OpenWetWare:Steering committee/Publishing chairs

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Julius B. Lucks 08:49, 1 November 2007 (CDT): The following is a paraphrase of an email I sent out to the sc listt which proposes the idea.

What about promoting 'publishing' of oww materials on already has a quantitative biology section (, and I am willing to bet that essentially all papers coming out of the OWW community could fit into this section. The arXiv allows you to post paper pre-prints online for free, and it is completely open access. Every e-print has associated with it a unique id, that is completely referenceable in papers, etc. In addition, if you do publish your paper in a journal, you can update arXiv e-print metadata with the journal reference, or a DOI of the journal article.

Compared to an alliance with Nature or some other body, promoting 'publishing' on the arXiv has many advantages:

1.) It already exists and no agreement or negotiations need to be made to use it. There is a very mild form of control in that people that are new to the arXiv system must be 'endorsed' by existing people, but this can be gotten around until enough OWW people are themselves endorsers.

2.) It provides all the functionality we want - some sort of official stamp on an OWW document in the form of an e-print that is completely referenceable and is more like a paper than a wiki page. In fact, the arXiv supports the notion of versions, so that you can always submit a newer version of a resource, keeping complete access to older versions.

3.) There are many tools already in place, or being developed that we can integrate the arXiv with OWW. As Bill knows, the arXiv already has an API that allows you to pull content from the arXiv into OWW trivially (by just specifying e-print id). In addition, this API supplies journal references and DOI's if they are present, so it would be very easy to create references in the biblio extension for both the e-print and the published version. Also, there is an ingest API in active development (and soon to be released) with which we could easily create our long-dreamed-of 'publish' button on OWW that could automatically publish an OWW page.

4.) Journals will accept papers that have been posted on the arXiv already. In particular, Nature has committed to this as is evident on the Nature Proceedings page (

"Nature Precedings hosts manuscripts that may be submitted to any journal of any publisher. Nature and all Nature journals have a policy that permits such posts on recognized pre- or e-print servers such as Nature Precedings and arXiv without affecting their eligibility for publication, whether or not such postings result in discussion on other sites and in the media. We cannot take responsibility for the possibility of scooping by competitors. Authors submitting to other journals are advised to check their policies about prior postings before sending manuscripts to Nature Precedings."

(In fact, Nature Precedings was heavily inspired by the arXiv.)

5.) If the quantitative biology community grows and needs more of a refined categorization (such as synthetic biology, etc.), the arXiv can expand its categorization scheme (which is how the q-bio section started in the first place).

6.) Integrating with the arXiv integrates what OWW is doing with the physics, math and computer science communities.

7.) There are a bunch of 'overlay' journals built on top of the arXiv already. Basically editors use the arXiv as their whole submission system, put papers through peer review of some sort, then create their journal as a series of links to arXiv posts. It would be completely natural for OWW to create something like this if we ever wanted to get into the publishing arena ourselves. There is a lot of flexibility with this.

The advantage to going with the arXiv with respect to rolling out something ourselves is that:

1.) The arXiv has been around since 1991 and they are very good at what they do. They also are supported by Cornell, and will be around for a long time to come. They also have huge recognition within the open access community, and are unaffiliated with publishers.

2.) Having worked at the arXiv, it is actually a complicated beast beneath the surface. I don't think we would want to get into this arena quite yet. We can always try things out on the arXiv, and if it is a real hit and the arXiv does not provide the flexibility we want, we can make our own system and import our old arXiv postings.


Julius B. Lucks 08:52, 1 November 2007 (CDT): I have talked with the arXiv and they think this sounds like a great idea. We at OWW now have to figure out how best we want to use this resource.