From: Jonas Sundberg (gussujon$##$student.gu.se)
Date: Thu Feb 23 2006 - 11:45:19 EST
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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