I was trying to work out a suitable journal to where I could submit a paper on sepCV, the PSI ontology for sample preparation and separation techniques. I found my self drawing up a table, so I thought I would blog it. My initial remit is that is should be in a proteomics relevant journal as well as bioinformatics, as we are trying to encourage a greater community contribution for term collection. In this respect it has to be open access. I would also prefer the journal to accept LateX instead on proprietary formats such as word. I was really disappointed with the number of journals that only accept word documents, even PlosOne refuses anything other than word or rft, tut, tut.
Based on this loose criteria, Proteome science comes top closely followed by Journal of Proteomics and Bioinformatics (if I sacrifice using word for open access). BMC Bioinformatics also ticks all the boxes but it misses out on the proteomics audience. The table below also includes Impact factor, but I did not really take that into consideration. Wouldn’t it be nice is there was an app that you could just enter in criteria like this, target audience, submission format, copyright, etc and get back the journals that meet these requirements. Something like this would save me an afternoon trawling through the web building spreadsheets.
How do you select your journal?
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fgibson.com 
#1 by PlausibleAccuracy on April 21, 2008 - 2:51 pm
I applaud your criteria! It’s great that you’re interested in publishing in an OA journal, and I’m always glad to see other people using LaTeX. I actually recently wrote about how I thought accepting LaTeX would be easier for journals, since they could simply apply their own style file in order to format the article for publication.
#2 by bill on April 21, 2008 - 5:03 pm
An app to do that would be great, but for no reason I can fathom journals seem to keep much of the relevant information effectively hidden — see, e.g., the “can’t find” in your own table there. I’ve tried a few times to get numbers on various things OA-related, and even with resources like the DOAJ it remains difficult.
Perhaps one could populate the database behind your putative application by assigning homework to science communication classes around the world — one journal per week per class or something? I’m thinking of a Heather Piwowar’s thesis meets Jean-Claude Bradley’s methodology sort of thing.
#3 by peanutbutter on April 30, 2008 - 9:42 am
@PlausibleAccuracy – I read your post on LateX, I have often wondered that myself, that is must be easier to format and publish latex than it is a word document. Some journals, like BMC, do provide latex templates, which match the final publication format.
@Bill – It certainly took a while compiling that relatively trivial table, and at the minute it looks as if manual curation is the only way to do it. If only the journals published their options as RDF……..
#4 by S. Gedela on July 12, 2008 - 12:16 pm
Yes i do agree with you!, Journal of Proteomics & Bioinformatics is the best choice of open access publication of proteomics and bioinformatics works
#5 by jim on August 27, 2008 - 10:12 am
How about Genome Biology?
Their scope says that they cover proteomics, they have an impact factor of 6.59, you can submit in Latex and it is open source.