From: Darren Rhodes (darren.rhodes$##$gmail.com)
Date: Thu Feb 23 2006 - 11:53:14 EST
---------- Forwarded message ----------
From: Darren Rhodes <darren.rhodes$##$gmail.com>
Date: Feb 23, 2006 4:52 PM
Subject: Re: ORGLIST: Synthetic Pages
To: Jonas Sundberg <gussujon$##$student.gu.se>
Dear Steve
Would you consider having a migration process of acceptance? The
first part being the posting of a procedure to a wiki; the second part
being a migration from the wiki to your current site.
This would address most of the concerns raised thus far in the discussion.
Darren.
On 2/23/06, Jonas Sundberg <gussujon$##$student.gu.se> wrote:
> Dear Steve
> Have you ever considered changing format of your homepage to a more
> wiki-oriented style? And is there a possibility that you in the future
> will change your copyright policies?
> I see both interactivity and the copyright issue being the main problems
> with your site, otherwise it looks great (and sadly I haven't seen it
> before it was mentioned on this list). I beleive in free information,
> and that this kind of data should be freely distributed and allowed to
> use in any context except for commercial purposes. I also think this
> kind of project would benefit from much more interactivity and ease of use.
> Best regards, Jonas
>
> stephen caddick wrote:
>
> > Derek,
> >
> > Thanks for your comment. I've seen MOLBANK and as you rightly point
> > out there are similarities. However unlike MOLBANK we do NOT
> > peer-review prior to publication - we edit and there is a significant
> > difference..As you can see from, for example
> > http://www.mdpi.net/molbank/molbank2006/m455.htm , a MOLBANK
> > submission is much more like a paper. For example look at the time
> > delay between acceptance and publication below: /Received: 28 December
> > 2005/ Accepted: 3 January 2006 / Published: 22 January 2006
> >
> > /Also I did not see a mechanism to allow users to add comments as with
> > synthetic pages - this is an essential feature of what we do. I think
> > MOLBANK is very good but it is, I think, a journal online, synthetic
> > pages is a database.
> >
> > However many thanks for bringing this up.
> >
> > Best wishes
> >
> > Steve
> >
> >
> > */djmcphee$##$sympatico.ca/* wrote:
> >
> > There are similar products already out there. MDPI has published
> > for many years (since 1977) its MolBank
> > (http://www.mdpi.org/molbank/) with one-page-per-compound peer
> > reviewed synthetic preparations, which are freely accessible.
> >
> > Derek
> > ============================================================
> > From: stephen caddick
> > Date: 2006/02/23 Thu AM 07:49:50 EST
> > To: deadlyvices$##$hotmail.com
> > CC: everybody$##$orglist.net
> > Subject: ORGLIST: Synthetic Pages
> >
> > Dear All,
> >
> > I have watched the debate regarding the Synthetic Pages web-site
> > with interest. As one of the founders I thought it might be useful
> > to offer some comments to members of ORGLIST.
> >
> > (a) Copyright. We do ask for a transfer of copyright. This is
> > because we wish to retain the right to keep material on the site.
> > We discussed this at some length but in the end wanted to be able
> > to maintain the database for the community. If we had not done
> > this then we would have been subject to individual contributors
> > removing material which we felt would have been counter-productive
> > to the value of the database. However in our terms and conditions
> > we do make it clear that we do not wish to constrain authors.
> >
> > see http://www.syntheticpages.org/static/about.php
> >
> > 'Can I publish after submitting a procedure to SyntheticPages?
> >
> > Yes. Although you transfer copyright of the SyntheticPage to us,
> > you may also incorporate the information into a paper (subject of
> > course to the third party's terms and conditions) or elsewhere.
> > For this, no copyright notice is required. You should, however,
> > consider that submitting a SyntheticPages may affect your right to
> > claim a patent on the material at a later date. Our Terms and
> > Conditions are posted in full at http://www.syntheticpages.org.'
> >
> >
> > (b) Peer-review. We do not peer-review the material before it goes
> > on the web, because as has been rightly pointed out in this
> > discussion, this would simply make us an online journal. We do not
> > wish to constrain people as to the material that is put on the
> > site. However we do edit for some pretty obvious good reasons.
> > Three founders of the site are Professors of Chemistry in UK
> > universities so we have a good feel for providing a light touch
> > edit - hopefully to simply provide a little improvement if needed
> > (grammar etc.). We believe that most material should be made
> > available so that the community can use it, ignore it or modify /
> > correct it. The Synthetic Pages allows individual procedures to be
> > improved and updated, by the submission of comments on procedures.
> > We think that this interactive component does use the power of the
> > internet to improve the user experience.
> >
> > (c) Format. We do have a standard format which we feel will lead
> > to pages which enhance user experience. However we want to
> > encourage the type of material and level of detail that is
> > provided. So when authors submit we ask them to consider providing
> > all types of information that will be useful. For example scale,
> > number of times a procedure has been done etc. For a really good
> > example of a page see: http://www.syntheticpages.org/pages/195 i.e
> > the generation of an organolithium from an alkyl halide. The style
> > and level of detail here is we believe greater than you would find
> > elsewhere. It is hard to make comments on the restrictive nature
> > of the format until one goes through the submission process. SO we
> > hope that ORGLIST members will try the site out by lodging a
> > procedure.
> >
> > (d) Content. It is true that we only have a few hundred protocols
> > but we think we understand why that is. We have good evidence that
> > it is not because the community is unsupportive, but rather that
> > writing up experiments can be something of a barrier. We are
> > consid ering ways in which we can increase content.
> >
> > So in summary what we have tried to do is to provide a
> > sustainable, consistent database for allowing users in the
> > community to place procedures in synthetic chemistry on the web.
> > We do not formally peer-review and we do not restrict an authors
> > ability to further publish the protocol (but we do not want people
> > to reproduce the 'synthetic pages format'). However we do edit, we
> > do try to maintain some consistency in presentation, we do check
> > to ensure that nothing too controversial is place on our site, and
> > we do allow for user comment (i.e. an interactive user experience).
> >
> > We are sure that there are many elements of the site that could be
> > better. However if we have got the entire concept wrong, then the
> > community will tell is by not using it and it will cease to exist.
> > However we have very good evidence that the site is useful in
> > terms of visits, searches and members. I understand some of the
> > comments that have been made abo ut the site, but some of the
> > points raised may indicate a lack of understanding of what we are
> > trying to achieve. However we welcome comments for improvements
> > and if in the end anyone else wishes to set up a database which is
> > better at supporting the community then that is very reasonable.
> > So if a new endeavour is undertaken I hope that it is successful.
> >
> > I hope these comments are useful
> >
> > Stephen Caddick
> >
> > On behalf of syntheticpages
> >
> >
> > Clyde Davies wrote: I have to say that I find the notion that
> > copyright of a chemical procedure
> > that is to say that it is impossible to reproduce the same
> > procedure word
> > -for-word in another format - residing totally with the publisher
> > to be
> > absolutely preposterous.
> >
> > I think the problem with Synthetic Pages is that it is taking 20th
> > century
> > notions of scientific publishing and trying to apply them to a
> > very 21st
> > century medium - the Internet. Peer-review existed back in the
> > days of the
> > printed page to ensure that the quality of the material being
> > published was
> > sufficient before committing it to the expensive process of
> > printing. Now,
> > with a wiki, if something proves to be wrong we can
> > retrospectively correct
> > it. My only concern is to do with *safety* issues: advocating the
> > sloshing-about of trichloromethyl chloroformate without pointing
> > out that it
> > generates phosgene vapour, for example would be very irresponsible.
> >
> > So I think that the reason why Synthetic Pages is as thin as it is, is
> > simply because the process does not 'leverage' the inherently
> > flexible and
> > dynamic nature of the medium. There is still a submissions
> > procedure, peer
> > review, predefined (and rigid) format etc etc...none of which
> > makes the
> > slightest acknowledgement that there are new and better ways of
> > doing things
> > now.
> >
> > >From the (largely positive) feedback I have received here I will be
> > progressing with this project. A number of people have already pledged
> > their support (you know who you are) and I will be contacting them
> > shortly
> > to see how we take this idea forward, resources permitting.
> >
> > Dr Clyde Davies
> >
> > -----Original Message-----
> > From: everybody-bounces$##$orglist.net
> > [mailto:everybody-bounces$##$orglist.net]
> > On Behalf Of nigel$##$pierpoint.u-net.com
> > Sent: 22 February 2006 11:22
> > To: Eugen Leitl
> > Cc: everybody$##$orglist.net
> > Subject: Re: ORGLIST: Synthetic Methods Wiki
> >
> > As a purely UK web based operation
> > (http://www.syntheticpages.org/static/pwstatement.html)
> > its not unreasonable to expect communication to be performed via
> > email,
> > hence
> >
> > editor$##$syntheticpages.org.
> >
> > would be the obvious place to contact them.
> >
> > Maybe someone should forward these comments onto the editors and
> > see if
> > there is a response.
> >
> > I don't really think it is a huge problem with copyright.
> > Don't you reference other authors when you use their work/ideas in
> > your own
> > research especially when writing papers?
> >
> > Also when references the site it helps publicise it which would
> > advertise it
> >
> > to a larger audience and possibly increase the number of submissions.
> >
> > As to accessing books and journals to glean information about
> > procedures,
> > how many of you have been performing a reaction done countless
> > times in the
> > lab before but by someone else and you can't get it to work? You're
> > following the prep word by word but still can't recreate the ideal
> > conditions that ensures 100 % yield!
> >
> > Only when you ask that person do they say (Oh actually I found
> > that........does the trick). This information is not included in the
> > original prep, nor written up else where.
> >
> > Its this "trivial" information that Syntheticpages tries to fill and
> > remember it FREE!!!
> >
> >
> > Cheers
> >
> > Nigel
> >
> >
> >
> >
> >
> >
> > Eugen Leitl writes:
> >
> > > On Tue, Feb 21, 2006 at 07:54:57PM +0100, Jonas Sun dberg wrote:
> > >
> > >> Yes, that looks like a big problem.
> > >
> > > I wonder what the motivation behind this restrictive copyright
> > > was. Do the operators of http://www.syntheticpages.org/ (I kept
> > > looking for a contact address, but was unable to find any)
> > eventually
> > > intend to raise a profit from operating it?
> > >
> > >> But I think it will be hard to get traffic/active writers, as
> > there seem
> > >> to be a lack of organic chemists that surf the web. Still I
> > think it's
> > >> worth a try! It doesn't cost anything else than the time wasted
> > setting
> > >> it up, and it could both be fun and educative. But I think we
> > need more
> > >> than a wiki of organic synthesis. A think a general wiki about
> > organic
> > >> chemistry with a special section dedicated to preparatory
> > methods would
> > >> work better, and maybe run a forum too.
> > >
> > > I'm a chemist by training, currently work in cheminfor matics, and
> > > have several machines in the rack by way of hobby. Assuming
> > people here
> > > would contribute content, we can easily cook up something
> > useful, and then
> > see
> > > where it goes from there. There's plenty of such projects in
> > biological
> > > sciences (e.g. http://openwetware.org/wiki/Main_Page etc.), but
> > I always
> > > considered organic chemists to be a too conservative bunch.
> > >
> > > Is there at all an interest here in such a project?
> > >
> > >> /Jonas
> > >>
> > >> Eugen Leitl wrote:
> > >>
> > >> >On Mon, Feb 20, 2006 at 06:46:45PM +0000, will jones wrote:
> > >> >
> > >> >
> > >> >
> > >> >>I've tried using that site before and also found it a bit
> > thin. If you
> > >> >>
> > >> >>
> > >> >
> > >> >I see bigger problems here:
> > http://www.syntheticpages.org/static/terms.php
> > >> >
> > >> >Copyright
> > >> >
> > >> > * SyntheticPages owns the copyright and any other rights to all
> > >> > materials on this website
> > >> > * SyntheticPages authorises you to:
> > >> > o browse and download the material
> > >> > o print out the material for teaching or research activities,
> > >> > provided that the copyright notice is included (Copyright
> > >> > SyntheticPages C )
> > >> > * You are not authorised to:
> > >> > o alter the material in any way
> > >> > o reproduce or store any part of this web site in any other
> > >> > public or private storage medium, electronic or otherwise,
> > >> > without written permission from SyntheticPages.
> > >> >
> > >> >
> > >> >
> > >> >
> > >> >>could make the submission process easy, and somehow have the
> > ability to
> >
> > >> >>search by structure, then I guess you would be onto a winner.
> > >> >>
> > >> >>
> > >> >
> > >> >These are GIFs, so in order to be able to search the images would
> > >> >have to be reentered manually, and exported into a suitable format
> > >> >(SMILEs, InChI, SDF, etc.) for searching (in a pinch, obgrep
> > would do).
> > >> >
> > >> >
> > >> >
> > >> >>If you could also put in a 'section of failed reactions, but
> > should
> > have
> > >> >>worked' then that would be awesome.
> > >> >>
> > >> >>
> > >> >
> > >> >
> > >> >
> > >>
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