From: djmcphee$##$sympatico.ca
Date: Thu Feb 23 2006 - 10:47:41 EST
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
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From: stephen caddick <stephen.caddick$##$talk21.com>
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 considering 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 about 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 <deadlyvices$##$hotmail.com> 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 Sundberg 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 cheminformatics, 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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> --
> Eugen* Leitl leitl http://leitl.org
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