EPA Communities of Practice
Chemoinformatics

Community of Practice

The Chemoinformatics workgroup is proposed to be formed in Summer 2005 to facilitate, coordinate and integrate efforts to address the challenges of chemical structure annotation (or indexing), retrieval, and mining of chemically-related data and documents, including newer toxicogenomics and metabonomics data, across EPA Program Offices, Labs and Centers. Much of EPA's public and internal chemical data records and databases currently are indexed only by chemical name (imprecise and non-unique) and CAS registry numbers (proprietary) and are not searchable by the more universal and informative metric of chemical structure. Additionally, there is unnecessary duplication of efforts and lack of coordination in the area of chemical structure-annotation and quality review of chemical information (e.g., structures, CAS) across diverse EPA databases. Finally, no Agency-wide chemical structure searching capability currently exists to enable EPA scientists, regulators, and outside parties to efficiently and precisely locate Agency chemical information based on chemical structure.

The Chemoinformatics workgroup would invite members of various Offices, Labs and centers currently involved in either chemical database construction or use, to coordinate ongoing efforts in the area of chemical-structure annotation and structure-searchability of EPA records and data, and to help chart a path forward for expanded Agency-wide adoption of capabilities in these areas. One of the first tasks of this workgroup would be to consider and refine the elements of the draft charter below, and create a finalized charter for the workgroup.

A draft charter of this Chemoinformatics workgroup is suggested to include the following functions:

Facilitate communication and co-ordination among the Agency personnel who are directly using, developing, or managing chemical information data records, including those associated with newer toxicogenomics and metabonomics technologies, particularly in ORD, OPP and OPPT whose duties involve chemical searching and structure-activity assessments.
Propose adoption of application-independent standards for chemical structure representation (including information pertaining to the characterization of mixtures, racemic chemicals, polymers, and stereochemistry) that will facilitate the broadest possible utility and compatibility of such information, both within and outside of EPA.
Guide the creation of a consolidated EPA database of chemical identification information (structure, CAS, name), obtained from public sources (chemfinder.com, PubChem, NLM ChemID) but having undergone additional levels of quality consistency review, to serve as a common resource for the structural annotation of EPA records or databases. [Note that physical/chemical properties can be measured or derived from the accurate chemical structures by a variety of algorithms and means; hence, such property annotation of chemical information resources will be considered as a separate and distinct task of chemical annotation not included in the initial charter of this workgroup.]
Create procedures and guidelines for chemical annotation of Agency data and records, as an adjunct to EPA Information Quality Guidelines, to improve consistency, quality, and efficiency related to storage, retrieval and mining of chemical information within the Agency.
Exchange information and experiences regarding available public and commercial approaches and initiatives in the areas of chemical structure representation, chemical searching, and managing and modeling of chemical data.
Evaluate and recommend which of the available approaches and initiatives might be adopted or coordinated to best serve EPA's long-term needs in this area, and serve as an information resource to other Agency personnel on these matters.
Evaluate and provide guidance concerning the needs and requirements of an Agency-wide chemical structure-searching capability, possibly from publicly available or open-source parties, that would offer low-cost, flexible solutions to enable EPA scientists or others to locate records or data pertaining to chemical information on EPA's intranet or internet websites.
Facilitate the development of training materials and programs for scientists, chemical managers and risk assessors that assist in the implementation and wider use of these chemical information resources and technologies.
Report regularly (every six months) to the ORD science council on issues, progress, and outputs

Office/Division/Branch managers across various research offices, including ORD, OPP and OPPT, will be invited to appoint representatives to this workgroup who would benefit most from, and contribute most to these discussions, as well as who would serve as a conduit of information to and from their respective Branch/Division/Office.

EPA Communities of PracticeChemoinformatics

Community of Practice

A draft charter of this Chemoinformatics workgroup is suggested to include the following functions:

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EPA Communities of Practice
Chemoinformatics