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Reports and Articles Chemical Structure Association Trust Bursaries The Chemical Structure Association Trust awarded travel bursaries to Horst Bögel from the University of Hallé, Germany, and to M. Karthikeyan from Pune, India, to enable them to attend the ChemInt’99 meeting in Georgetown, Washington D.C. in September. Their reports are given below.
ChemInt’99 – Report by Horst Bögel The second International “Chemistry and the Internet” ChemInt’99 conference was held 25-27 September 1999 at the Georgetown University Conference Center/Marriott Hotel at the Georgetown University in Washington, DC. Approximately 100 scientists from many countries (mainly from US and some from Europe) presented and discussed some important trends in using the Internet in chemistry. The organizers were Steven Bachrach (Chairman), Trinity University (firstname.lastname@example.org), Stephen R. Heller, NIST (email@example.com), Henry Rzepa, Imperial College, London (firstname.lastname@example.org) and Kimberley Cousins (Poster Talks Coordinator), California State University, San Bernardino (email@example.com); the conference office was organized by Scherago International, Inc., New York, NY, 10001 USA.
The Georgetown University Conference Center is located in the campus of the university next to the Georgetown University hospital in the historical Georgetown. In walking distance were the downtown restaurants, shops, museums, business and administration centres of the city. The conference site is approximately 25 miles from the Dulles International Airport and could be easily reached only by taxi. The hotel special conference room rates were relatively high, at $130 per night, but a mild climate and some sunny days at the end of September provided a good and stimulating atmosphere for the meeting. The conference had been designed for maximum interaction among the participants so talks and panel sessions were held in the morning and afternoon, with free time later. Participants were asked to dress informally for the meeting and speakers were encouraged NOT to wear suits (or even ties). Lunches were served in a restaurant on the same floor. Near the conference room there was enough space for poster sessions, commercial presentations, and to make use of the personal computers provided for accessing the Internet.
The exhibitors from ACD (Advanced Chemistry Development, Inc.), American Chemical Society (ACS), Chemical Abstracts Service (CAS) ChemWeb, Cherwell Scientific, MDL Information Systems, LabSeek.com, and Synopsys presented their most recent services and products and contributed to the various coffee breaks and receptions.
In the opening paper on Friday, MDL presented the very convenient CHIME plug-in for web-browsers to visualize 3D molecular structures in World Wide Web documents. The topics covered in the main part of the conference are summarised below, and each session concluded with a panel discussion.
Economic Issue / E-Commerce
Bill Town, Director of Operations at ChemWeb.com, opened the first session with a talk on “E- commerce – why bother?” With the convergence of telecommunications and computing technologies, increasing computing power and better speeds across the Internet, he believes E-commerce will succeed. E-commerce is already accepted for purchase in on-line catalogues of books, music, travel, entertainment, software, computers, cars, chemicals and laboratory equipment at consumer web sites, and for payment. We expect the following from an online shopping mall: access to a wide selection of products, up-dated prices, enhanced productivity, service and support at reduced costs. The design of web-offers should take care of clear navigation, ensure privacy, short response time, fast delivery of products, modular architecture and simplicity of use. “It’s not easy, it’s not cheap and it’s not optional,” he said quoting a well-known US consultant. E-commerce sites can cost between $2 million and $40 million to build, and in the region of $2 million to $50 million per year to maintain. There are already some key players in the chemistry E-commerce markets such as chemicals (ChemConnect, Chemdex, CheMatch, e-Chemicals, Sigma-Aldrich), laboratory equipment (LabX, chromatography.net), laboratory supplies (SciQuest.com), books/software and information (ChemWeb.com).
A second contribution by Jerome Reichman reported on using databases in relation to copyright and intellectual property rights in non-copyrightable collections of data and explored the potentially adverse impact that the emerging legal infrastructure could have on scientific, technical, and educational users of factual data and information.
Electronic publishing provides a lot of advantages, but it seems that the use of E-publishing is lagging behind the technical possibilities. Chris Parkinson reported on Collaborative Authoring: a Remote Document System (RDS) recently released from the Environmental Molecular Sciences Laboratory at PNNL addresses the issues of multiple-authoring and document-sharing over a heterogeneous networking environment. The tool is written in Java and allows for drag and drop in documents; in December a new public release is expected (http://www.emsl.pnl.gov:2080/proj/cip/rds.html).
As Robert Bovenschulte from ACS told us, the journal “Organic Letters” is available online and the new technology provides many advantages and enhancements, but at the first glance at no reduced costs. There are still questions concerning the pricing models for reading and using articles online.
The “Internet Journal of Chemistry” founded by Steven M Bachrach is a wholly electronic journal publishing in all areas of chemistry (http://www.ijc.com/) and it has been operational since January 1998. Subscription is $48 per year; last year 38 articles were refereed, prepared and published. There is a user-friendly handling of 3D structures and units (e.g. energies).
In the panel discussion it was stated that using XML (eXtended Markup Language) instead of HTML code, data (author), style (publisher) and query (reader) types can be handled.
It has become increasingly clear in recent years that students can come to a true understanding of the principles of chemistry only by being active participants in the learning process. Thus we have been searching for ways to increase student involvement both inside the classroom and outside, principally through electronic media. Don DeCoste reported in his paper “Teaching Chemistry in the Electronic Age” that the students have to answer the question correctly. The instructor sees the number of unsuccessful trials of the student and the grades are stored automatically (http://hexane.chem.uiuc.ed/ with guest login).
Alan Arnold from New South Wales, Australia, described the “The MetaChem and Janus Projects Down Under” as gateways to chemical information. Effective and high-quality teaching and research in the molecular sciences requires timely access to a very large body of reliable information. Printed chemical information sources are well organized but with the advent of the Internet, a huge range of additional electronic resources has become available and the institutions are unable to pay for the services. The development of the MetaChem http://metachem.ch.adfa.edu.au/ mSQL database evaluated information sources and services was initiated in 1996. In addition, the Janus Centres will provide a focus for national collaborative purchasing in their disciplines, and provide one-stop shops for access to research information in those disciplines, including chemistry.
The importance of combining structural data with spectral information was the central point in Robert Lancashire’s paper. He has, for some time, incorporated visualizations in his learning modules (http://wwwchem.uwimona.edu.jm:1104/courses/). More recently with the aid of CHIME and the inclusion of our JCAMP-DX spectral viewer, it has been possible to extend this to cover spectroscopic topics. Interactive pages have been produced and, from displays of both spectra and molecular graphics, it is possible to link peaks in IR spectra to animations of the vibrational modes or links from NMR spectra to highlight the atoms responsible.
Learning Polymer Science was the title of Lon J Mathias’ lecture where he stated that browser-based multimedia allows the viewer to explore, ask questions and get immediate answers, facilitating discovery-based learning. Empowering students and teachers in the organization and presentation of information in multimedia format increases learning: we learn better when we teach others. This “learning by teaching” applies to both method and content. The Macrogalleria has been developed, a resource in the basics of polymer science (what polymers are, how they’re made and where they’re used) at http://www.psrc.usm.edu/macrog.
Corporate Internet / Intranet Strategy
Very often the use of different software tools to solve small parts of a huge problems causes difficulties and delays. Yvonne C Martin (Abbott Labs) initiated the SPARK project to solve these problems. To the user, SPARK looks like a single application. It can search databases or read files to identify structures; retrieve biological data from databases or files; perform similarity and substructure searches on collections of compounds; calculate and look up physical properties of molecules such as octanol- water logP, pKa, water solubility, number of hydrogen-bonding groups, etc; process collections of molecules to calculate the mean and standard deviation of properties and cluster similar molecules together; provide plotting and statistical analysis capabilities; and export HTML reports and standard file format for use by other programs.
Thomas Pierce (Rohm & Haas) reported the ups and downs and acceptance of using the www in the company. Current successes include web video for seminars and distance learning and a few internal computational chemistry applications.
At the beginning of the nineties, Bayer AG established an “Integrated Chemistry Information System (ICS)” as a framework for the development of an integrated set of PC-client/server systems which address the whole spectrum of central chemical information. Achim Zielesny reported that with the advance of Web technology in the middle of the decade there was a growing motivation to utilize the Web as a new system platform for elaborated scientific IT applications – despite the obvious technical hurdles and the web’s reputation to be good for PR presentations only. In 1996 Bayer made the strategic decision to set up a central chemical information infrastructure on the corporate Intranet: The ICS Web. The goals to be achieved were a considerably improved level of system integration (the basic benefit of the Web), reduced maintenance costs, easy and world-wide access as well as enhanced user friendliness.
Stephen Boyer (IBM Almaden Research Center) presented the IBM Intellectual Property Network (Patent Server) (http://www.patents.ibm.com/) as one of the most complete repositories of patents & patent applications (PCT’s) that is publicly available on the Internet today and it’s free. It currently makes available all US patents (text & images) from 1971 to present, as well as European Patents and patent applications. Users can search the various collections and view the actual patent documents from their web browsers.
Gary Mallard explained that the NIST Chemistry WebBook (http://webbook.nist.gov/) is an ongoing project to provide a full range of chemical data on the web. Very useful data and chemical information on thousands of chemicals can be searched for in different ways (e.g. by formula, compound name, 2D- substructure search via Java Applet).
Lewis Jardine (Cherwell Scientific) developed JavaBeans components for building clients for corporate intranets and advanced interactive webpages. Recently an extended ChemSymphony has been developed which allows access to and integration of databases and server side computational engines. The new Data Relationship Model has made it possible to methodically assimilate and collate data from differing sources within the same data pool. For convenience, this can be accessed and manipulated by a drag-and-drop spreadsheet viewer which makes extensive use of JavaBeans components.
An enhanced version of the CACTVS browser, the “Enhanced NCI Database Browser” (presented by Marc C Nicklaus), based on publicly available structural data of the National Cancer Institute, currently comprises more than 246,000 structures. They are searchable by various criteria, such a molecular formula, full structure, substructure, molecular similarity, biological test data and more. Hit lists are displayed in tabular form. Individual hits can be displayed and downloaded in various formats, including an Image Gallery and web-specific formats such as VRML viewable with appropriate browser plug-ins. One new feature is the 3D-pharmacophore search capability.
The panel discussions, the poster presentations and the commercial presentations contributed considerably to the great success of this conference.
A complete list of abstracts of the contributions can be found for the 18 lectures at (http://www.chemint.org/chemint99/abstracts/lectures.html) and for the 22 posters at (http://www.chemint.org/chemint99/abstracts/posters.html)
The next conference “Chemistry and the Internet – ChemInt2000” will be at the same place Georgetown University Washington, DC, from September 23-26, 2000; for details, see (http://www.chemint.org). Poster Abstract Submissions will be activated in February 2000. ChemInt2000 will look into the current and future technologies, developments, and applications for chemistry using the Internet. The Internet has become a major avenue for communication among scientists. ChemInt2000 will again gather together the leaders and innovators in developing Internet resources for chemists, to discuss what future innovations will bring to chemists. Chemists who use the Internet on a regular basis, web masters and web developers for chemistry sites, and web publishers will benefit greatly from this conference. In addition working chemists who want to learn from leaders in this high growth and high visibility area what the current and future value of the Internet will also find the conference of great value.
ChemInt’99 – Report from Dr. M. Karthikeyan, Scientist, ARDE, Pune, India In June of 1996, when I was doing my Ph.D at National Chemical Laboratory, I was awarded a Chemical Structure Association Trust bursary to attend 4th International Conference on Chemical Structures, in The Netherlands. It helped me to get more information and exposure to chemical information activities in the world. The encouragement and motivation gained during the conference through informal discussion with experts in the field was the driving force to pursue further research in this area, and helped to extend the ICIS (Interactive Chemical Information System) program developed for educational purposes.
The primitive version of the ICIS program with animation capabilities, was completely rewritten to generate automatic chemical structure database (virtual library). A part of the work was presented as an abstract in the 5th International Conference on Chemical Structures in June 1999. Though I could not physically attend the conference I could do it by virtual means using Internet. The presentation entitled “Computer search for High Energetic Organic Compounds from the automatically generated Chemical structure database” was made available online via WWW. The template method was used rather than atom-atom connectivity, and the program was extended to store chemical structures as intelligent pixels in a compressed GIF format compatible for internet file transfer. The algorithm developed entitled “Algorithm for compact storage and Retrieval of Chemical structures as Intelligent pixels” was presented in the poster session of ChemInt’99, in Washington DC, USA. This program and presentation materials are available on request.
This conference ChemInt’99 is of unique type held once in a year, started in 1998, due to overwhelming response from academic, industrial and government departments, it is continued this year also. The theme of the conference was to communicate chemical information across the globe via Internet. A Chemical Structure Association Trust award in the form of a bursary to meet my travel expenses, in turn helped me to get permission and additional grants from the Ministry of Defence, India.
Attendees of the conference, especially from software companies and research organizations such as Molecular Design Limited, Advanced Chemistry Development and NIST shown keen interest in the work, and appreciated the efforts made in developing a strategy to store chemical information in a very compact format. They also suggested publication of papers in appropriate journals in order to communicate the results with the scientific community.
Though the theme of the conference was to communicate chemical information via internet, additional topics were presented in the conference: E-commerce, Database security, Collaborative authoring of remote document systems, Electronic journals (past, present and future), Teaching chemistry in the electronic age, Gateways to chemical information, Multimedia applications in chemistry, Interactive Web page documents, Structure Activity relationship, Chemists and Web Applications, and Free electronic online chemical databases (Material Safety Data Sheets, Commercial Chemicals, Physico- chemical property data etc.)
During the electronic presentation, a version of ACS, IPX formats was discussed with experts. The experts discussed the problem of integrating academic research project into an industrial environment, and re-engineering for designing interfaces. They compared the present program with the commercial chemical data bases made in the past three decades, and appreciated the algorithm and attempt to use modern programming techniques.
The informal discussion with experts of the respective fields gave an insight into the emerging technologies for effective utilization in our scientific research. It is always advantageous for scientists from government organizations to attend conferences of such technological importance and to get more information for implementation in their research areas. It also opens a channel among researchers to do collaborative work across the globe in chemical information systems.
Participants came from industries, Scientific Organizations, Universities / Research Institutes / Colleges: Union Carbide, Cambridge Soft Corporation, Sigma-Aldrich Research, IBM, Bayer Corporation, Synopsys Scientific, Advanced Chemistry Development, Abbott Laboratories, Molecular Design Limited, American Chemical Society, American Physical Society, Chemical Abstracts Service, OPCW, DRDO, California State University, Georgetown University, University of Illinois, Scripps Research Institute, European Patent Office, ChemWeb, University of California, Max Plank Institute of Chemical Ecology, Vienna University of Technology, University College / Australian Defence Force
The Chemical Structure Association Trust’s help to promote education and research in chemical information system is highly appreciated. I personally thank the Trust for giving me such an opportunity and recognition in the form of a bursary.
3rd International Conference for Chemical Information Users, Manchester, 16th – 17th November 1999, Manchester, UK Some 70 or so people gathered together under the increasingly darkening skies, well it was Manchester, to attend this now regular conference and were treated to a really excellent and packed programme. More’s the pity that the numbers were not greater. Maybe we’ve suffered from chemical information meeting overload in 1999?
After the welcoming remarks from Janet Ash, our CSA Chairman, the conference was opened by Diana Leitch, Director of John Ryland’s library at Manchester University, speaking about “Electronic Journals in the higher education community”. Diana promised to be controversial and she was! She started by saying that she gets heart palpitations at the mention of electronic journals, and most of her talk centred round the maxim that E-journals do not offer academia good value for money. There are over-bureaucratic procedures; remote access really means …”on what PCs do you want access?” and the method of access is governed by the Publisher. Terms & conditions of service are a minefield and need to be completed by every single person using the service; there are numerous different formats of the e-journal and the crunch is the COST. Despite an increased budget, the subscription to one publisher’s journals has had to be suspended as it was unaffordable.
Then followed a paper by Elspeth Hyams on Copyright in the digital environment. Elspeth contends that information published digitally can be “broadcast” and, therefore, different regulations apply to electronic publications from those governing materials in print media. In effect, digital licenses mean NO copying and the concept of fair dealing falls by the wayside. Also, there is a greater tendency to charge on a transactional basis. Publishers and users need to talk to each other much more, to avoid the situation where publishers cannot afford to launch new publications and users cannot afford to buy them.
Harry Boyle (CAS) presented a paper, co-authored by Eileen Shanbrom, on “A collaborative approach to integrated searching and full-text delivery via the Web”. Mainly with reference to ChemPort, Harry was describing the way to link to Publishers’ sites, Patent Office sites and the customers’ in-house holdings to deliver this full text solution. The barriers between primary and secondary publishing are being broken down. Harry also discussed the problem of costs, and felt that everyone sees the web as an opportunity to make more money. The academic community is having to adopt the behaviour of the commercial sector to survive.
Tuesday’s session on “Electronic Journals and Document Delivery”, was completed by Andrew Braid from the British Library Document Supply Centre, who spoke about this topic in relation to “Is this a challenge or an opportunity?” Although, we’ve been exposed to the statistics coming out of the BLDSC before, nevertheless they still are quite mind boggling – over 4M requests/year of which 90% are satisfied from their own stocks! The answer to the question is, as far as BLDSC is concerned, no prizes – an opportunity. Andrew’s conclusion was that their original role can be replicated in the digital age as no library is self-sufficient, even when using electronic publications.
Then followed a series of product reviews from the exhibitors, strictly controlled by Doug Veal, Chairman of the RSC Chemical Information Group. There were 9 presentations each allocated 8 minutes for their review, but in some cases it turned out to be 6.75 minutes because of the time taken to set up the technology (why couldn’t all the Power Point presentations have been pre-loaded onto a single machine?). The companies represented were Synopsys; Blackwells; CAS; Chemical Concepts; ISI; STN; Oxford Molecular; MIMAS and there was also a presentation from the World Health Organization.
The day concluded with a sherry reception, dinner and wine all provided by the kind sponsors – Beilstein, ChemWeb and ISI in that order.
Wednesday’s morning session on “Education and Industry: Information Training for Chemists” was opened by Engelbert Zass from ETH in Zurich. He presented a number of initiatives to teach chemical information via the Web, in particular “TopClass”. Engelbert also described the VSC distance learning project (multi-media teaching modules) undertaken by a number of, mainly, German universities in which Johnny Gasteiger at Erlangen is responsible for the chemical information module and the Virtual Campus project in Switzerland.
Mark Winter from the University of Sheffield described their “WebElements” source of information about the periodic table and how this has grown and developed since its inception in 1993. The visualisation of information is important, and the WebElements site uses many different methods to display information about the periodic table. Mark expects it will not be long before we are all using palm top computers to access information, and the way of displaying that information will be vitally important.
“Virtual Communities” was the subject of Wendy Warr’s talk, which concentrated particularly on the RSC ChemSoc and ACS ChemCenter. She discussed the design and content of these services and their value to the chemical community and she concluded that running virtual communities and e- commerce sites is extremely expensive.
Barry Dunne (SII/CAS) then spoke about SciFinder Scholar and how this has developed as a direct response to the expressed requirements of academic users. He covered other key resources available to the academic community and mentioned the setting up of the Resource Discovery Network for higher education in the UK. Barry feels that information training should be part of all chemistry courses, to avoid the situation where Research becomes re-search!
The morning session was concluded by Elisabeth Goodman from SmithKline Beecham whose paper covered knowledge management and the opportunities available for chemists in the pharmaceutical industries especially with regard to how these resources can be exploited. Knowledge management involves pulling together all the information sources available, and, more importantly, sharing that knowledge with others in your organisation. One way to do this is to put the information scientists amongst the research workers, rather than isolate them in the library. Some organisations offer incentives for sharing knowledge amongst the staff, by offering rewards.
The final session of the conference was entitled “New methods of representing Chemical Structures on the Web”. The first speaker was John Hollerton from GlaxoWellcome whose paper, intriguingly titled “Chemistry on the Web – cracking or crackers?” dealt with the various technologies used to deliver chemical information through the Web and the advantages/disadvantages of the Web as a delivery mechanism for chemical information. There are so many options available and so many points to consider when designing web-based systems. He concluded that success will come only by choosing the right tools for the right job at the right time.
The next speaker was Jean Holt from MDL who spoke about a number of MDL’s products that fit into the corporate web environment including ISIS/Direct their new data cartridge. The web is more important for what it enables than for what it is, and Jean sees the future in XML and Java!
Bill Town then described the services offered to the chemical community by ChemWeb especially with regard to structure searching tools and plug-ins and the various structure databases that they offer. ChemWeb now has over 150,000 members and is recording some 40,000 page transmissions per day. The chemistry whiteboard facility on ChemWeb, based on ChemSymphony Beans, provides a unique way for chemists to communicate remotely using a structure diagram, which can be modified online by chemists logged in at different sites.
Keith Harrington (Synopsys) spoke about the various flavours of Accord and specifically recent advances in chemical representation within the Accord Chemistry Engine leading to simple solutions to complex enumeration problems. He felt that biologists had solved the HTS problem and it is now time for chemistry software to catch up.
The conference was ended by Peter Murray-Rust, from the University of Nottingham, in his usual inimitable style talking about the XML “revolution” – open, available, vendor independent, structured format supported by W3C (WorldWideWeb consortium). Peter’s view is that “chemistry” is in danger of bepassed in this area, because chemistry suffers from having no agreed approaches to inter- operability, with the drive coming from e-commerce. Peter then went on to describe their Chemical Markup Language (CML), which he hopes will be adopted by the whole of the chemistry community.
The organisers are particularly grateful to all the sponsors for helping to keep down the cost of attending the meeting, which was good value for money. In addition to the sponsors of the evening events, CAS provided some excellent conference folders and ChemWeb also sponsored the conference web site, which enabled us to organise much of the meeting electronically.
We must end by expressing our sincere thanks and appreciation to the RSC Chemical Information Group, who co-organised this conference, and to Helen Schofield, the local organiser, who put so much hard work into making this conference such a success.
Peter Nichols and Janet Ash
PDR AGM The Pharma Documentation Ring (PDR) held its 41st Annual General meeting in Copenhagen, Denmark from the 29th September to the 1st October 1999. The PDR is an association whose members represent the scientific information departments of the leading R&D-based pharmaceutical corporations. The 28 Companies, who were represented, account for more than half of the total global turnover ($296 billion) of ethical drugs in 1999. This year’s successful meeting, excellently organised by Novo Nordisk, was attended by 40 delegates from the member companies, with Lundbeck represented for the first time. The total number of member companies has shown a slight fall over the last 3 years due to continuing consolidation in the Pharmaceutical Industry. The existing PDR Board was re-elected for a further term of 2 years.
Each Annual General Meeting has a special theme and this year’s was devoted to the Intranet – The Second Generation. This was particularly timely as several of the PDR Companies are in the process of re-engineering and redeveloping their Intranets. Following presentations by several PDR representatives, three external speakers from Verity, Autonomy and IHS Dataware gave presentations on their commercial indexing and searching products.
Mike Tansey, CEO of Thomson Science and Technology and Managing Director of Derwent Information gave an interesting and valuable insight into Derwent’s future plans for developing its products and meeting the future needs of its customers. It was clear that closer co-operation between the Institute for Scientific Information (ISI) and Derwent (both members of the Thomson Group) could lead to improved products for the R&D based Pharmaceutical Industry.
A key development reported during the meeting was the progress that had been on the development of a model licensing agreement for electronic journals with representatives of the Scientific Technical and Medical (STM) publishers. Considerable progress had been made by a small working party consisting of representatives from both the PDR and STM publishers. Two of the PDR representatives involved had been invited to address an STM Meeting taking place in October at the Frankfurt Book Fair. It is expected that the model licence proposal will be completed by the end of 1999.
The remainder of the meeting was concerned with the sharing of knowledge and experience amongst the representatives from the different Pharmaceutical Companies. Each representative gave a short report on developments that have taken place in their company during the previous 12 months. This enables participants to discuss with their PDR colleagues in other companies the individual approaches that have been taken on common issues and problems.
PDR company representatives also provide an annual report on the developments that have taken place in an information topic of their choice.
The results of several PDR member surveys were presented and discussed. These covered topics as varied as document management, newsfeeds and the quality of drug pipeline and other commercial databases.
Some selected highlights from the presentations and ensuing discussions were:
- The majority of PDR companies are re-engineering and enhancing their Intranet services to deliver improved customer facilities. Over the last few years, member companies have learnt a great deal about how to design effective interfaces to published and proprietary information and the new services being developed capitalise on this learning.
- Most PDR companies are now accessing a large number of scientific technical and medical journals in electronic form. Substantive differences in the individual licensing agreements with each publisher increases the overall administration needed to establish each new agreement and to monitor compliance with specific terms and conditions. It is hoped that the model licensing agreement discussed previously will reduce this administration.
- Several information vendors are enhancing their products by providing links from secondary to primary sources and vice versa. This is seen as a valuable development by PDR representatives, though some concern was expressed that the linking may become somewhat fragmented with some secondary sources deciding to provide links to only certain selected primary sources. Such a situation could severely restrict the value of the links for R&D users of the services. It was agreed that ‘Linking’ should be the topic of a Special PDR Meeting to be held next spring.
- PDR companies would like to continue to migrate some of their stand alone and networked CD-ROM applications to an Intranet environment but in some cases, for example pharmacopoeias, the high licensing costs are proving prohibitive (even for the CD-ROMs)
- The improved timeliness of pharmaceutical patent information from the main database producers – Chemical Abstracts Service and Derwent Publications Ltd. – was warmly welcomed. A new patent alerting service Current Patents Gazette from Current Drugs had also attracted a good deal of interest.
- Following a successful Special PDR Meeting on Knowledge Management held in June, PDR Companies have continued to develop applications that support improved capture and sharing of acquired knowledge and information within their organisations.
- A number of PDR Companies reported that they were encouraged that the long term support of in- house TRIP database applications has been secured due to the acquisition of this text retrieval software by the Tieto Group.
The 42nd PDR AGM will be held on 27th Sept. – 29th September 2000 in Cheshire, England and will be hosted by AstraZeneca.
In summary, the meeting was very successful and a survey conducted amongst PDR members who attended the meeting indicated a very high level of relevant and quality presentations by members and invited speakers. An enthusiastic and individual approach to the different topics was strongly evident, helping to make these AGMs one of the annual highlights of the information scene in the pharmaceutical sector.
The PDR web site, launched in 1999, can be found at http://www.p-d-r.com/.
Forthcoming Meetings Joint CINF/CSA Symposium, March 2000 A special joint session of the American Chemical Society’s (ACS) Chemical Information Division (CINF) and the CSA will take place on Tuesday 28th March 2000.
The Joint CSA/CINF Symposium, entitled “Chemical Information and E-Commerce” is a full day session forming part of the 219th National Meeting of the ACS, 26 – 30 March 2000 – San Francisco, California. The session will be chaired by Bryan Vickery, Community Development Manager, ChemWeb.com [http://chemweb.com/].
The call for abstracts was met with enthusiasm by all chemical e-commerce platforms operating today, and even by some about to launch. Recent articles in Chemical & Engineering News (C&EN, 12 July 1999, 11-18) have highlighted the explosion in the area of e-commerce in the chemicals industry – which includes retail (books, software) and business-to-business (b2b) platforms.
The session is now organised and the titles, speakers and organisations are listed here:
- Integration of technical information with on-line buying increases the chemical procurement efficiency John Custer, Internet Strategies, Sigma-Aldrich Research [http://www.sigma-aldrich.com/]
- Demand aggregation in real-time as a new model for e-commerce Lane S. Yago, PowerPurchasing Group [http://www.powerpurchasing.com/]
- Bringing clarity to e-commerce in the industry Brad Lich, Vice President of Marketing, e-Chemicals Inc [http://www.e-chemicals.com/]
- Chemical information and e-commerce in the 21st century: The role of the infomediary in online commodities trading Arlyn R Sibille, Vice President Analytical Testing, WorldWideTesting.com [http://worldwidetesting.com/]
- Integrating reagent selection, ordering and inventory management Charles D. Sullivan, Maurizio Bronzetti, and David A. Evans. MDL Information Systems, Inc [http://www.mdli.com/]
- Leveraging e-procurement in pharmaceutical R&D Mark Robillard, Vice President of Electronic Commerce, EMAX Solution Partners [http://www.emax.com/]
- E-commerce models: changing the way vertical industries do business Kevin Wenta, CheMatch [http://www.chematch.com/]
- Proven Benefits of e-commerce for chemical buyers and sellers John Beasley, ChemConnect [http://www.chemconnect.com/]The session will be concluded by a panel discussion: Online marketplaces: Strategies for reaching customers through electronic commerce to include many of the speakers and David A. Weber, Supplier Relations, Chemdex [http://www.chemdex.com/]
Bioinformatics meetings CCP11 is an academic project hosted by the Human Genome Mapping Project Resource Centre, an institute of the Medical Research Council, UK. Our remit is to foster the bioinformatics community through our website ‘The Bioinformatics Resource’ (http://www.hgmp.mrc.ac.uk/CCP11/), newsletter, and regular conferences and training courses. There are two CCP11 conferences (details below) which may be of interest to CSA members. Early registration for these events is advisable.
To be kept up-to-date with other articles of bioinformatics news, subscribe to the news service: http://www.hgmp.mrc.ac.uk/CCP11/news_subscribe.html
CCP11 International Meeting On Developing Software Tools for Bioinformatics
Hinxton Hall Conference Centre, Hinxton, Cambridge, UK 17 December 1999
Register at: http://www.hgmp.mrc.ac.uk/CCP11/meeting2/
This meeting will bring the state of art in bioinformatics software development to the broad community of software developers. The meeting consists of two sessions. The day session is a lecture series given by leaders in the field of”source code available” programming libraries. This is followed by a discussion session for researchers actively involved in development of bioinformatics programming libraries. The meeting will provide valuable information for researchers of all levels of experience.
The Sixth Genes, Proteins and Computers Conference (GPCVI)
Chester College, Chester, UK. 26 – 28 April 2000 http://www.hgmp.mrc.ac.uk/CCP11/gpcvi/
An International Conference for Bioinformatics and the Molecular Biologist
Bringing bioinformatics to the molecular biology community, this established international conference will bring together leading experts in the fields of functional genomics and proteomics, structural genomics, biosequence analysis and phylogeny. The emphasis is the solving of molecular biological problems by using computational approaches, and the relevance of this to the molecular biology community.
For further information about the above, contact:
Dr J.C. Ison
Bioinformatics Applications Group
UK MRC Human Genome Mapping Project Resource Centre
Hinxton, Cambridge, CB10 1SB, UK
E-mail : firstname.lastname@example.org
Tel : 01223 49-4548
The CCP11 Project : http://www.hgmp.mrc.ac.uk/CCP11/
Information Fellowship New information fellowship at Indiana University The School of Library and Information Science at Indiana University is pleased to announce a new fellowship: The Charles A. and Charles H. Davis Fellowship in Scientific Information. The donors are providing $100,000 to initiate the award. Named after Charles A. Davis, a pioneer in forensic science, and his son, Charles H. Davis, a chemist with advanced degrees in library and information science, the fellowship will assist promising graduate students in scientific information–for example, the School’s specialization in chemical information.
Charles A. Davis headed the Indiana State Police Headquarters Laboratory and later that agency’s Criminal Investigation Division. A zoology major at Indiana University during the 1930s, he worked throughout his career with friends and colleagues on the IU faculty in anthropology, chemistry, toxicology, medicine, dentistry, and law. He also chaired the original Indiana State Commission on Forensic Sciences.
Charles H. Davis has three degrees from IU and studied postgraduate chemistry at the University of Munich on a fellowship awarded by the German government. He has a graduate minor in toxicology and has spent most of his career in information science, working first as an editor for Chemical Abstracts before entering academic life. He has taught at Drexel University and the University of Michigan and served for several years as a dean, first at the University of Alberta, Canada, and more recently at the University of Illinois at Urbana-Champaign, where he now holds the rank of Professor Emeritus. He is also a Senior Fellow in Library and Information Science at IU and teaches as an adjunct professor at both the IUPUI and Bloomington campuses of Indiana University.
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Synopsys At the American Chemical Society Conference in New Orleans in August, Synopsys Scientific Systems Ltd. and Oracle Corporation announced the release of the Accord DataCartridge module for Oracle 8 (“Accord for Oracle8”) that, for the first time, transforms chemistry into a first-class datatype, searchable alongside numbers and text via standard SQL. Tight integration of the Accord Chemistry Engine within Oracle fundamentally changes how chemical structures and reactions can be stored, searched and analysed within a relational framework. Gone is the need for separate chemical servers, integration layers and development skills. With Accord for Oracle, industry standard tools and technologies can be utilized to develop fully-featured chemical applications as diverse as compound registration, combinatorial chemistry and Web chemistry publishing.
Synopsys and Oracle have combined their respective strengths in chemical information and object- relational technology to develop a scalable, robust solution to the problem of storing and searching chemical structures and reactions. Accord for Oracle provides a rich, documented set of SQL functions and operators that allow chemical moieties to be stored and searched by exact structure or substructure; converted to and from standard chemical formats, such as SMILES strings and MDL Molfiles; and molecular properties, calculated as required by an application directly within the relational server. All the power of the Accord Software Development Kit (SDK) can be harnessed via PL/SQL to develop chemical business rules and registration procedures.
Application developers can use the Accord for Oracle server in conjunction with Accord client-side components to deliver active chemical content via n-tier Web or more traditional client-server solutions. The Accord ActiveX Chemistry Control can be used for query preparation and chemical depiction within a wide variety environments that can communicate with Oracle via ODBC. Standard interfaces to Oracle, such as the Oracle Web Application Server and Oracle CLI, can be used to communicate chemistry to and from the server. In addition, Accord for Access applications can link directly to Accord or Oracle tables to provide a fully-featured, out-of-the-box client. In summary, Accord and Oracle 8 offer complementary capabilities and shared strengths that, together, promise to change the way we think about developing and deploying chemical database applications.
Because Accord for Oracle implements up-to-date chemical indexing algorithms within the underlying relational database server, chemical searching of enterprise data repositories is fast and scalable. SQL statements can seamlessly combine chemical, numeric and text SQL terms. And because the Accord DataCartridge tunes Oracle 8 into chemistry ‘under the hood’, complex issues such as query optimisation, indexing and backup/recovery are all taken care of by the system. This allows users to focus on their application logic and leverage Oracle to its fullest, utilising Accord components when and where required on the client, the middle tier or the database server.
“Thanks to the open component-based design of both Oracle’s and Synopsys’ software and the teamwork between staff from both companies, the migration to Oracle 8 was effected in record time,” said Olivier Cabot, Director of Oracle Design and Migration Services. He continued: “The Pharmaceutical sector is an important market for Oracle and we look to specialist software providers like Synopsys to provide value-added capabilities that benefit our joint customers.”
Dr. Glen Hopkinson, Managing Director at Synopsys, commented, “The extensibility of Oracle 8 has, for the first time, offered us the opportunity to marry traditional relational data with active chemical content on the server. Accord for Oracle will enable Synopsys and our customers to develop a new range of chemical applications that are based on one scalable, robust, chemistry-enabled database server with all the benefits that this brings.”
Dr. Keith Harrington, Director of Geographic Sales & Marketing at Synopsys commented: “By working together with industry partners, we are seeking to provide customers with better, more robust solutions that seamlessly combine best-of-breed technologies to meet their corporate chemical information needs. Our focus as a company is to deliver component-based chemical tools and solutions that are second to none. This is the way of the future – not only on the client, but also on application and database server platforms.”
Accord for Oracle is fully compatible with Oracle 8 and with Accord 3.0 desktop products and visual chemical components, including Accord for Access and the Accord ActiveX Chemistry Control. It is available now on Windows NT Server and Sun Solaris. A ‘FastStart’ package is available that includes on-site installation, training and consultancy support. Contact Synopsys for details regarding pricing and additional platform availability.
Tripos Tripos, Inc. announced in September the introduction of Charisma™, a software tool that clusters compounds according to their most common substructures. Using Charisma, scientists in the pharmaceutical and biotechnology fields will easily observe the relationship between molecular substructures and specific properties to accelerate their drug discovery. “Visualization of structure- activity relationships and identification of chemical structures that are critical to biological activity are fundamental steps in drug design,” says Trevor Heritage, Ph.D., vice president of Tripos Discovery Software. “Until now, no software has been able to quickly elucidate structure-activity patterns within large data sets, and communicate those patterns in terms of real chemical features that can readily be used by medicinal chemists.”
Charisma is a hierarchical clustering tool that classifies compounds according to their most common substructures. It organizes substructure information in an interactive dendrogram, which looks much like a family tree in genealogy. Each intersection of tree branches represents a substructure and the compounds containing that substructure. By averaging a specific property, such as activity, for the compounds at an intersection and then coloring each branch according to this average, Charisma can visually relate substructures to activity.
“Unlike other clustering tools that relate numerical descriptors to properties, Charisma relates the components of actual structure to chemical or biological properties. This facilitates next generation design by the chemists,” says Rob Jilek, Tripos diversity product manager. “For Charisma, the structure is the descriptor.”
Because Charisma sorts and categorizes compounds as would a medicinal or synthetic chemist, researchers can objectively evaluate their own conclusions about structure-activity relationships. Charisma exploits the power of the human eye at pattern recognition of chemical structures, building a colored roadmap that shows how incremental changes in structure add to or detract from the specific property being analyzed.
Charisma will be available in the SYBYL™ 6.6 release scheduled for late October. SYBYL is Tripos’ complete computational tool kit for molecular design and analysis. At the heart of Tripos’ suite of discovery software, SYBYL provides essential construction and analysis tools for both large and small molecular structures.
In a move to further provide researchers with access to information, EBSCO Subscription Services and Chemical Abstracts Service (CAS) have announced a linking partnership. Once these links are completed in the first quarter of 2000, researchers will be able to link from CAS database resources via the ChemPort (SM) Connection to the full text of journal articles contained on EBSCO Online (R).
“We see the linking agreement with CAS as a significant step toward our goal of providing our customers all of the information choices that they expect,” said Mark Williams, manager of Electronic Content Development for EBSCO Online. “EBSCO Online’s strategic aim is to provide every logical partnership possible so users can search and seamlessly link to full text.”
“CAS is delighted to join with EBSCO Online in making a wealth of science-related literature more readily available to our customers,” said CAS marketing director Suzan A. Brown. “The CAS/EBSCO linking partnership puts users in touch with a prestigious group of publishers collaborating to build a unique digital research environment for scientists.” STN users searching with STN Express with Discover, STN Easy or STN on the Web; SciFinder or SciFinder Scholar users; and CA on CD customers will be able to link from search results directly to full text articles available on EBSCO Online.
EBSCO Online is a World Wide Web-based service that provides a single source for all aspects of a comprehensive electronic journal collection. Users can go to one URL and use one search engine to search across journal content from a variety of publishers and access the full text. Administrators can choose from a variety of authentication methods to make access easy for users depending on their needs.
“Linking has become synonymous to total customer satisfaction in electronic information delivery,” Williams said. “This is what the ChemPort Connection/EBSCO Online linking agreement is intended to deliver.”
EBSCO customers have access to more than 3,600 electronic journals through EBSCO ONLINE, and content is available from a number of publishers, including more than 350,000 articles from more than 30,000 individual issues. “Our content is among the richest in the industry,” Williams added. “STM publishers from around the world and in leading disciplines are included in this service. We aggregate much of the content and provide links to those publishers that wish to aggregate content themselves.”
CAS, a division of the American Chemical Society, produces the world’s largest and most comprehensive databases of chemical information, including more than 18 million abstracts of chemistry-related literature and patents and more than 20 million substance records. CAS publishes Chemical Abstracts (CA), related publications and CD-ROM services; operates the CAS Chemical Registry; produces a family of online databases; and offers the SciFinder desktop research tool. CAS operates STN International, a network of scientific and technical databases, in association with FIZ Karlsruhe in Germany and Japan Science and Technology Corporation. The CAS Web site is at http://www.cas.org/
EBSCO Subscription Services is part of the EBSCO Information Services Group, which provides fully integrated serials access and delivery solutions worldwide through print and electronic subscription services, reference database development and production and online multi-database access. The EBSCO Information Services group also includes EBSCO Publishing. For more information, please visit the EBSCO World Wide Web site at http://www.ebsco.com/.
ACD Advanced Chemistry Development announced the implementation of SIMPLE, a system for Strategic Information Management in a Process and Laboratory Environment. This application has been developed for Pfizer’s Analytical Research and Development Department in Sandwich, UK. This is a web-based system capable of tracking, scheduling and reporting of analytical data generated from and during the development process and builds upon the functionality developed for ACD/SLIMS. SLIMS is a full-featured sample manager allowing desktop access to sample information, chemical structures and analytical spectra (NMR, MS, IR, UV-VIS). Each aspect of the LIMS system is integrated to the appropriate helped application tool for textual reporting, molecular structure drawing and spectral processing and manipulation. For SIMPLE, the intention is to extend the functionality of the system to include the integration of automated system alongside the implementation of electronic notebook functionality.
ACD also announced the release of HPLC Simulator, which allows you to input one or more chemical structures and then predict the relative retention times on a high performance liquid chromatography column. If experimental data are known for some of the structures, the accuracy of the predictions can be significantly improved through system training. LogD, the octanol/water partition coefficient for dissociative systems, is the crucial component in the prediction of the retention times of different compounds in reversed phase HPLC and ion exchange HPLC analyses. Additionally, in some cases the values of molar refractivity, molar volume and MW are also involved. For large structures containing more than 10 acidic protons the logP values (the octanol/water partition coefficient for neutral forms) instead of logD values are used. ACD/HPLC Simulator allows the user to input the experimental values of retention time for any set of three or more structures and obtain the prediction equation. Using this equation, the program predicts the retention time for any new structure under the experimental conditions. It also allows the user to calibrate a column using the Conditional Charge coefficient without entering the experimental retention times. Furthermore, the obtained calibration can be used for the prediction of the elution order for any set of structures.
Richard Hong, President of Hawk Scientific Systems, New Jersey, USA
Eva Hendrick, Manager of Registry Products at CAS, Columbus, Ohio, USA
Andrew Berks, Senior Information Scientist at Merck & Co, Rahway, New Jersey, USA
Dr. Kimito Funatsu, Associate Professor, Toyohashi University, Tempaka, Japan
Ms Shouko Nakayama, Fuji Photo Film, Japan
Dr. Elean Lasterra, Celltech Chiroscience, Cambridge, UK
Greg Banik has moved to Bio-Rad Laboratories, Sadtler Division, where he is General Manager.
Edlyn Simmons is now Section Head, Business Information Services, with Procter & Gamble in Cincinnati, Ohio.
Jim Lohr (of CAS fame) has been appointed CEO of Columbus Molecular Software. Others in the management team at this company will be known to CSA members: Wayne Johnson, President and Vice President of Technology, Paul Blower, Chief Scientific Officer, Glenn Myatt, Vice President of Scientific Development, Kevin Cross, Director of Development, and Julie Roberts, Director of Marketing and Professional Services.