The Application of Chemical Multipurpose Internet Mail Extensions
(Chemical MIME) Internet Standards to Electronic Mail and World-Wide
Web information exchange
Henry S. Rzepa,* a Peter Murray-Rustb and Benjamin J. Whitakerc
aDepartment of Chemistry, Imperial College, London, SW7
2AY; E-mail: rzepa@ic.ac.uk
bVirtual School of Molecular Science, Department of Pharmacy, University of Nottingham, Nottingham.
cSchool of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
Summary: The proposal and subsequent global use of an Internet standard
based on chemical primary Multipurpose Internet Mail Extensions (chemical
MIME) media type is reviewed. Examples of the configuration of this standard for
use with Internet based electronic mail and World-Wide Web clients are shown. The
long term objectives of the integration and inter-operability of chemical
information across the boundaries of Internet-based electronic journals,
conferences, virtual courses, databases, modelling and newly emerging information
handling and modelling tools are set out. We believe that one way forward is by concentrating on
more finely grained chemical information components, using generic tools based on
XML (eXtensible markup language) and its support in chemistry via CML (chemical
markup language).
Introduction
The development of Internet-based document and information delivery systems
during the last four years has been rapid,1 with a particular focus on
the creation and delivery of chemically oriented World-Wide Web (WWW) based
documents. This has in turn introduced to many concepts such as the use of
structured and interlinked document collections specified by languages such as
HTML (Hypertext Markup Language). This review will focus on one aspect of this
revolution, the chemical application of an Internet standard known as MIME
(Multipurpose Internet Mail Extensions) to the World-Wide Web and electronic mail
(email) handling. We will discuss how a transparent integration of e-mail and
WWW based exchanges of chemical information with chemical modelling and
information handling tools can be achieved using this mechanism, and present some ideas
for how we believe development beyond the MIME mechanism should proceed.
Multipurpose Internet Mail Extensions (MIME)
Despite the attention given to the development of the World-Wide Web, email
arguably remains the more frequently used mechanism for electronic information
exchange by scientists. Email is often regarded however as a temporary and
informal communication medium, not well suited for the precisely defined exchange
of structured information in a subject area such as chemistry. Its increasing
adoption by chemists over the last 15 years or so has concentrated on the
exchange of loosely structured messages based on ASCII text, which rarely if ever
contain any explicit markup (chemical or otherwise) or easily machine-parsable
semantics. In 1992, Borenstein and Freed recognised that the absence of a
structuring mechanism was a serious deficiency in email, and proposed a MIME
protocol2 for achieving this, which was subsequently adopted as an
Internet standard by the Internet Engineering Task Force (IETF). MIME defined how
a specified document could be associated with an email message body, and how it
should be handled upon receipt by a suitable client program.
The MIME protocol comprises two components. The first defines how binary computer
files must be encoded to achieve so-called 7-bit transparency for compatibility
with most text-based Internet mail routers (so-called base-64 encoding) and is
not discussed further here. The second component defines a standard mechanism
whereby computer files can be associated with an email message via
appropriate headers and delimiters, and allows the appropriate processing of such
enclosures by mail handling programs in the possession of the email recipient.
Borenstein and Freed envisaged a multi-component structure to an email message,
in which the first compoent would comprise the informal and unstructured message
body, whilst subsequent components could include structured and well defined data
files which could be handled by programs other than the basic email client. These
components were to be known as media types, and in the original proposal, a
number of such primary media types were defined, each sufficiently generic that
default handling schemes could, at least in principle, be applied their content.
Thus it is clearly apparent that different processing and display mechanisms are
required for the primary defined media types TEXT, IMAGE, AUDIO and VIDEO. The
APPLICATION media type has less well defined boundaries, and tends to be used for
the resolution of proprietary data types defined by the developers of software
applications. A MULTIPART type was defined to allow the multi-component
collection to be created. Most recently, the MODEL primary type has been added to
allow the processing of numerical and symbolic data for three and higher
dimensional models. The MIME protocol also defines a secondary media type header
which allows the definition of more specific information on the expected content
of a message attachment. For example, image/jpeg defines a bit-mapped
image file in the specific standard format defined by the Joint Photographic
Experts Group. The two level mechanism also allows a separate name space to be
defined for each primary media type.
In early 1994, we considered3 how the MIME mechanism could be used to
allow the exchange of standard (ratified or de facto) chemical data types
using either email mechanisms or the then emerging medium of the World-Wide Web.
Whilst many of the so-called chemical legacy formats are not always fully
documented and specified in the literature, and some such as the Brookhaven
protein databank format have spawned a number of variants and mutations over the
years, we nevertheless felt that the concept of "chemical" as a new
primary MIME media type would have a number of distinct advantages. Firstly, it
was apparent that none of the original or subsequently proposed primary media
types would allow any sensible component of default handling of implicit chemical
information contained in a data file. Secondly, the MIME mechanism operates by
assigning three or four letter filename extensions to the data files, and hence
each primary type must operate within a closely regulated name space convention.
By assigning a primary type CHEMICAL, this name space could be delegated to the
community that defines the media type, rather than the less manageable Internet
community as a whole. Finally, the adoption of CHEMICAL as a primary media type
was seen as the first step in achieving a closer integration between the exchange
of chemical information via document server systems such as the World-Wide
Web and the exchange of the same data types using electronic mail mechanisms.
Chemical MIME Types
In the four years or more that have elapsed since the original proposal for
chemical MIME types, their use via the World-Wide Web has become common.
Listed in Table 1 are the chemical MIME types which as far as we are aware have
actually been used to a greater or less extent during this period,4
almost always in the context of the WWW rather than email, together with
suggestions for appropriate programs capable of processing and/or displaying the
associated chemical content. In many cases, such programs can also serve as the
starting basis for molecular modelling applications and database
queries,5 electronic journal6 and conference
browsing,7 and numerous other applications. In this sense, chemical
MIME has served as the infra-structure which has started to
catalyse the development of a new generation of Internet-based chemistry tools.1
Chemical MIME types can be applied in three different contexts.
- MIME types which have been configured for WWW (HTTP) document
servers operating on an Internet-wide scale, i.e. associated with
publically published documents. Such configuration is normally accomplished
via a privileged account, and the use of standard types is essential so
that different servers allow documents of the same type to be access by remote
users in an identical manner. The precise manner in which any individual server
is configured may differ, but a typical entry in a "mime.types"
configuration file might appear as follows
chemical/x-mdl-molfile mol
This simply serves as an instruction to the server that any document associated
with a filename extension .mol is issued upon request with a document
header containing a specification of the MIME type as
chemical/x-mdl-molfile.
- In an Intranet environment, i.e. one associated with documents which
are only accessible in a controlled private environment, it is common to define
additional non-standard MIME types for local use. The responsibility for
coordinating the use of such private types lies entirely within the organisation.
This is to be contrasted with the use of public types, for which articles such as
this serve to co-ordinate globally.
- The configuration of client-side software for MIME is accomplished quite
differently from that for servers. A number of the MIME types listed in Table 1
in fact derive from so-called "plug-ins"8 which can be used to enhance
the basic capability of a World-Wide Web browser and/or email software, and
which removes much of the burden of installation of the MIME mechanism from the
user. An alternative is for the user to pro-actively specify that a designated
"helper" program be used to resolve the chemical document. In some
cases, such as the Netscape Communicator program, the same software package can
be used for handling both WWW documents or email messages, and the user's
configuration for both is handled via a single plug-in installation
process. For other programs, such as stand-alone email clients, the user will
have to do the configuration process explicitly.
Application of chemical MIME using Email and WWW-based Client Software
An overview of how MIME can be applied to the transport of specific chemical data
types using the two principle Internet mechanisms of email and the WWW is
illustrated in Scheme 1. Four distinct
data storage areas can be identified on any individual user's computer file system. These
include the general user file area, an area specified by the user for receipt of
email attachments, a temporary area associated with the WWW-client cache if
specified by the user and finally a WWW document collection area if the user has
specified a personal WWW-server or has access to a central WWW server. Chemical
MIME at least in part provides one mechanism for achieving self-consistency in
the handling of chemical files across these file areas. To illustrate this
process, some specific examples of how MIME headers are added are shown below.
Examples of chemical MIME Headers
A WWW client which makes a HTTP (Hypertext transfer protocol) GET request to a WWW server
configured to support chemical MIME types results in the following
response;
GET /atp.pdb http/1.0
HTTP 200 Document follows
Date: Mon, 30 Mar 1998 13:54:40 GMT
Server: NCSA/1.5.2
Last-modified: Fri, 19 Aug 1994 15:46:58 GMT
Content-type: chemical/x-pdb
Content-length: 2916
The received MIME type is resolved via a suitable internal look-up table
available to the WWW client which maps the MIME types to an application program
or plug-in capable of parsing, processing and/or displaying the chemical data, in
this example a simple PDB format file.
An email client which makes a SMTP (Simple mail transfer protocol)
request to an email relay will receive the following related set of headers;
Mime-Version: 1.0
Content-Type: multipart/mixed; boundary="===_-1320854989==_===="
Date: Mon, 30 Mar 1998 15:18:23 +0100
To: recipient@somewhere
From: "Sender"
Subject: Illustration of chemical MIME headers
Status: O
--====_-1320854989==_====
Content-Type: text/plain; charset="us-ascii"
This message contains a chemical attachment
--====_-1320854988==_D====
Content-Type: chemical/x-pdb; name="ferrocene.pdb"
Content-Disposition: attachment; filename="ferrocene.pdb"
Content-Transfer-Encoding: base64
Q09NUE5EICAgIGZlcnJvY2VuZS5...
The email program can be used to extract the appropriate component of the
multipart message attachment (in this example separated by the unique string
1320854989), decoding it if necessary from the base-64 scheme
adopted to ensure 7-bit transparency of the file, and to save the file to the
user's filebase in a segregated area identified for such attachments. If the user
wishes to view the contents of the attachment, a mapping between the MIME types
and a suitable application program can be achieved either via a specific look-up
table associated with the email client, or by invoking a WWW-client to perform
this task.
Application of chemical MIME to add value to Document Exchange
During the last four years, it has become increasingly common place to attach
documents of various types to text email messages via the implicit use of
MIME protocols. The most common types of attached documents tend to be either
bit-mapped images (MIME type image/gif or image/jpeg) or 7-bit
encodings of binary word-processor documents (e.g. MIME type
application/msword). The use of such non-chemical MIME types almost
certainly means that any chemical information contained in the documents will
inevitably degrade. Recovering chemical data from such formats into an active and
reusable form firstly requires knowledge that the document actually does contain
chemical information, and secondly it requires information about the likely
structure of that information. It is precisely this missing information which the
explicit use of the chemical MIME protocol will provide, via the primary and
secondary types. To highlight the advantages of this still infrequently used
method of attachment, we include here specific details of how the
mechanism can be used for three typical email environments. These examples should also
serve as prototypes for setting up other commonly used email handling systems
that support MIME.
Example 1. Chemical MIME Handling using the Unix Pine email Client
This mechanism in fact constitutes the original Unix-based method
developed by Borenstein and Freed2 to test their MIME proposal. For
outgoing email messages, the chemical MIME headers are added according to a look-up
table present on the users home directory called .mime.types. A typical
entry is as follows
chemical/x-pdb pdb
For incoming email messages, the association of a document MIME type with a
program suitable for its resolution is accomplished using a look-up table
present on the users home directory called .mailcap
chemical/x-pdb; netscape %s
Example 2. Chemical MIME Handling using the Eudora email Client.
Eudora is a stand-alone email client available for Windows and MacOS operating
systems. This program allows hyperlink-style resolution of an enclosed message
attachment by a program designated by the recipient. Unlike a WWW client such as
Netscape, where the chemical MIME types are simply defined on all three major
platforms by adding an appropriate plug-in (Table 1), the configuration of
Eudora both for sending and receiving chemical attachments is operating system
dependent. On MacOS, a chemical MIME plug-in10 is placed in the same
folder as the Eudora application. To achieve the equivalent functionality on
Windows 95/98/NT, the file Eudora.ini present in the application folder must have
an entry of the following type added for each of the MIME types required;
both=pdb,pdb,TEXT,chemical,x-pdb
When receiving email messages which include a chemical MIME
attachment, users will have to specify an appropriate program to
resolve the attachment. This has to be done only once for each MIME
type. This can be by e.g. adding the filename
extension appropriate for each type of MIME attachment via the Windows
Registry file, or by specifying this within the email program.
Example 3. Chemical MIME Handling using Netscape Communicator
illustrating Integration of WWW and email Clients.
Netscape Communicator (at the time of writing at version 4.05) represents,
inter alia, an integrated WWW client (Navigator) and an email client
(Messenger). Configuration of chemical MIME types can be accomplished in two
generic ways. The simplest is via the Netscape plug-in mechanism. Several
plug-ins offer support for chemical MIME types (Table 1) and their installation
automatically configures both the WWW and email client components of Netscape
with the MIME types supported by the plug-in. This automatic mechanism can also
be over-ridden by a user configuration option which will allow additionally
defined or redefined chemical MIME types to be associated with other specific
programs for processing any individual data type.
In operation, the application of chemical MIME is almost entirely transparent to
the user. Any chemical data set defined by the MIME types which is received by
the WWW client Navigator will be displayed as either an in-lined model using an
appropriate chemical plug-in or in an external window using a user specified
program. We note here that all incoming data files can also be saved in the
Netscape client local disk cache, where in principle the chemical MIME labelling
could be used to create a persistently stored chemical database using suitable
software. A chemical attachment received by the email client Messenger can be
passed to the browser window for resolution with the MIME headers being processed
internally between Messenger and Navigator, or externally via the file
system and the filename extensions.
When Netscape Messenger is used to send an chemical email attachment to an email
relay, the user selects the appropriate filename, and Messenger will insert the
appropriate MIME headers by appropriately mapping the filename extensions. This
mapping is as before defined either via the plug-in support, or by explicit
declaration in the configuration.
The Netscape implementation is the only one that works transparently across Unix,
Windows and MacOS client-based operating systems. One test of operating system
transparency is for the test originator to attach a simple chemical co-ordinate
file8 to an email message and to send this to a remote recipient. The
entire process is then reversed by the recipient retrieving the received file
from their email attachments folder (Scheme 1) and sending it back to the
original sender. The process will be regarded as successful if the test file
received back is identical with the originally sent file, and can be suitably and
automatically resolved by both parties via an appropriate 3D coordinate
display program or plug-in using either email or WWW clients.
Example 4. Using chemical MIME handling to add value to an Internet Chemical Database.
The fourth example illustrates how chemical MIME can be applied
outside an email environment. The application of chemical MIME in areas such as electronic conferences and
journals has been amply documented elsewhere.1 This example
illustrates how MIME can be used to enhance a database of degradation schemes
for atmospherically significant volatile organic compounds (VOCs).11
In the Leeds Master Chemical Mechanism (MCM), simplified degradation schemes for
120 such VOCs have been constructed. The information contained in the database
is however difficult to navigate because the degradation products and
intermediates of one reaction may be reagents in an other. In the Leeds scheme
the organic component of the MCM contains in the region of 7000 reactions and
2500 chemical species. Such a complex web of information is best presented as a
hypertext document, within which the chemical structures are represented using
the SMILES notation (Table 1). The SMILES string can be interpreted by spawning
an external viewer as a helper application (Table 1) using the chemical MIME
mechanism, thus achieving a linkage between structural and kinetic information in
the database. Furthermore the chemical structural information contained within
the database remains active and reusable in other contexts, for example
substructure searching of other databases.
Beyond chemical MIME: Chemical Information Components
Chemical MIME was an experiment in the sense of initiating activity and
collecting data. In the spirit of the WWW, we had few preconceptions about what
would happen, and our original choice of chemical MIME types was in part designed
to stimulate development. A retrospective assessment is that the major use has
been for distributing simple chemical information components, or what we have
termed "legacy formats" deriving from older databases or program input
files, rather than for multi-component documents such as envisaged in newer
structured formats such as CIF, ASN.1 etc. Given the direction of the World-Wide
Web community, this is entirely reasonable and has given an excellent platform
for the next stage, which we outline here.
Most chemical information is a complex mixture of different components
and disciplines. For example, a "compound data card" usually consists
of:
- a molecular connection table
- citations/references/authorship
- physicochemical properties
- (possibly) graphics, spectra
- links to other information.
Of these only the first is specifically "chemical", and the others are
found in many other disciplines.
Starting in 1997, the W3C (World Wide Web Consortium)12 has been
developing a set of generic, discipline-independent protocols for the
transmission of documents. These protocols allow for the description,
encapsulation and inter-operability of "information objects" from
specific disciplines. For example, in a cooperative international forum including
support from the American Mathematical Society, a protocol for WWW-based
transmission of "mathematics" has been developed (MathML). This is
specifically designed so that it will interoperate with existing (HTML) and
emerging (XML) protocols. In a similar fashion, a W3C group is devising a
protocol for meta data (RDF, or Resource definition framework and DC, or Dublin
Core) which will allow simple and complex descriptions of the role and content of
documents. For example, the authorship, authenticity, location, ownership and
related attributed of a document can be described in RDF/DC framework. We
believe that it should always be appropriate to examine these generic approaches
before devising yet another proprietary format.
What the W3C has also made clear is that there are generic operations which apply
to any sort of document and that these are often not trivial. They include:
- authoring
- editing
- validation
- parsing
- rendering
- merging
- filtering
- searching
- transformation
To develop tools for each of these from scratch is expensive and error-prone. The
approach taken by the W3C is resulting in generic tools which apply to all
document types, and we shall outline the general principles.
A document (which is not limited to text and can contain or consist of
non-textual objects) is composed of smaller components. It contains sequence
information (the order of the components can matter) and structure (one component
can contain another). Thus a book consists of chapters in sequence; the chapters
can contain sections, which contain subsections. In a similar way we can we could
describe a labNoteBook as containing compoundDataCards and text. The
compoundDataCards can contain molecules, spectra, etc. The other important
concept is the identification of the components themselves through markup.
The markup shows the limits of a component, and gives a handle (tag) by which it
can be identified or linked to semantic resources.
The W3C has now created a language (eXtensible Markup Language, XML)13
for managing general structured documents on the WWW. XML is formally a very
simple subset of SGML, but for those unfamiliar with SGML, it may help to think
of it as an abstraction of the HTML-approach. It is not a language, but a tool
for creating one's own language in such a way that it is compatible with existing
and future WWW technology. At time of writing (April 1998) it seems certain to be
a ubiquitous component of all major manufacturers' WWW tools.
The XML effort is currently tackling the problem of how to manage documents with
components from several domains. This has to address cases where the individual
markup languages have been developed in ignorance of each other. An example would
be a document containing text (HTML), maths (MathML) and chemistry (CML). The
solution to this will initially be through the use of namespaces which guarantee
that tags from the different domains will not clash.
It is clear, therefore, that a very important trend is towards multi-domain
documents using XML syntax. We believe that much information in molecular science
is ideally suited to such an approach, and suggest that additional means of
identifying chemical information will be required. In some cases this could be
the existing chemical MIME types (XML has a mechanism for encapsulating MIME),
but will increasingly use other methods based on XML.
A survey of a number of technical publications suggests that there are a
relatively small number of different abstractions of information components. For
example, although the content of an image could vary widely, the basic technology
to read and render it is domain-independent. The commonest components (with
existing technology) are:
- text (HTML)
- images (GIF, JPEG)
- structured graphics
- tables [*]
- graphs [*]
- numeric quantities with units [*]
- arrays and matrices [*]
- citations (RDF, Dublin Core)
- links (XLL)
- mathematics (MathML)
For components labelled [*] there are existing solutions but they are fragmented
and not yet developed for the WWW/XML. Note that many components which are
apparently chemistry-specific (e.g. spectra, schemes) are simply concrete
examples of these abstract types (e.g. a spectrum and an index of stock prices
can use identical technology). The challenge is semantic, how do we attach
meaning to the labels or other components? In a similar way, reaction schemes can
be described as molecular components embedded in a general semantic network.
A key feature of XML is the separation of syntax from semantics. Thus XML
guarantees that the document will be platform and software-independent. However,
when it "arrives at the reader" there must be a mechanism for adding
semantic information, e.g. what does MOL mean?. In many cases this is
supplied by styles sheets (e.g. formatting the document such that its
meaning becomes clearer) but for technical data additional processes are
required. Tags and attributes can be linked to glossaries. Thus
<ITEM CONVENTION="mmCIF"
TERM="_cell.length_a">23.4</ITEM>
can be linked to the International Union of Crystallography's mmCIF dictionary
for macromolecules.14 This defines the quantity as the cell length
(in Angstrom units by default). It will be a major advance if those with data
dictionaries can make them available electronically. The Virtual Hyperglossary
Technology15 has been developed as a prototype to provide XML-based
technology for such linking. Alternatively it is possible to link the document to
actions provided by software. One such method is with Java classes, which can be
specifically linked to given tags as in the JUMBO browser.16
The most challenging types of information to distribute are those that describe
the relation of one quantity to another. Sometimes this can be done by
containment (e.g. a spectrum and a molecule can be linked by being contained in a
compoundDataCard). But for more complex mapping we require either semantic
networks as in RDF or hypermedia(as in XLL. These provide ways of connecting
components in arbitrarily complex manners. Thus XLL could e.g. provide links from
functional groups to peaks in a spectrum.
If we accept that XML and related standards (XLL, XSL stylesheets, RDF, DC and
DOM or Document Object Model) will provide the generic capabilities then the
task facing chemistry becomes more clearly defined: to provide extensible markup
for chemistry-specific components and to analyse common relationships in
chemistry.
To this end a prototype XML language has been developed termed Chemical Markup
Language.17 This is provided as a starting point for the process of
supporting chemistry in XML. Current elementTypes or tags have been deliberately
kept simple:
- ATOM
- ATOMS (simplifies handling of large molecules)
- BOND
- BONDS
- ELECTRON
- FORMULA
These can be qualified with a small number of hard coded attributes (e.g. ELSYM,
X2, Y2, etc. for ATOM, ORDER, STER, etc. for BOND) Different conventions can be
set with a CONVENTION attribute. In this way most simple descriptions of
molecules can be captured. The contents of these can be arbitrarily complex and
could support, say, orbital components on atoms, quadrupoles, 13C shifts, etc.
Since much chemistry is solid-state we include CRYST, and for macromolecules
supply SEQUENCE and FEATURE. The key point is that XML has been developed in an
open collaborative process (which has included many companies which compete
vigorously in the markets). We believe this is appropriate for chemistry as well
and offer CML as a starting point for such a process.
Conclusion.
During the period 1970-1994, chemical applications of the Internet were largely
based on a set of generic file and text transmission protocols, such as terminal
(Telnet), file transfer (FTP), email transfer (SMTP) and document handling
systems (HTTP), methods where little explicit labelling and structuring of the
chemical content was available and where little inter-operability existed between
either the chemical content itself or with non-chemical content in other
disciplines.
During the period 1994-1998, mechanisms such as chemical MIME set the scene for
a convergence both within the chemical community and with other scientific areas,
bringing together applications such as electronic mail with database and
modelling tools, electronic conferences, journals, books and taught courses. In
the future, more finely grained mechanisms such as XML/CML will undoubtedly
enable further convergence to the point that the Internet will become a far
better and more powerful "resource discovery" tool for the chemical and
scientific communities.
Acknowledgements
Funding from the UK JISC e-Lib programme for the CLIC electronic journal
project, and the JISC JTAP programme for the VChemLab project is gratefully
acknowledged.
Notes and References
- H. S. Rzepa, P. Murray-Rust and B. J. Whitaker, Chem. Soc.
Revs, 1997, 1-10.
- N. Borenstein and N. Freed, "MIME (Multipurpose Internet
Mail Extensions) Part One: Mechanisms for Specifying and Describing
the Format of Internet Message Bodies", Internet RFC 1521,
Bellcore, Innosoft, September 1993.
- H. S. Rzepa, B. J. Whitaker and M. J. Winter, J.
Chem. Soc., Chem. Commun., 1994, 1907; H. S. Rzepa,
Comp. Networks and ISDN Systems, 1994, 27,
317-318; H. S. Rzepa, Chem. Design Auto.
News, 1994, 9, 1; H. S. Rzepa, in "The
Internet: A Guide for Chemists", Ed. S. Bachrach, American
Chemical Society, 1995; M. J. Winter, H. S. Rzepa and B. J. Whitaker,
Chem. Brit., 1995, 685;
A. N. Davies, Spectroscopy Europe, 1996, 8, 42;
H. S. Rzepa, Science
Progress, 1996, 79, 97; B. J. Whitaker, H. S. Rzepa,
Proc. Int. Chem. Inf. Conf. (Ed. H. Collier), 1995,
62-71; H. S. Rzepa, O. Casher and B J. Whitaker, Proc. Int.
Chem. Inf. Conf. (Ed. H. Collier), 1996, 141-148; H. S. Rzepa,
W. Locke, P. Murray-Rust and B. J. Whitaker in Perspect. Protein
Eng. '96, (Ed. M. J. Geisow), 1996, Paper No. 19; H. S. Rzepa,
P. Murray-Rust and B. J. Whitaker, Chem. Intl.,
1997, 19, 17.
- A description of the definitive list will be published elsewhere; H. S.
Rzepa, P. Murray-Rust and B. J. Whitaker, Pure & App Chemistry, in preparation.
The latest information is available on-line at http://www.ch.ic.ac.uk/chemime/
- H. S. Rzepa, "Internet-based
Computational Chemistry Tools", in Encyclopaedia of Computational
Chemistry, Wiley, 1998, in press.
- An example of the use of chemical MIME to integrate a variety of chemical
data types into the body of an electronic journal is the CLIC Electronic Journal
Project; D. James, B. J. Whitaker, C. Hildyard, H. S. Rzepa, O. Casher, J. M.
Goodman, D. Riddick and P. Murray-Rust, New. Rev. Information
Networking, 1996, 61. For the project itself, see http://www.rsc.org/is/journals/current/chemcomm/cccenha.htm
or the original site at http://chemcomm.clic.ac.uk/. For details
of how a "chemically enhanced" article was prepared, see O. Casher and
H. S. Rzepa, in Proc. E. Conf. Trends in Organomet. Chem.: ECTOC-3
(Eds H. S. Rzepa and C. Leach), Royal Society of Chemistry, 1998. ISBN (CD-ROM)
0-85404-889-8.
- For examples of the application of chemical MIME to electronic
conferencing, see C. Leach and H. S. Rzepa (Eds), ECTOC-1, Royal
Society of Chemistry, 1996. Also ECHET96, 1997; ECTOC-3, 1998, ECHET98, 1998. The
conferences are on-line at http://www.ch.ic.ac.uk/ectoc/.
- T. Maffett and B. van Vliet, MDL Information systems, 1996. For further
details of Chime, see http://www.mdli.com/chemscape/chime/.
This plug-in derives from the Rasmol program written by R. Sayle and applied
within the chemical MIME project as described in 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.
- A simple test molecule is available at
http://www.ch.ic.ac.uk/rzepa/jcics/molecule.pdb A site for testing
an extended set of chemical MIME types is available at
http://www-dsed.llnl.gov/documents/tests/chem.html
- H. S. Rzepa, available as
http://www.ch.ic.ac.uk/rzepa/jcics/chemical10.hqx
- M. J. Pilling, S. Saunders, M. Jenkin
and D. Derwent, "Tropospheric Chemistry",
http://www.chem.leeds.ac.uk/Atmospheric/MCM/main.html.
- For details of all W3C (World-Wide Web Consortium) recommendations, proposed
recommendations, working drafts and notes,
see http://www.w3.org/TR/
- P. Murray-Rust, "Chemical Markup Language, A simple introduction to
structured documents", in "XML, Principles, Tools and Techniques" (Ed. D. Connolly,),
O'Reilly, 1997, pp 135-149.
- For specifications see P. E. Bourne, H. M. Berman, B. McMahon, K. D.
Watenpaugh, J. Westbrook and P. M. D. Fitzgerald. Meth. Enzymol,
1997, 277, 571-590. See also http://www.iucr.org and http://www.iucr.org/cif/mm/index.html
- P. Murray-Rust and L. West, ASLIB Managing Information, 1997, 4, 36-39.
See also http://www.vhg.org.uk/
- P. Murray-Rust in Proc. E. Conf. Trends in
Organomet. Chem.: ECTOC-3 (Eds H. S. Rzepa and C.
Leach), Royal Society of Chemistry, 1998. ISBN (CD-ROM) 0-85404-889-8.
A fully working version of JUMBO is included on this CD-ROM. See also Ref 13,
pp 197-207.
- The CML project was first described in P. Murray-Rust, C. Leach and H. S.
Rzepa, Abs. Papers Am. Chem. Soc , 1995, 210, pp.40-COMP (http://www.ch.ic.ac.uk/cml/) and in P.
Murray-Rust and H. S. Rzepa, Abs. Papers Am. Chem. Soc, 1997,
214, pp.23-COMP. Details of CML itself are available in Refs 13 and 16.
Further details will be published in a forthcoming paper.