Bookmark and Share

Standardization News Search
Tech News
Call for Experts to Standardize Bioinformatics Data

ASTM International invites bioinformatics professionals to develop standards for bioinformatics sequence markup language (BSMLTM). The standards will describe a uniform encoded language that meets the expanding needs of biotech researchers.

Individuals in the healthcare informatics, biotechnical, pharmaceutical, and computer fields are strongly urged to participate. Contact Dan Smith, director, Technical Committee Operations (phone: 610/832-9727).

ASTM Committee E31 on Healthcare Informatics initiated the activity in May. Coordinating the effort are Peter L. Elkin, M.D., associate professor, Medicine and Medical Informatics, Mayo Clinic, Rochester, Minn., and Jeff R. Spitzner, Ph.D., chief science officer, LabBook, Inc., Columbus, Ohio, a biomedical information-solutions provider.

Elkin is committee vice chairman and chairs a subcommittee that develops standards for controlled health vocabularies and data representation. Spitzner helped to create BSML with other LabBook scientists. Spitzner, Elkin, and participating individuals will draft LabBook’s BSML as a proposed ASTM standard and present it to the committee for ballot.

LabBook explains on their Web site that “BSML encodes biological sequence information and includes graphical representations of biologically meaningful objects such as sequences, genes, electrophoresis gels, and multiple alignments.”

Spitzner and Elkin say the objective of the ASTM activity is to “identify or develop overlapping sets of standards that together encompass the entire span of life sciences research and clinical information in order to meet the needs of the community.”

“BSML allows life sciences researchers, suppliers, and content and service providers to interact and exchange information through a universal data language that captures the richness of genome research data in documents that retain the biological meanings and relationships of the underlying information,” explains Spitzner. “BSML represents a method for encoding information about biological molecules (DNA, RNA and protein sequences), including sequence data, feature tables, references, and associated tabular data (e.g., gene expression values), as well as optional visualization and interaction with these bioinformatics objects.

Elkin says, “BSML was an easy choice. It is the most mature and comprehensive standard today for bioinformatics, and it has been widely accepted by the industry. Furthermore, its development was funded by the NHGRI [National Human Genome Research Institute], and this XML [extensive markup language] data specification has always been made available to the public domain since its initial release in 1997. The industry’s use of standards such as BSML will have tremendous impact on basic research, biotechnology, and human health.”

ASTM Committee E31 on Healthcare Informatics formed in 1970 to promote the knowledge and development of standards for health information systems. The standards developed by this ANSI-accredited committee cover architecture, content, portability, storage, privacy, security, and computer data procedures for healthcare information.

For further information, contact Dan Smith, director, Technical Committee Operations, ASTM International (phone: 610/832-9727). //

Copyright 2002, ASTM