If you have any comments, please mail any of the principal authors of this document (rzepa@ic.ac.uk, p.murray-rust@mail.cryst.bbk.ac.uk, benw@chemistry.leeds.ac.uk) or send a comment to the discussion forum chemime@ic.ac.uk)

Contents.

1. Background and History to the Project
2. Why do we Need Chemical Internet Standards?
3. Chemical MIME Types included in the May - October 1995 IETF draft
4. New types Proposed since the Original IETF Draft
5. The Chemime Discussion list archives
6. Uptake of Chemical MIME Usage (Alta Vista Statistics)
7. A List of Projects Utilising Chemical MIME
8. Software which supports chemical MIME media types directly
9. Background articles and other information about chemical MIME

1. Background and History to the Project

(a) Electronic mail evolved from purely text based communication, to systems where "attachments" to the message could be included. For the first time, it became possible to include attachments which could have chemical content.
(b) A mechanism for document delivery called the World-Wide Web was introduced. Here too, a document could be associated with chemical content via a device known as a "hyperlink".

It became obvious during 1993 that the enormous potential for exchange of structured information that the Internet now offered would have to be matched by globally accepted standards for such information. At this stage, we considered that "chemical" information represented a potentially definable class of "media type" that had certain unique characteristics that would require particular handling by the recipient of such information. We started a project in January 1994 which we called "Chemical MIME". This was first announced during the Chemistry workshop at the First WWW International Conference, held at CERN in May 1994.

Our intention was to establish a set of standard "headers" that would unambiguously identify "chemical content" in Internet Electronic Mail message bodies and World-Wide Web documents. 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. 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 each expired after six months of discussion. In July 1995, we presented our case in person at the IETF meeting in Stockholm. Out of this meeting there emerged several conclusions.

• The IETF mechanisms for discussing and accepting such enhancements of the MIME standards were not functioning efficiently at that time.
• The IETF committees were focused largely on Electronic Mail handling and as a result, discussion centered on a relatively non-productive attempt at semantic distinction between "chemistry" as a "subject type" and "chemical" as a "media type". Here, the sociological question of whether all subject disciplines would rush to register their own discipline as a MIME type was the perceived danger
• Application of MIME to the World-Wide Web was viewed by some purists as departing from the original strict interpretation of the MIME standard, and the interaction between the two communities appeared strained and at the time unproductive.

2. Why do we Need Chemical Internet Standards?

Communities are usually suspicious of organisations that 'go it alone' in developing informatics tools and this often results in competing systems developed under a veils of secrecy; there is a built-in disadvantage to those outside the developer's organisation. This is evidenced by the flame-wars that are common on many public newsgroups and discussion groups at present.

Chemistry has inherited a large number of legacy approaches to information and whilst these are useful for some subsets of the discipline, we feel strongly that the tools of the future will only come through public debate and cooperation. Also, however, we need a variety of ideas and approaches so it is valuable to see which ones 'evolve' as well as being planned. If a subcommunity finds a useful de facto standard, that may well be worthy of recognition as such; but it may also need careful tailoring so that it interfaces well with other areas. This can only come through public activity.

Many tools developed by single organisations in a competitive situation are not future-proof; i.e. they may not be interpretable in a few years' time and the information may be effectively lost. This is particularly likely for binary files, but may also happen when numbers or abbreviations are used. Examples of this are common, and it would be presumptuous to guess which products were still supported in the future.

Terms are often given different semantics or used with default units. It is therefore important to agree with the rest of the community how a term is to be interpreted, and ideally there should be algorithms to convert to related terms.

Guidelines

General

• All developers of informatics tools commit to these guidelines; there should be no reason to depart from them without warning and discussion.
• Organisations should be prepared, where appropriate, to enter the standards creation process in a constructive manner.
• Chemical information exchanged in the public arena should follow these guidelines.
• All documentation required to interpret the syntax and semantics of the information in a document should be publicly accessible.
• Documents should be validatable against this documentation.
• Where possible, developers should make code available for reading and writing documents in a given format.
• Where possible, distributors of information should use the chemical/* MIME approach described below.
• New technology opens new ways of managing information, some of which may challenge or undermine the guidelines here. All developers should try to anticipate this by raising such issues with the community, and not pre-empt the communal view by inappropriate use of technology.

Chemical/* MIME

• The number of types should be strictly limited. (Usually each type requires specific software to read it, thus placing a burden on readers).
• MIME types should not be used or developed as a means of gaining a market monopoly; it is required that the description of a document's format be made public and reading/writing software is encouraged.
• New versions of exisiting types must not be introduced without prior discusssion and acceptance. This includes clear versioning procedures and detailed documentation of revisions.
• New subtypes will be discouraged if there is already a subtype which is capable of carrying that information. chemical/* should not be seen as simply a means of authenticating current legacy systems.
• The use of chemical/* should not be used as a means of adding apparent authority to an organisation's project or system if this has not already been discussed. The use of chemical/* in the public arena in ways not sanctioned is deprecated.
• Developers are urged to use markup languages where possible (e.g. CIF, ASN.1, CML) and to define the semantics of use (e.g. through glossaries of terms). These definitions should be public, and if possible equivalences to other definitions should be given.

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

4. New types Proposed since the Original IETF Draft

5. The Chemime Discussion list archives. During the Period November 1994 - present, a discussion list has been active for people to discuss various aspects of the proposals. Users can subscribe by sending a message to listserver@ic.ac.uk with the content
subscribe chemime your name
The discussions of this forum are archived under
http://www.ch.ic.ac.uk/hypermail/chemime/

6. Uptake of Chemical MIME Usage (Alta Vista Statistics)

7. A List of Projects Utilising Chemical MIME

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 Collections
14. Chemical and Drug Structure Display at the NIH

8. Software which supports chemical MIME media types directly

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

9. 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