[QSAR-devel] Chemical Semantic Web and Thanks (fwd from pm286|at|cam.ac.uk)

----- Forwarded message from Peter Murray-Rust <pm286|at|cam.ac.uk>
 From: Peter Murray-Rust <pm286|at|cam.ac.uk>
 Date: Wed, 08 Dec 2004 09:50:16 +0000
 To: JOELib devel <joelib-devel|at|lists.sourceforge.net>,
 	JOELib help <joelib-help|at|lists.sourceforge.net>,
 	cdk <cdk-devel|at|lists.sourceforge.net>,
 	Octet Developer <octet-devel|at|lists.sourceforge.net>,
 	QSAR Development <qsar-devel|at|lists.sourceforge.net>,
 	Beda Kosata <beda|at|zirael.org>
 Subject: [QSAR-devel] Chemical Semantic Web and Thanks
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 [Crossposted to several OpenSource lists - please reply thoughtfully. I
 will collate significant replies]
 I presented an invited lecture at the Royal Soc Chem yesterday on "The
 Chemical Semantic Web" and highlighted the impressive contribution of the
 Open Source movement in chemistry. I hope I managed to acknowledge most
 people's contributions. It generated a lively discussion in which, I think,
 the Open Source approach came out very positively.
 Two common negative questions were presented:
 "Who pays for it"
  the implication was that if there was no commercial development the
 software was second-class and there was no future for it. My response was
 that the code would be eagerly adopted by the bioinformatics community
 (strongly confirmed by Mike Ashburner) and we are starting to set up strong
 links with the Bioinformatics community on small molecules. This question
 came from the pharma industry and so I challenged them to put something
 back into the communal process. It's noticeable that the pharma industry is
 a consumer of our efforts but has not contributed anything in return and
 continues to pay for overpriced software products that do not use modern
 methodology. (I spent 15 years in Glaxo so I feel I have a right to
 criticise the industry). I know that pharma industry reads this list and I
 would be delighted if there were some who wished to support communal
 activity. [I would suggest they mail me directly and I will summarise
 replies. All replies will be assumed to be Open unless specifically
 indicated]. One approach would be to support a physical workshop on
 chemical open source. Particular topics could be:
 - markup languages
 - communal chemical ontologies (e.g. descriptors)
 - Open datasets
 - use of InChI (we are very excited about this)
 - graphical components
 - common code libraries
 - web services (I'll mail later)
 The only contribution that I know of from the pharma industry to
 chemoinformatics is the JME editor which is free, but despite repeated
 requests is not Open and not likely to be. It could be withdrawn at any time.
 "Open source is unfair to commercial developers"
 I think this attitude is particularly strong in the US and perhaps Germany.
 The idea is that public funding should not be used to compete against
 commercial organisations. As Mike Ashburner replied, most Open software in
 bioinformatics is written by people on short term contracts often with no
 possibility of extension. I know that made contributors to these lists do
 not have jobs. I developed much of CML when I was unemployed after being
 made redundant from Glaxo.
 I would be more (slightly) more sympathetic to this view if the chemical
 software industry provided anything substantial to the community. I know of
 no support for Open efforts from the chemical software industry other than
 a very undersupported effort to get an Open Management Group spec for
 chemistry. I was invited to contribute CML as the core of this spec, but
 even then it was made clear that I would not even have my (foreign) travel
 expenses paid - even though I had no job.
 Note that "free" is not good enough and may even by counterproductive.
 Closed software often stifles development as there is no API and the
 software can be withdrawn at any time. That is why we are so keen to see a
 JChempaint component as a universal Open chemical editor for the web.
 In fact I think the tide is turning. The components that you are all
 developing are ideal for Web Services, which will have the potential to
 rapidly become a major player in the chemoinformatics market. Between the
 members of this community we have standards, data, transformers,
 algorithms, repositories, query languages, graphics and much more. I'll put
 forward a strategy in the next mail(s).
 Meanwhile - when you are hacking the latest set of bugs at 0200 in the
 morning, take heart - it really is appreciated - and yes - the day of Open
 Source for "chemistry" is dawning. In fact I think the centre of
 gravity of
 chemical software development is starting to shift towards bioscience [and
 materials] so that people will simply refer to the informatics of small
 molecules as "bioinformatics"
 Many thanks to those who have sponsored our Open Source development: Royal
 Soc. Chemistry, Nature Publishing Group, Cyprotex. More about this later.
 Peter Murray-Rust
 Unilever Centre for Molecular Informatics
 Chemistry Department, Cambridge University
 Lensfield Road, CAMBRIDGE, CB2 1EW, UK
 Tel: +44-1223-763069
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