Publishing BioWiki Databases: Call for Pre-submission Inquiries

[Alexander Pico]

Hi all,

We are exploring the idea of coordinating a block of publications on biowiki
databases in the next annual NAR Database Issue. Do we have a critical mass
of interest? Are there enough examples of reliable, well-maintained, active
and useful biowikis to warrant a concerted effort?

Carefully review the criteria for submitting to the NAR Database Issue:
http://www.oxfordjournals.org/our_journals/nar/for_authors/msprep_database.h
tml
In particular, consider whether your biowiki has demonstrated maturity. How
does your content quality, breadth and reliability compare to related
databases? Does your biowiki service a broad community of users? Do you
provide useful accessibility or analysis functions?

Here are some recent examples:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808918/
http://nar.oxfordjournals.org/content/39/suppl_1/D141.full
http://database.oxfordjournals.org/content/2010/baq009.abstract

This would not be a Database Issue *about* biowikis. Thus, the criteria for
acceptance would not be biased just by the fact that your resource *is* a
wiki.

Reply to this thread if you are interested, so we can gauge the level of
coordination needed. Here is the timeline for submissions:

* Pre-submission inquiry -- 1 July
* Paper submission -- 15 August
* Published online starting in November
* Issue finalized by mid-December

Cheers,
Alex

[Justin Preece]

The Jaiswal Lab at Oregon State is interested in participating.

We are developing a wiki for genotype/phenotype annotation in plant species, using SMW as the primary platform.

Please keep us posted on the coordination schedule.

Justin Preece
Bioinformatics
Jaiswal Lab, Dept. of Botany & Plant Pathology
o: 541-737-6511
f: 541-737-3573
Oregon State University

[Dave Clements]

Hello all,

Something worth thinking about is contacting the journal Database (where the PDBWiki paper was published) about a virtual wiki database issue.  They have done this for biocuration (see http://www.oxfordjournals.org/our_journals/databa/biocuration_virtual_issue.html) and are willing to do it for other topics as well.  Contact the editors at database.edi...@oup.com.

NAR is great, but the database issue has become so large that any sense or relatedness between papers might be lost in the sheer volume of papers.  This concept is explicitly supported at Database.

Dave C.

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[Pascale G]

Hello,

I agree that DATABASE would be a perfect venue for this. You would have much more freedom on the format of the different papers, and you could also probably ask to get a 'special issue', which would give the topic a lot of visibility.


Pascale Gaudet

[Thomas Kelder]

Hello,

I also like the idea of a special issue in Database, however it might
be worth to consider the desired target audience as well. This is one
of the reasons we initially decided to publish WikiPathways in a
biological journal (PLoS Biology) instead of a more bioinformatics
focused journal, since we really wanted to reach the potential
curators at the first place.

I'm not sure what the actual audience of the Database journal is, but
I suspect that with publishing in NAR we may reach more biologists.
What do you think?

Best wishes,
Thomas

[Evelo Chris (BIGCAT)]

Dear all,

To be honest I think that neither Database nor the database issue of NAR are well read by biologists. Although people often don't even read journals anymore a reference to a to technical sounding journal might indeed prevent people from reading it.

I think with the NAR database issue you would in fact primarily reach bioinformaticians, with Database you would also reach curators and with for instance BMC Genomics you would get closer to biologists. Of course you would have to talk with such a journal, but they might be willing to do a special issue as well.

This all assumes that the content really is about separate Biowiki's, their content and their usefulness. If you would also want to pay attention to wiki technology itself, interoperability between wiki's and for instance common ontologies or user engagement issues, the choice might be different.

Best wishes, Chris

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Verzonden: Wed Feb 16 10:09:39 2011
Onderwerp: Re: [BioWiki] Publishing BioWiki Databases: Call for Pre-submission Inquiries

[barend mons]

Agree with Chris and will soon share some interesting text with you
about citation of the databases (and wiki's) themselves in the near
future, but give me some time, please....

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Dr. Barend Mons
Scientific Director
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Netherlands Bioinformatics Centre (NBIC)
http://www.nbic.nl
and Biosemantics Group
Leiden University Medical Centre
http://www.biosemantics.org
Mobile: +31-624879779
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[Dave Clements]

Hello all,

I'm wondering if a two-pronged approach would work.  This thread started as a proposal for a block of publications on biowikis.  A block of papers seems like a natural fit for Database and NAR Database.  Would it be worth writing a block of papers in one of those (I favor Database), and then writing a summary/trends paper for publication in another more biologist friendly publication?  The trends paper could heavily reference, say, a special Database issue.  I think Chris is right.  If want to reach large numbers of biologists, Database and NAR (on their own) might not be the ticket.

Dave C.

Onderwerp: Re: [BioWiki] Publishing BioWiki Databases: Call for Pre-submission Inquiries

--

[Wyeth Wasserman]

Hello All,

I think the key item is to promote the unity and growth of the community by putting a block of publications in one place.  Each project has a very distinct research focus, making it difficult to target an optimal journal for the biologist perspective.  As I sit on the editorial board for DATABASE, I may be a little biased, but I think it would be a suitable place for this effort.  I also agree with Dave that putting some highlights pieces out in the bio/medical journals could call attention to the papers.

Wyeth

-- 
---
Wyeth W. Wasserman, Ph.D.
Senior Scientist and Associate Director, Centre for Molecular Medicine and Therapeutics
Scientist Level 3, Child and Family Research Institute
Professor, Department of Medical Genetics
University of British Columbia 
Vancouver BC
Canada

[Dan Bolser]

Hi All,

One idea behind the table of biowikis was that it could form the basis
of a table in a biowiki review paper. For this reason, I'd like to
encourage you to visit that site to check, update and add information
about your favourite biowiki projects.

http://bifx.org/wiki/BioWiki

Any feedback on the site would be welcome.

Cheers,
Dan.