From: Clyde Davies (deadlyvices$##$hotmail.com)
Date: Sat Feb 25 2006 - 02:36:13 EST
Hi to all,
I have stirred up what has been a vigorous and stimulating debate, so thanks
to all for taking part. I must admit I hadn't had time to think through
*all* the implications of changing the publishing model for this kind of
information, which is exactly why I put the proposal up for discussion.
People have put very strong points for and against the proposal.
For me, the paramount consideration has to be health and safety. Lab
procedures are inherently risky operations, and any development which
increases the risk to both publisher and reader is totally unacceptable. It
is easy to see how a wiki could increase this risk by abdicating
responsibility for the content. Stephen quite rightly points this out, as
well as the copyright issues involved in publishing other people's work.
I suppose what matters most to me is that I have given us all some food for
thought. I still believe that we have some way to go until the flexibility
and power of Internet publishing is harnessed fully. I would therefore
still like to experiment with various ways of presenting this information,
under the proviso that any material is strictly proof-of-concept and not to
be used as an authoritative source. Hopefully then any learning arising
from such experiments could be put to use in improving already established
sites, such as Synthetic Pages, which is something I would wholeheartedly
support.
I just want to thank everyone, and especially Stephen, for taking the time
to participate in this debate. I feel it has been a very usefully
experience.
Regards
Clyde Davies
_____
From: everybody-bounces$##$orglist.net [mailto:everybody-bounces$##$orglist.net]
On Behalf Of stephen caddick
Sent: 23 February 2006 17:38
To: gussujon$##$student.gu.se
Cc: everybody$##$orglist.net
Subject: Re: Fwd: ORGLIST: Synthetic Pages
Dear All,
The reason we would probably not move to a wiki-format is that we believe
that there must be some editorial control to make sure that there is some
safeguard and validation to the procedures on the site. So as far as I can
see the idea of allowing anyone to edit content as in a wiki, could lead to
some very unsafe or ambiguous information being present on our site and as
you known, site-owners have responsibilities and legal obligations regarding
content. Its also important that people recognise that when they put
something on the web it is a disclosure and may compromise any patent
position for the future, we highlight this in out T & C.
The position on copyright has been very difficult for us to resolve and in
the end we decided to go down what is a fairly conventional route. However
we do not in any way wish to impede authors and as stated on the site,
people can make their con tent available elsewhere without a copyright
notice (people are free to incorporate their syntheticpages procedures in
papers and in other media) BUT we must retain the right to continue to make
freely-available the content which would not be the case if we did not have
the copyright. There is another point which is that we must protect the
syntheticpages style - because otherwise someone could copy the whole site,
claim the copyright and stop us (and others) using it. We have taken advice
on this and it seems that there is not really any other way of protecting
the site and ensuring sustainability
When we conceived of the site we wanted to be sure that we had some
safeguards but we did not want to be an online journal. In the end we do not
generally make a value judgement about content submitted, unless its
nonsensical, but we do edit to improve the user experience. Its worth noting
that in using this format we place a much greater burden of work on
ourselves, but we thi nk its important. If you let anyone freely edit,
comment etc. on content without any safeguard there is a danger that the
information will become less useful and possibly dangerous.
We have had enormously positive response from the community about the site.
Remember that our copyright policy is much more liberal than most journals
and we have harnessed the interactive nature of the internet (by allowing
members to comment). However we do think that some form of validation is
important and that the guidelines for use of the site provide a good
framework for a valuable resource in synthetic chemistry.
Best wishes
Steve
Darren Rhodes <darren.rhodes$##$gmail.com> wrote:
---------- Forwarded message ----------
From: Darren Rhodes
Date: Feb 23, 2006 4:52 PM
Subject: Re: ORGLIST: Synthetic Pages
T o: Jonas Sundberg
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 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 fe ature 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 aft er 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 o bvious 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 co nsider 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 imposs ible 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
&g t; > 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
&g t; >
> > -----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 r eference 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 pr ocess 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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