/) - Evolution, development,
and random biological ejaculations from a godless libera (PZ Myers) - debate
on evolution vs. creation / intelligent design debate with its huge number of
posts and even greater number of comments).
• RealClimate (http://www.realclimate.org) - commentary site on climate
science by working climate scientists for the interested public and journalists.
We aim to provide a quick response to developing stories and provide the
context sometimes missing in mainstream commentary. The discussion here
is restricted to scientific topics and will not get involved in any political or
economic implications of the science.
Can we measure the web impact factor (WIF) of these science blogs?
Definition of WIF
WIF = number of blogs linking to a website in the last six months (A)/ number of
posts on the blog in the last 6 month (B)
(WIF – calculation has been slightly moderated from original definition as by Peter
Ingwersen, 1998. He calculated the WIF as a snapshot of the search engine
database at a specific time. Here, we introduce a certain time period = 6 month to be
able to use the Technorati Authority number as (A)).
Example: http://scienceblogs.com/pharyngula/:
(A) you may use Technorati Authority: www.technorati.com -> Advanced Search
(October 2007 – March 2008): 2854 (authority is given near to a post)
(B) Blog Post on Pharyngula between October 2007 and March 2008
(Number from the Archive at http://scienceblogs.com/pharyngula/archives.php):
1290
WIF = 2854/1290 = 2.21 (March 2008)
WIF Limitedness:
 Depends on search engines’ web coverage
 Some singular websites (within a Webpage) may cause the largest inlinks
frequency
 Inlink frequency only tells us something about popularity not about impact or
quality
 You can “pimp” each WIF
Source: A. Noruzi (2006). The web impact factor: a critical review. The Electronic
Library, 24.
Familiarize Yourself with the Wordpress Technology
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
12







Build your own Blog
Choose a Design for your Blog
Navigation of your new Blog
Write and edit a Post
Publish a Post
Comment on a Post
Links and Images
www.wordpress.com
The Network of Interest: Keeping up-to-date about the news in a certain topic
Example:
• There has been an open-access article, followed by interesting discussions in
several blogs
• Additionally, there has been a posting about some related ideas (and the
follow-up discussion in some other blogs)
Question: How could a researcher working on a review about the topic follow the
discussion?
Some terms:
 Trackback: a normally automatic notification to a post that it has been cited
by the blog of the ‘citer’ – will increase citation index of the respective post
and show the citation network.
 RSS-Feed: within the Feed only the newest posts (title, first paragraph,
Permalink) show up. The feedlink can automatically used by search engines,
feed readers
RSS-Feed-Reader: e.g. http://www.bloglines.com will help to track changes in
several information sources simultaneously. Feed Reader aggregate the ‘blogline’ of
several subscribed RSS-Feeds simultaneously.
Exercise: Create your Feedroll on a topic of interest – including some OpenAccess
Journal, Nature, Science …
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
13
OpenAccess
Article 1
Discussion
in Blog 1
Discussion
in Blog 2
RSS Feeds
Review
Trackbacks
Discussion
in Blog 3
Post 1
Discussion
in Blog 4
Zurich-Basel Plant Science Center
Dr. Melanie Paschke
Following
Trackbacks
14