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FW: RE: Chemistry and the Semantic Web

From: Hammond, Tony <T.Hammond@nature.com>
Date: Thu, 1 Jul 2004 13:15:37 +0100
Message-ID: <125F7834E11A5741A7D79412EE3504F90AEF6510@UK1APPS2.nature.com>
To: "'public-semweb-lifesci@w3.org'" <public-semweb-lifesci@w3.org>

[Forwarded to the list on behalf of Peter Murray-Rust who's having
difficulty posting.]

>Date: Thu, 01 Jul 2004 08:55:26 +0100
>To: <Eric.Neumann@aventis.com>,
>From: Peter Murray-Rust <pm286@cam.ac.uk>
>Subject: RE: Chemistry and the Semantic Web
>Cc: h.rzepa@ic.ac.uk
>At 14:45 30/06/2004 -0400, Eric.Neumann@aventis.com wrote:
>I am excited to see the discussion on Chemistry and the Semantic Web 
>hope that this can read to some real progress.
>When we (Henry Rzepa and I) developed Chemical Markup Language (CML -
>please use this precise acronym) 10 years ago we saw the  potential for 
>semantic processing. CML was one of the very first non-textual 
>content-based markup languages and as such requires its own toolset for 
>authoring, editing, transformation, databases and much else. About 10 
>years ago we showed that MIME helper applications could add valuable 
>semantic to chemical information and urged the use of SGML (and now XML).
>CML is now a mainstream scientific XML language. Last week I was 
>to present to the NSF/NationalScienceDigitalLibrary meeting in Washington 
>which looked to support the interoperability of major multidisciplinary 
>languages (primarily physical sciences). Forward-looking publishers now 
>see XML (and thereby these markup languages) as the main way forward for 
>rich re-usable content.
>We have continued to develop CML technology and investigated most of 
>mature W3C technologies and their applicability to chemistry. These
>- DTD
>- XMLSchema
>- RDF
>- RSS
>- XMLSignature
>- namespaces
>- SVG
>We now have components deployed and can create examples of the Chemical
>Semantic Web.  Two examples:
>- CML Rss (http://wwmm.ch.cam.ac.uk/moin/CmlRss). This allows 
>authors/publishers to create an RSS feed where items include CML. We have 
>developed a CML-sensitive RSS client with a complete download kit and we 
>urge you all to have a look! This has enormous potential for chemical 
>publishing - a publisher can include complete information on a compound - 
>2D structure, 3D structure, properties, etc. The client can display, 
>aggregate or filter this. We especially thank Timo Hannay and Ben Lund of 
>Nature Publishing Group for showing us the proper way of adding RDF. Their 
>urchin (http://urchin.sf.net) is capable of aggregating many such feeds. 
>If authors adopted this then chemistry could become on of the first real 
>semantic web applications
>- WWMM (world wide molecular matrix). http://wwmm.ch.cam.ac.uk/Bob  In 
>this vision we tackle the problem of creating a knowledge resource for 
>chemistry. Users can donate micro-information (e.g. a single structure for 
>which they get a free high-quality calculation of molecular properties 
>using quantum mechanics methods. The only stipulation is that the results 
>are then Openly available to the community (in CML). In this way the world 
>can gain grow a semantic resource.
>These are only two examples of possible semantically enhanced web
>technologies. Both could be deployed within enterprises.
>Technically, therefore, the chemical semantic web is already
>possible.Unfortunately there is a major cultural  problem, which I hope 
>isn't out of scope on this list. (BTW I spent may years working in pharma 
>industry (Glaxo) and shall particularly comment on the potential and 
>difficulties there)
>In our opinions the first generation of the semantic web will be built 
>open systems on the public Internet. For rapid development the resources 
>must be open. (Current robots give up when asked to register for a site, 
>add their names and emails, etc.). In biosciences this has been 
>spectacular and a robot can access and re-use a wide range of high quality 
>and comprehensive data (genomes, sequences, structures, etc.) Much of the 
>full-text literature is now being made Openly available and bioscience 
>publishers are looking at new publication models. This would allow the 
>primary literature to become a primary knowledge base for the semantic web.
>In chemistry almost all information is "owned". An author signs over 
>copyright to the publisher which usually forbids them to post the full 
>text on the Web, even years after publication. Thus Henry and I cannot 
>send you the text of our manuscripts on the Chemical Semantic Web - you 
>will have to subscribe to the American Chemical Society. My views on the 
>inappropriateness of this are well publicised, but I believe that 
>copyright should be honoured. Similarly all data is "owned" by secondary 
>data producers such as Chemical Abstracts, Beilstein , Derwent, Thomson , 
>etc. In the days of paper this had to be created by manual rekeying, but 
>we now have tools that can read and understand primary chemical 
>publications. Whether they can be legally deployed and for what purpose is 
>unclear. It would seem that a low cost human may extract and key 
>information but it is less clear whether a robot can do the same. But this 
>has to be where the future lies.
>The chemical semantic web requires tools. The markup languages for 
>geography, etc. are supported by commercial suppliers. Chemical software 
>producers have been very slow to adopt XML ("there is no market for it") 
>and prefer byzantine proprietary formats as a way of maintaining market 
>share. We have therefore had to develop our own on a communal voluntary 
>basis - all main Open Source chemical tools promote CML. There are signs 
>that the commercial manufacturers are starting to see the value of CML, 
>but they do this on a sporadic and uncoordinated basis. For example the 
>OMG lifesciences effort had ca 50 members in the biosciences and ca 2.5 in 
>chemistry. This effort was based on CML but we are normally expected to 
>contribute to this development at our own expense.
>The pharmaceutical industry has been slow to see the value of XML as a
>communal infrastructure - I have worked with WHO and FDA who see the 
>potential and have been trying to develop this approach. For example the 
>dossier that the FDA requires for a new drug runs to millions of page 
>equivalents and needs to integrate information from many sources. XML is 
>essential and valuable for this, but progress is slow.
>The main visionaries for CML include:
>- government (Patents, drug regulatory, environment, safety)
>- health (drug discovery, safety)
>- a few publishers (often outside chemistry)
>- generic web technologists (e.g. IT companies)
>It is disappointing how little interest there has been from pharma. I
>don't know how widely this list is read, but let me make a plea for a 
>concerted effort here. I have worked with several other industries (media 
>, finance, energy, aerospace) where the need for a communal information 
>infrastructure at a precompetitive level is widely recognised.  XML is the 
>universal approach.
>IMO the pharma industry has many areas where it desperately needs a
>communal information infrastructure. This include regulatory, drug 
>information and safety, basic ADMETox data, etc. I don't even know of a 
>site where I can get reliable information on current marketed drugs which 
>I can re-use without having to pay or violate copyright.
>Minor comments follow:
>> From my understanding of XPaths
>> (http://www.w3.org/TR/xpath#section-Introduction), they can be used 
>> "within" URIs. So mapping an RDF statement to a specific Chem-XML node 
>> or group should be doable.
>CMLRSS already does this for CML (sic).
>>Eric.Neumann@aventis.com wrote:
>> > Question: How would one apply RDF for such cases? Would one use CML 
>> > (chemical markup language) to describe the chemical structure and 
>> > have an RDF statement refer to part of that doc via 
>> > XPath/XPointers?
>>  How
>> > about other structural formats like SMILE and CHUCKLES?
>These are semantically void in an XML environment. There is no 
>for discovering their semantics and there is virtually no non-commercial 
>software for their re-use.
>>  Would the
>>This is an interesting question, and certainly also relevant to any 
>>classical bioinformatics data sources that contain more quantitative 
>>than qualitative data (e.g. 3D structures, 2D gel images and 
>>microarray data). I don't really have any solutions, just some ideas:
>I believe that biosciences can and should take the lead here by 
>source of high quality structure/property databases for molecules of 
>interest to bioscience.
>>In those cases where it is possible to embed identifiers in the data, 
>>these could be referenced with identifiers such as 
>>urn:lsid:foo.org:bar:10. A resolution server can then be set up to 
>>extract the referenced data when required. Note that the original 
>>format need not contain full LSIDs.
>We have a mechanism for embedding and referencing identifiers. The main
>task is to have public repositories of agreed identifiers.
>Peter Murray-Rust
>Unilever Centre for Molecular Informatics
>Chemistry Department, Cambridge University
>Lensfield Road, CAMBRIDGE, CB2 1EW, UK
>Tel: +44-1223-763069

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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