Guidelines for
the use of the Internet by IUPAC bodies
(Technical Report)
A.N. Davies,
S.R. Heller and J. W. Jost
ABSTRACT
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INTERNET HOMEPAGE DESIGN - SOME DO'S AND
DON'TS
Basic Principles
It is important not to lose sight of the reason for the presence of
a particular IUPAC body on the Internet. The delivery of information
is either to a restricted group of people or to a wider audience than
would usually be the case. Whichever is the case, the presence of the
required information should be clear and retrieval easy.
Some Do's and Don'ts
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RECOMMENDATION TO USE CHEMICAL MULTIPURPOSE
INTERNET MAIL EXTENSIONS ON IUPAC INTERNET WEB SITES
A CPEP working party is finalizing a publication defining Multipurpose
Internet Mail Extensions (MIME) types for chemistry and these should
be implemented wherever possible on IUPAC Internet Web Sites.
A brief overview of the current status and a table of the data file
extensions covered is given below but please refer to the web site at
the following URL: http://www.ch.ic.ac.uk/chemime/
for the latest information.
Multipurpose Internet Mail Extensions
In order to identify different types of data the Internet Engineering
Task Force (IETF) has approved MIME protocols. MIME types are used to
identify content of files or parts of files on the internet. MIME types
consist of a primary and sub-type. The primary type defines the general
type of data in the file, while the sub-type defines the exact file
format.
Examples of primary file types include text, image, audio and video.
A couple of examples of MIME types are video/quicktime for QuickTime
movies and audio/x-wav for wave audio files.
Chemical MIME
A proposal to include common scientific file formats in chemistry as
a primary MIME type 'chemical' has been pioneered by Henry Rzepa of
Imperial College, London, UK ([email protected])
and his colleagues and adopted as a topic for a IUPAC working party.*
A draft table of some of the chemical MIME types is given in table 1
below.
What this basically means is that an internet aware software should
recognize a file called mydata.gau as a gaussian input file. And a file
called myspectrum.dx should be recognized as a JCAMP-DX spectrum and
treated as such. The 'x-' refers to the MIME type as being experimental.
This will be dropped when adopted by the IETF.
Table 1. Suggested internet chemical mime types.
| Primary/sub-type |
Suggested qualifier(s) |
| chemical/x-cxf |
cxf |
| chemical/x-mif |
mif |
| chemical/x-pdb |
pdb |
| chemical/x-cif |
cif |
| chemical/x-mdl-molfile |
mol |
| chemical/x-mdl-sdfile |
sdf |
| chemical/x-mdl-rdfile |
rdf |
| chemical/x-mdl-rxnfile |
rxn |
| chemical/x-embl-dl-nucleotide |
emb, embl |
| chemical/x-genbank |
gen |
| chemical/x-ncbi-asn1 |
asn |
| chemical/x-gcg8-sequence |
gcg |
| chemical/x-daylight-smiles |
smi |
| chemical/x-rosdal |
ros |
| chemical/x-macromodel-input |
mmd, mmod |
| chemical/x-mopac-input |
mop |
| chemical/x-gaussian-input |
gau |
| chemical/x-jcamp-dx |
dx, jdx |
| chemical/x-kinemage |
kin |
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CHEMICAL MARKUP LANGUAGE
It has been suggested that a short description of the Chemical Markup
Language (CML) would also be appropriate here although its implementation
on IUPAC internet sites cannot currently be recommended due to a lack
of available software support. This is a developing field which may
have relevance in the future for reporting chemistry on the internet
and IUPAC bodies should be aware of its existence, especially in case
of any overlap with current or future projects.
CML is an application of the extensible markup language (XML) and is
being developed to contain chemical information within electronic documents.
Currently work is concentrated on chemical structure information but
IUPAC bodies should watch the web site at: http://www.xml-cml.org/
for developments. There is also a large amount of background information
to this project available here.
Many large mainstream development projects on the Internet involve
the use of XML owing to the need for and value in electronic commerce.
It is therefore only a matter of time before XML, and its chemical child,
CML, will find widespread use see: http://www.xml.org/
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GLOSSARY
CML Chemical Markup Language
CPEP Committee on Printed and Electronic Publications
DTD Document Type Definition is the formal definition of the
elements, structures, and rules for marking up a given type of SGML
document. You can store a DTD at the beginning of the document or externally
in a separate file.
HTML Hypertext Markup Language
IETF Internet Engineering Task Force
MIME Multipurpose Internet Mail Extensions
PDF Adobe Portable Document Format
SGML Standard Generalized Markup Language is an international
standard (ISO 8879) published in 1986.
WWW World Wide Web
XML Extensible Markup Language
