The Chemical MIME Project: A Working Example

Henry S. Rzepa,^(a) Wyn Locke,^(a) Peter-Murray Rust,^(b) Benjamin Whitaker^(c)

August, 1996

Contents.

1. Background and History to the Project
2. Chemical MIME Types included in the May - October 1995 IETF draft
3. New types Proposed since the Original IETF Draft
4. Uptake of Chemical MIME Usage (Alta Vista Statistics)
5. A List of Projects Utilising Chemical MIME
6. Software which supports chemical MIME media types directly
7. A Working Example Utilising Chime
8. Background articles and other information about chemical MIME

1. Background and History to the Project

This project started in January 1994, and was first announced during the Chemistry workshop at the First WWW International Conference, held at CERN in May 1994.

The intention of the project was to establish a set of standard file "headers" that would unambiguously identify "chemical content" in Internet-based transactions such as electronic mail, and more recently the World-Wide Web. The latter in particular allows chemical content to be integrated into document delivery using the Hyperlink concept, a concept around which this very CD-ROM product is built. We originally identified a small number of relatively standard file types containing chemical information, which together with the addition of a chemical MIME header, would enable the content to be sensibly processed by the recipient of the information. Essentially, this was an addition to the MIME standard which had been proposed and ratified via a body called the IETF (Internet Engineering Task Force) in 1993. Since chemical MIME was envisaged as primarily an Internet Standard, we initially approached the IETF with our proposal, via a discussion document called an Internet Draft. The first version of this was published during May-October 1994, and a second revised version during April-September 1995. These two proposals resulted widespread adopted throughout the community. Currently, the focus is on acting via the IUPAC organisation for chemical standards. A "home" page is located at
http://www.ch.ic.ac.uk/chemime/
where the second Internet draft, up to date information, guidelines for standards and other background information is available. A discussion list is archived under
http://www.ch.ic.ac.uk/hypermail/chemime/ Users can subscribe by sending a message to listserver@ic.ac.uk with the content
subscribe chemime your name

The remainder of this article will focus on various sources of information and pointers to working examples of chemical MIME. One specific illustration of a small molecule database will be included here.

2. Chemical MIME Types included in the May - October 1995 draft as part of a "standards track" process.

The following list of chemical MIME types forms the main body of the IETF Internet draft valid during the period May - October 1995.

3. New types Proposed for Inclusion since the Original IETF Draft

4. Uptake of Chemical MIME (Alta Vista Statistics)

The following url fragments represent Alta Vista (http://www.altavista.digital.com/) searches using the Advanced Query feature after the keyword "link:" (e.g. link:www.ch.ic.ac.uk). It can report an estimate or actual count of the number of pages pointing to a particular link. This search was performed on July 23, 1996.

5. A Partial List of Projects Utilising Chemical MIME

This list (and others in this document) point to internet based documents. To access them, you will have to have an active Internet connection on your computer.

1. Original Examples at Imperial and Leeds Universities.
2. NCBI Project at NIH
3. Brookhaven Protein Databank
4. Molecules R Us facility at the NIH
5. Protein Science E-Journal
6. Journal of Molecular Modelling
7. Nature Science Journal
8. Electronic Conferences in Trends in Organic Chemistry: ECTOC-1 and ECHET96
9. Klotho Project at WUSTL.
10. Project CORINA at Erlangen University
11. ChemFinder Project by CambridgeSoft
12. Demos by Daylight Software.
13. Molecule-of-the-Month Collection
14. Chemical and Drug Structure Display at the NIH
15. A Molecular Hyperglossary: Organic Molecular information in Hypermedia Form

6. Software which supports chemical MIME media types directly

1. Chemscape Chime by MDLI: A Netscape plug-in.

7. A Working Example which Utilises the Chime Plug-in

The purpose of this working example is simply to show how chemical MIME can serve to integrate chemical content within a Hypertext document. We do NOT address issues such as "hyperglossary" construction, indexing, database maintenance and user contributions, and integration of e.g. analytical data and so forth. All these themes are the subject of current activity, both in our laboratories, and elsewhere. If you are interested, see the chemical MIME home page for current information.

8. Background articles and other information about chemical MIME.

1. Antony N. Davies, "Internet Chemical MIME", Spectroscopy Europe, 1996, 8(1), 42.
2. H. S. Rzepa, B. J. Whitaker and M. J. Winter, J. Chem. Soc., Chem. Commun., 1994, 1907.
3. O. Casher, G. Chandramohan, M. Hargreaves, C. Leach, P. Murray-Rust, R. Sayle, H. S. Rzepa and B. J. Whitaker, J. Chem. Soc., Perkin Trans 2, 1995, 7.
4. S. M. Bachrach, P. Murray-Rust, H. S. Rzepa and B. J. Whitaker, Network Science, March, 1996.
5. Maryilyn Dunker, Indiana University, Chemical Information Viewers: A Collection of programs that can be used with chemical MIME datasets.
6. Scott Nelson, Lawrence Livermore National Laboratory, A test page for checking your MIME Configurations

© H. S. Rzepa, W. Locke, P. Murray-Rust, B. J. Whitaker. 1996.