Chemical Informatics Letters

Volume 10, Issue 6; June 2005

Editor: Jonathan M Goodman

Chemistry 2000 [c2k]
Chemistry 2000 (c2k) is continuing to provide up to date information about chemistry departments, learned societies and chemistry journals around the world. Since the last report in June 2004 (Chem. Inf. Lett. 2004, 8, #6, 69). The database now lists 1857 departments from 138 countries. The United States of America has the most department (642), followed by France (103) and then Britain and Germany almost equal. The French academic system is not arranged in the same was as the British one, and this probably inflates the number of departments listed. There are now 3062 sites listed in total (departments, learned societies and journals), of which about twenty are inaccessible in a typical month. The database has grown by 2.4 % in the last year.

Google Scholar
How good is Google Scholar? A 2004 review has now been updated (June 2005). The reviews conclude that Google Scholar has some way to go before it can compete with subscription-based systems. The tool is probably more effective for disciplines with a tradition of open access publication than for subjects such as chemistry, where most content is available only by subscription.

PageRank algorithm
Google is based on the PageRank algorithm, which is described on a Stanford website. A patent application (20050071741 - for more details just type this number into Google) has now been submitted for this area. This can be used to help understand how Google ranks its lists. Google also provided information on this, on April 1st, 2002.

Accessibility of Crystal Structure Data
Small molecule crystal structure data can be most easily searched through the Cambridge Crystallographic Data Centre, which is available by subscription. However, the request-a-structure service is accessible from the CCDC home page, and does not require a fee. The Crystallography Open Database provides everything freely, but is smaller and does not have the same long tradition of curation. The COD is running a petition asking for (crystal data or powder patterns) to be available at no cost on the Web.

Nearly half a million acronyms are available through a recently announced search engine. Several languages are available, although English dominates. How useful is it to have a general search engine for acronyms? Can this work well for chemistry? A few simple synthetic chemistry acronyms (DMP, DMAP, DIBAL) were tested and all drew blanks. However, AM1 and DFT both were decoded correctly, although there were fourteen suggestions for the latter, only one of which was related to chemistry. A smaller, chemistry focussed index is also available at Indiana University. The same five test acronyms gave identical results, except for DFT, which only found thirteen suggestions - all except one of which were chemistry-focussed.

Scientometrics is the study or measurement of scientific texts and information. There are at least two journals in this area, Scientometrics and Cybermetrics, and also a society: International Society for Scientometrics and informetrics. Not content with the quantitative analysis of general scientific information, there has been a recent bibliometric analysis of scientometrics.

Open Knowledge Initiative
The Open Knowledge Initiative, which started at at MIT in 2001, develops ways of allowing learning management systems interact with enterprise systems. The website includes a list of e-learning products.

Scopus vs Web of Science
Scopus and the The Web of Science are both resources for searching the scholarly scientific literature. Scopus developed since 2002, was launched at the end of 2004. It is distinct from Scirus, a free scientific search engine also produced by Elsevier. The Web of Science, from Thomson, developed from the Science Citation Index. This comparison recommends buying both, if possible, but notes that Scopus appears to be slower to update its database.

Simon the Virtual Stockroom Manager
Sigma-Aldrich has developed a 'virtual stockroom' displaying its catalogue as a stockroom. The resources include substructure searching of chemicals in the catalog.

ACS Web Subscriptions
The ACS is changing its web subscription system for 2006. Instead of rolling access to the last four years and the current year, which meant that a year of access was lost each new calendar year, institutional subscribers to ACS web editions will have access from 1996 to the present. Articles published between 1879 and 1995 will be renamed the ACS Legacy Archives and will be available either for an annual fee or a one-off payment with a 'with a "nominal" annual fee'. The '"nominal"' fee is less than an annual subscription for most journals.

Google raises search word limit to 32
This will allow for more complicated search queries, which may be important for searching for specific chemical entities.

ACS and PubChem
CAS and the ACS are concerned about PubChem. Is a publicly-funded organisation competing with a commercial one? Is this a good use of tax-payers money? This argument may seem strange in the UK, where it is accepted that taxes are spent on hospitals and schools, and there are also commercial hospitals and schools, which do a good business by providing more than the state-funded alternatives, at a cost. However, a similar argument was used to close PubScience (Chem. Inf. Lett. 2001, 3, #1, and Chem. Inf. Lett. 2002, 5, #6, 3).

The ACS published a statement on the issue, and ACS President William F Carroll has written an open letter about the situation, in which he reaffirms that the 'increase and diffusion of chemical knowledge is the conerstone of the ACS mission and its Congressional Charter.' C & E News also has an article on the issue.

Does PubChem compete with CAS? According to an article in Nature, Bob Massie, the head of CAS, thinks that every chemical researcher understands that PubChem is a substitute for CAS. Many people have expressed views disagreeing with the ACS position, and pointed out that CAS, a tax-exempt organization, has received public funding to develop its database. A history of the development of CAS is available to subscribers to J. Chem. Inf. Comput. Sci. The University of California Office of Scholarly Communication has a page commenting on the issue. The Scholarly Publishing and Academic Resources Coalition (SPARC) supports PubChem. Discussions between the NIH and the ACS continued, but the argument then moved to Congress.

On 10th June, the House voted on the 2006 budget for the NIH. PubChem represents a tiny fraction of the NIH budget. A small increase was approved, but one that falls short of inflation. The report accompanying the bill did not ask the NIH to restrict the scope of PubChem, but "urges NIH to work with private sector providers to avoid unnecessary duplication and competition with private sector chemical databases." The ACS noted is was pleased with the report language. Supporters of PubChem see the report language as a victory for the NIH.

© 2005 J M Goodman, Cambridge
Cambridge Chemistry Home Page CIL Chemical Calculations Goodman Research Group Webmaster: J M Goodman