Chemical Informatics Letters

Volume 9, Issue 5; November 2004

Editor: Jonathan M Goodman

Journal Colours
Journals are colour-coded according to their policies on author self-archiving. There are at least two schemes for doing this:
  • RoMEO (Rights Metadata for Open archiving)
    • White: self-archiving not allowed
    • Yellow: pre-print archiving permitted (pre-refereeing)
    • Blue: post-print archiving permitted (final draft, post-refereeing)
    • Green: pre-print and post-print archiving permitted
  • Hanard (Summary statistics)
    • Gray: no green light to self-archiving
    • Pale green: pre-print archiving permitted (pre-refereeing)
    • Bright green: post-print archiving permitted (final draft, post-refereeing)
All the journals listed in the Directory of Open Access Journals are gold, which means they are available on open-access, whereas articles in green journals are only openly available if the author chooses to make them so. Gold journals, therefore, are also green (both bright and pale) blue and yellow.

W3C Workshop on Semantic Web for Life Sciences
This workshop ran in October 2004 in Cambridge Massachusetts. One focus of interest was the LSID (Life sciences identifier), which addresses the need for a naming schema for biological entities. This is a more ambitious aim than naming chemical entities, but Inchi may play a role in this. An archive of submissions is available.

The PGM Database
The Platinum Group Metals Database is now live. This database comprises a large collection of physical, mechanical and chemical data for platinum, palladium, rhodium, iridium, osmium and ruthenium. Information is available on more than four hundred alloys and more than six hundred pages of related data.

Open clip art
This project aims to create an archive of clip art that can be freely used for any purpose. Currently, the archive is rather short of chemistry-related pictures, but a few are available.

RSS News Feeds for U.S. Pregrant Patent Publications
This news feeds covers the latest patent publications in the USA. There is also a Museum of Obscure Patents which profiles some surprising patent claims. It is clear that patents are not restricted by the laws of physics.

Enhanced Public Access to NIH Research Information
The NIH has sought public comments regarding NIH's plans to facilitate enhanced public access to NIH health related research information. The comment period is now closed. Background information is available. Donald E. Knuth has written on the crisis in scientific publishing (PDF). According to the Budapest Open Access Initiative "an old tradition and a new technology have converged to make possible an unprecedented public good".

Notes on Molecular Orbital Calculations
The text book Notes on Molecular Orbital Calculations by John D. Roberts is now on the web as a PDF file. The book was published in 1961.

CrossRef is a collaborative, cross-publisher reference linking service that turns citations into hyperlinks, allowing researchers to navigate online literature at the article level. A group of twenty nine leading journal publishers are participating in a CrossRef Search Pilot, including the American Physical Society, Annual Reviews, Institute of Physics, IUCR, Nature, PNAS, Wiley and Oxford University Press. *Google(tm) technology* CrossRef Search has been developed by CrossRef in partnership with Google.

Open Source mathematics packages
There are many commercial mathematics packages, including Maple, Matlab and Mathematica. Open source alternatives include Maxima, Octave, Axiom, Yacas, SciLab and JACAL. There are also lower-level packages available.

Many databases of Material Safety Data Sheets are available on-line, and some of these are free. Most have disclaimers about the limited liability of the data providers should the information turn out to be inaccurate.

MedLibraryAlert is an automated search engine that scans daily for your customized updates in the PubMed and MEDLINE databases and automatically e-mails you the results.

Applications of Cheminformatics and Chemical Modelling to Drug Discovery
This conference ran in November, and information on the talks is available on-line.

© 2004 J M Goodman, Cambridge
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