Chemical Informatics Letters

Volume 11, Issue 4; October 2005

Editor: Jonathan M Goodman

Citations to internet resources
Scientific papers may well have references to internet resources as well as to traditionally published papers. Sometimes these references are given simply as a URL. This is a pointer to a resource which may be transient, so it seems inappropriate to provide less information than in a traditional citation.

Most publishers require a list of authors, the name, year, volume and pages of the paper, for citations to journals, and this information contains some redundancy. It is usually possible to find the paper if there is a minor typographical error, or even several minor errors, in the citation. Even if the journal information is completely erroneous, the list of authors may be enough to identify the publication.

Citation by a single URL provides much less than this. An error in a single letter may make the resource hard or impossible to identify. Websites are not archived by national institutions, as printed journals are.

The ACS Journal of Chemical Education recommends listing the author, the title of the site, the URL and the date accessed. The American Psychological Association has similar recommendations. The ACS guidelines do not mention the issue in this summary of recommendations.

In order to help ensuer that the information in the URL will be available for as long as possible, it would be useful to give even more information. An improved format would be:

  • Author(s)
  • Institution
  • Section of Institution
  • Title of site
  • URL
  • date of access
If the website has disappeared when a reader tries to access it, this format provides several lines of enquiry. A search for an author may find many people, but a search for an author linked with an institution will probably be more successful. For large companies or universities, information about the role of the author within the organisation will also be useful. An academic might have moved the resource on moving institution. A company might maintain a resource with different people.

This form of citation might take slightly more space than a citation for a traditional journal, but this reflects the lower longevity and long-term accessibility of websites than journals. Following this recommendation should be a dramatic improvement on simply citing a plain URL.

IUPAC is continuing to develop Joint Committee on Atomic and Molecular Physical Data Exchange (JCAMP-DX) protocols, and the latest provisional recommendations are now available.

Wellcome Trust position on open access
The Wellcome Trust updated its position statement on open access in September 2005. It supports unrestricted access to the published output of research as a fundamental part of its charitable mission and a public benefit to be encouraged wherever possible.

Website access for disabled people
This summary of UK law from the RNIB explains the legal requirements for making websites accessible to disabled people. The Sydney Olympics Organising Committee was fined for not fulfilling these obligations. The RNIB recommend aiming for AA compliance (passing priority one and priority two checkpoints), as defined by the W3C. This can be checked using tools such as WebXACT.

German Conference on Chemoinformatics will be held in Goslar, Germany, November 13-15, 2005. It is organized by the Chemistry-Information-Computers (CIC) division of the German Chemical Society.
  • Chemoinformatics and Drug Development
  • Chemical Information Systems and Scientific Publishing
  • Computational/Theoretical Chemistry
  • eTeaching/eLearning

Chemoinformatics in Europe: Research and Teaching will be held in Obernai (near Strasbourg), France, 29 May - 1 June 2006

  • Encoding chemical structures (safe exchange of information, > descriptors, fingerprints, phramacophores, .)
  • Databases and data sources.
  • Property predictions (ADME, environmental related applications).
  • "In silico" design of new compounds (virtual combinatorial libraries, similarity search).
  • Drug design: Linking chemo- and bio-informatics.
  • Teaching: chemoinformatics in graduate and undergraduate curricula.

Digital Chemistry
Barnard Chemical Information is now Digital Chemistry, which was started on 20th September 2005 by Julian Hayward, the Managing Director, and John Barnard, Tony Cook, Geoff Downs, and Matthew Wright The company's goals are to deliver sophisticated software tools and services which address the cheminformatics needs of researchers within the pharmaceutical and related industries. Initial products will be based on the well-known BCI Toolkit and will include new web services.

world standards
As before (Chem. Inf. Lett. 2003, 7, #3, 31), the World Standards Day will be celebrated by the ISO on Friday 14th October, 2005. In 2004, the US NIST followed the ISO's lead on the date. The American National Standards Institute (ANSI), however, is celebrating a world standards week, from October 3rd - 7th, and celebrates World Standards Day on October 6th.

Chinese data
How important is data from China? The Baidu database is a success with third quarter profits trebling, and Chinese databases are becoming available.

Public interest benchmarks for intellectual property
The Royal Society of Arts has launched the Adelphi Charter on Creativity, Innovation and Intellectual Property calling for a public interest test should be applied before granting intellectual property rights. This approach might effect companies that claim patents on XML or other standards. The Economist has recently discussed issues with intellectual property protection. The US patent office, however, has removed the requirement for business patents to be Technological Arts, which may expand the opportunities for patenting procedures.

Control of the internet
Who controls the internet? Currently a US organisation ICANN is the closest thing to a ruling body, although there are other important players, including VeriSign which will control the '.com' domain until 2012. Should other nations, or the UN be involved? There is pressure to widen control of the internet beyond the US. Some US senators and representatives disagree. The current system, however, is imperfect.

Are institutional repositories taking over the world?
A JIBS User Group seminar has addressed this question, as UK universities and research councils are establishing institutional repositories. Are these repositories the real answer to making research output more accessible? The speakers from academia and funding bodies were clear that repositories are important and will become much more so. The commercial publishers were more concerned about the drawbacks of these developments.

PubChem now has over five and a quarter million structures. William Carroll, the president of the ACS has written a third open letter about the relationship between PubChem and the ACS (for the second letter, see Chem. Inf. Lett. 2005, 11, #3, 25). Unfortunately, there was no time to discuss the issue of PubChem at the Open Meeting for the Joint Board-Council Committees on Chemical Abstracts Service at the ACS August 2005 National Meeting, and this was noted by Science (DOI: 10.1126/science.309.5743.1987e).

© 2005 J M Goodman, Cambridge
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