Re: Preprint time? (JSON-LD)

[Jerven Bolleman]

Second try sending this, now via personal account
On 24 Jan 2014, at 22:33, Jerven Bolleman <jerven....@isb-sib.ch> wrote:

> Hi Everyone,
>
> Let me first apologise for being of the radar for a month and not working on Faldo as promised.
>
> I think we are getting close.
> The major outstanding issues are Michel’s comments need to be integrated.
> The last classes need to be discussed in the OWL section (these are the set an bag options for the legacy joins).
>
> Otherwise we are quite close.
>
> We have two people who would like to cite something with a DOI.
> So if no one objects I would like to submit to the preprint server sunday morning.
> I would not be embarrassed by the general level of the paper now.
>
> The paper now also includes an example in JSON-LD hope that would be interesting for people.
>
> Regards,
> Jerven
>
>
> -------------------------------------------------------------------
> Jerven Bolleman Jerven....@isb-sib.ch
> SIB Swiss Institute of Bioinformatics Tel: +41 (0)22 379 58 85
> CMU, rue Michel Servet 1 Fax: +41 (0)22 379 58 58
> 1211 Geneve 4,
> Switzerland www.isb-sib.ch - www.uniprot.org
> Follow us at https://twitter.com/#!/uniprot
> -------------------------------------------------------------------
>

[Peter Cock]

Excellent :)

In terms of preprints, both PeerJ PrePrints and bioRxiv give a DOI,
while the older arXiv does not. Some journals don't like preprints,
with a DOI but I can't find any preprint policy information on the
Journal of Biomedical Semantics website. They're not on this list:
http://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy

Peter

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[Joachim Baran]

Hello,

  I just went over the paper again and sent another pull request.

  I would not submit the paper to a pre-print server, but incorporate Michel’s changes and submit the paper for peer review instead. There is no benefit of having people cite the pre-print DOI and it could even be argued that we loose two citations on the real paper due to that. In academic evaluations, the pre-print publication does simply not count.

Joachim

[Peter Cock]

On Sat, Jan 25, 2014 at 4:20 PM, Joachim Baran <joachi...@gmail.com> wrote:
> Hello,
>
> I just went over the paper again and sent another pull request.
>
> I would not submit the paper to a pre-print server, but incorporate
> Michel’s changes and submit the paper for peer review instead. There is no
> benefit of having people cite the pre-print DOI and it could even be argued
> that we loose two citations on the real paper due to that. In academic
> evaluations, the pre-print publication does simply not count.
>
> Joachim

It depends who is doing the counting (citing preprints on arXiv
is fairly common place in Physics and mathematics - Biology
is just backward on this), but I don't see how we can lose
citations by this, only gain.

Peter

[Joachim Baran]

On January 25, 2014 at 2:35:03 PM, Peter Cock (p.j.a...@googlemail.com) wrote:

It depends who is doing the counting (citing preprints on arXiv 
is fairly common place in Physics and mathematics - Biology 
is just backward on this), but I don't see how we can lose 
citations by this, only gain. 

  I think that a publication that cites the pre-print publication now, will not be corrected to reference the peer reviewed paper later. Since many of us are evaluated on peer reviewed publications, I would rather invest the little spare time that we have available in getting the FALDO paper ready for peer reviewed publication asap instead.

  I am not opposed to pre-print publication as such. I just believe that it will not have many benefits associated with it.

Joachim

[Michel Dumontier]

We can certainly put a paper on a pre-print server after submission to a journal.

m.

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Michel Dumontier

Associate Professor of Medicine (Biomedical Informatics), Stanford University

Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group

http://dumontierlab.com

[Joachim Baran]

On January 25, 2014 at 3:09:24 PM, Michel Dumontier (michel.d...@gmail.com) wrote:

We can certainly put a paper on a pre-print server after submission to a journal.

  That would be a good compromise.

Joachim

[Hilmar Lapp]

On Jan 25, 2014, at 7:53 AM, Peter Cock wrote:

> I can't find any preprint policy information on the Journal of Biomedical Semantics website. They're not on this list:
> http://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy

They are. It's a BMC journal, and thus preprints are allowed.

On Jan 25, 2014, at 11:20 AM, Joachim Baran wrote:

> I would not submit the paper to a pre-print server, but incorporate Michel’s changes and submit the paper for peer review instead. There is no benefit of having people cite the pre-print DOI and it could even be argued that we loose two citations on the real paper due to that.

I agree with the argument that preprint server submission should not delay peer review submission. I also agree that if it's not ready for peer review submission (but getting it ready is the target) then it's not quite ready for preprint submission either, another way of saying what Michel suggested (which is actually what we did for a recent JBMS paper, i.e., submit as preprint the version submitted to peer-review).

The concern of citation credit diversion is a valid one. However, if someone needs a citation now, they won't wait until the paper is through peer-review, which can be months from now. So then the question becomes lose two citations entirely, or have 2 on the preprint. In other words, by when the preprint becomes citable is under your control, whereas for the peer-reviewed paper it's not.

Just some thoughts from someone who has no skin in this, so better ignore ...

-hilmar
--
Hilmar Lapp -:- lappland.io

[Jerven Bolleman]

Hi All,

Quick list of things that need to be done as I understand it before
submitting for peer review.

Michel suggestion incorporation (ANS.1 included in
discussion/implementation, but others require more thinking (i.e.
suggestions welcome))
Grammar/spell check and standardisation on US or UK (Joachim's changes merged)
Double check faldo matches paper description (update small changes &
clarifications).
copy examples from paper to FALDO git repo.

I am not sure about the preprint now ( I don't mind the current state
being on a preprint server, it is decent enough ). I still think we
need to get our asses out there. I am horrible slow first author so
some motivation to finish is needed.

So I suggest we send out a preprint to http://biorxiv.org/ as it
allows preprint revision (i.e. final version). I would like to do so
at one o'clock monday Berlin time. If as an author you will not agree
to this then let me know.

Then I would suggest we send it for peer review the monday after on
the 3rd of February.
So we have one week to finish the issues mentioned above.

Hope to see your replies on Monday,

Regards,
Jerven

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[Joachim Baran]

On January 26, 2014 at 5:32:27 AM, Jerven Bolleman (m...@jerven.eu) wrote:

[…] I would like to do so 

at one o'clock monday Berlin time. If as an author you will not agree 
to this then let me know. 

Then I would suggest we send it for peer review the monday after on 
the 3rd of February. 

  If there is only one week difference between these submissions, then I would rather postpone the preprint submission and have it coincide with the journal submission a week later. I am with Hilmar here — if it is not ready for peer review, then it is probably also not ready for pre-print submission.

Joachim

[Jerven Bolleman]

Hi Joachim,

I personally feel it can be submitted for peer review as is. However, I also think it can be further improved.
Yet, at the same time some people would like to cite it. And as at biorxiv you can update the preprint later it
seemed like the best of both worlds. preprint as today for a week, then preprint as submitted for peer review
when ready.

Regards,
Jerven

[Peter Cock]

On Mon, Jan 27, 2014 at 2:03 PM, Jerven Bolleman <m...@jerven.eu> wrote:
> Hi Joachim,
>
> I personally feel it can be submitted for peer review as is. However, I also think it can be further improved.
> Yet, at the same time some people would like to cite it. And as at biorxiv you can update the preprint later it
> seemed like the best of both worlds. preprint as today for a week, then preprint as submitted for peer review
> when ready.
>
> Regards,
> Jerven

I agree - without the external pressure that people would like to cite
the preprint,
I would post the preprint simultaneously with formal submission to the journal.

All of biorxiv, arXiv and PeerJ PrePrints support revisions or
versions of preprints,
e.g. https://peerj.com/preprints/207v1/ and https://peerj.com/preprints/207v2/
so doing an early preprint (for the other papers which want to cite it
right now)
seems like a reasonable compromise.

Regards,

Peter

[Peter Cock]

Jerven and I did some more work on the paper today, incorporating
feedback etc. To assist anyone without a working LaTeX install, I've
attached a PDF as of this afternoon's commit:

https://github.com/JervenBolleman/FALDO-paper/commit/187b6db9c84e78f0a5127694d0c5d83e1d461102

I think the current text is fine for an early preprint as outlined above
(in order to capture a couple of early citations explicitly).

I agree with Jerven that we could still further improve this (and there
are some open issues on GitHub which cover specific points), but it
seems close to being ready for formal submission to the journal.

Regards,

Peter

[Joachim Baran]

Hello,

  I am currently not using my work computer and will not have access to it until tomorrow evening:

  Can someone please update the manuscript to reflect the license change to CC0? As far as I recall it, CC0 was pushed by Hilmar and the majority of authors agreed to use that license instead of an attribution license.

Joachim

[Peter Cock]

On Mon, Jan 27, 2014 at 6:52 PM, Joachim Baran <joachi...@gmail.com> wrote:
> Hello,
>
> I am currently not using my work computer and will not have access to it
> until tomorrow evening:
>
> Can someone please update the manuscript to reflect the license change to
> CC0? As far as I recall it, CC0 was pushed by Hilmar and the majority of
> authors agreed to use that license instead of an attribution license.
>
> Joachim

Good point - we were talking about this here:
https://github.com/JervenBolleman/FALDO/issues/7

I've made a note on the issue I'd filed against the FALDO paper
repository to consider moving from v3.0 to v4.0 of the CC licence :
https://github.com/JervenBolleman/FALDO-paper/issues/23

Peter