Subject: IUPAC Chemical Identifier Project (IChIP)

From: Steve Heller <[email-masked]>
Date: Sun, 2 Apr 2000 10:25:12 -0400 (EDT)

April 2, 2000

IUPAC Chemical Identifier Project (IChIP)

The initial meeting of the IUPAC Strategy Round Table: Representation of
Molecular Structure: Nomenclature and Its Alternatives, was held on March
10-11, 2000 at the National Academy of Sciences in Washington DC. As noted
in the minutes (see below) from that meeting, the group agreed to study
the feasibility of creating an IUPAC chemical identifier. Steve Heller and
Steve Stein (NIST) were asked to coordinate this task and provide a
feasibility report to the IUPAC Secretariat including a potential plan of
action by the fall of 2000.

This message is being sent to attendees of the meeting, as well as a wide
audience of chemists, information specialists, and others to solicit
comments and suggestions concerning technical issues involved in
developing a standard unique digital representation of chemical
structures. Steve Stein and I would appreciate a response from you by 1
May 2000. At this initial stage, we are particularly concerned with the
representation of well-defined covalently-bonded molecules. 

Please feel free to pass this information on to any colleague you believe
would be interested in this project.

A variety of methods have been proposed for deriving a unique digital
"name" from a defined chemical structure. We wish to begin by collecting
and comparing available methods that may be applied to this task along
with known deficiencies and other technical concerns.
 
Specifically, we wish to consider the pros and cons of various chemical
structure normalization rules (e.g., tautomerization, aromatization, etc.)
and related issues along with available "canonicalization" schemes leading
to a creation of a unique digital "name". In addition, we wish to consider
any standards that may be needed for structure entry to ensure unambiguous
name by any structure-drawing package. Finally, complete specification of
a single chemical substance will require additional qualifiers, including
stereochemistry, geometrical configuration, chemical state, charge,
electronic state, etc. We expect to include these as pre-defined fields
separable from the basic connectivity information.

It is intended that the rules leading to the formulation of a unique
digital representation from a chemical structure will be openly available
and capable of being extended to a wider range of chemical structures,
including, for example, organometallic compounds, polymers,
incompletely-defined structures and compound classes. 

Steve Heller/Steve Stein

------------
IUPAC - Summary of report the the IUAPC Executive Committee - San
Francisco, CA March 24-25, 2000

The IUPAC Executive Committee approved the formation of an ad hoc
Committee on Chemical Identity and Nomenclature Systems, with Dr. Alan
McNaught as Chairman. The CCINS will be responsible for developing systems
for conventional and computer-based chemical nomenclature; cooperating
with the four nomenclature Commissions (until the end of 2001);
coordinating interdisciplinary activities in the nomenclature field; and
recommending to the Bureau long-range strategy on chemical nomenclature.
It is expected that this body will provide the long-term central planning,
management and coordination of chemical nomenclature that would otherwise
be lost when the Commissions are discontinued at the end of 2001.  The
Executive Committee also approved a feasibility study of the Chemical
Identifier project, to be managed by the CCINS.

Chemical Identifier

A proposal by Dr. Stephen Heller for a major new IUPAC initiative was
extensively discussed and clarified during the IUPAC Nomenclature Round
Table.  Framed initially in terms of an "IUPAC chemical registry system,"
the proposal was recast as a "chemical identifier" - a meaningful
alphanumeric text string that can uniquely identify a chemical compound
and facilitate its handling in computer databases.  This code would be the
equivalent of an IUPAC systematic name but would be designed to be easily
used by computers.  The Identifier could also include other information
about the specific substance in question.  There are several issues to be
resolved as indicated below.  The participants recommended that the
feasibility of the project and resolution of these issues be carried out
as soon as possible by representatives of a wide range of interested
parties. Drs. Heller and Stein (NIST) were asked to recommend a list of
individuals and groups that should be consulted initially and to propose a
framework for addressing the issues.

The aim of the IUPAC Chemical Identifier (IChI) Project is to establish a
unique label, the IUPAC Chemical Identifier (IChI), which would be a
non-proprietary identifier for chemical substances that could be used in
printed and electronic data sources thus enabling easier linking of
diverse data compilations.

IChI will not require the establishment of a registry system. Unlike the
CAS Registry System, it will not depend on the existence of a database of
unique substance records to establish the next available sequence number
for any new chemical substance being assigned an IChI. It will use a, yet
to be defined, set of IUPAC structure conventions, and rules for
normalisation and canonicalisation of the structure representation to
establish the unique label. It will thus enable an automatic conversion of
a graphical representation of a chemical substance into the unique IChI
label which can be performed anywhere in the world and which could be
built into desktop chemical structure drawing packages (such as ChemDraw,
ISIS/Draw, etc.) and online chemical structure drawing applets (such as
ACD/Draw).

The brainstorming session after the IUPAC Strategy Round Table in
Washington suggested a number of mutually incompatible attributes for
IChI:

1. It should be short and easily usable by humans and contain a check
digit which could detect typing errors such as transposition of characters
(as in the CAS Registry number)

2. It should be fully reversible (i.e., a computer should be able to
convert IChI back into a structure representation which can be displayed)
which is likely to result in a representation too long to be used by
humans

3. It should contain intelligence (i.e., it should group families of
salts, stereo isomers, etc.) and thus be a type of classification system.
Consensus needs to be obtained by the working group set up to investigate
the feasibility of the project [or imposed by IUPAC management] before the
IChI project can proceed to establish working groups to look at structure
conventions and the rules for normalisation and canonicalisation.

The process flows from input by a chemist of a structure, using drawing
software, to the creation of the Identifier. IUPAC would define three
aspects of this process: the rules for drawing a structure, the form of
the in-memory representation of the structure diagram, and the
mathematical algorithm for converting the in memory representation to a
text string, the Identifier. The steps to convert from the drawn structure
to the machine representation, normalization and canonicalization, would
be done by vendor developed software. This part of the process has been
implemented by a number of software developers. The new aspect to be
introduced by IUPAC would be a standard data table structure.

The definition of a standard data table structure is necessary to allow
the next step, the conversion of the data table to an alphanumeric text
string. IUPAC would define the mathematical algorithm, the implementation
of the algorithm would be left to interested software developers. The
output from application of the algorithm would be the IUPAC Chemical
Identifier.

The process would be reversible if criterion 2 above is met, so that the
Identifier could be used to recreate the machine representation. This
would then allow either display of the structure or generation of the
IUPAC name. The Identifier would thus serve as the computer equivalent of
the IUPAC name for a molecule. This would facilitate searching the
internet and labeling information in electronic documents with the name of
the chemical substance in question.

----------------

Stephen R. Heller, Ph. D.
Guest Researcher
NIST/SRD, Mail Stop: 820/113
100 Bureau Drive
820 Diamond Avenue, Room 101
Gaithersburg, MD 20899-2310 USA
Phone: 301-975-3338    FAX: 301-926-0416
E-mail:  [email-masked]
WWW:     www.hellers.com/~steve
--------------------------------------------------
As a member of the Organizing Committee, I invite you to attend
Chemistry & the Internet - ChemInt2000; September 23-26, 2000;
Washington, DC.
http://www.chemint.org