Minutes of the Bioinformatics Standards Committee P1953 Meeting
Thursday, January 6, 2005, 5:30 PM PST

Betty Cheng: Introductions

Welcome to the working group of IEEE Standards Committee: Vicky Markstein, Acting Chair; Phil Bourne, Chair: Betty, Recording Secretary

Some background on the Bioinformatics Standards Committee (BSC) activities:

First task: Make roadmap of existing standards group in the field. Find group willing to go through the IEEE process. PSB is one of the open meetings. Others in ISCB, and CSB.

Active contact at conferences, e.g. Functional Genomics at Philadelphia. Regular teleconferences on a monthly basis. Mailing list set up. Any interested party can subscribe.

Suzanna Lewis volunteered Structural Ontology to go through the standards process. They (SO) are already started on a standardization effort.

Betty explains the IEEE process – ultimate proposed standard given to IEEE for public review to solicit standards. All remarks must be answered.

Standards undergo review, renewal, and updating. IEEE requires standard review every 5 years.

We are looking for people interested in working with the SO standard – looking for members of the Bioinformatics community to participate. We need people to review the standard when it is ready.

IEEE has expertise in related areas: legal, for example. We are seeking open access. We are trying to set a neutral platform – IEEE has developed a global community to disseminate a standard to the engineering community. It would expand to the biological community, and to the instrumentation of biological equipment.

Vicky: made remarks about how this activity started.

Q & A:

Relation with regulatory agencies, such as the FDA?
FDA may want to regulate microarrays

Relationship with European standardization organization?
Started talks with M. Ashburner, Carol Goble

Crystallography: standard of some sort is now being enforced.
Phil: PDB format goes back 20+ years. All software that deals with structure deals with PDB format. But PDB format is unable to deal with molecules that we get these days. International Union of Crystallography mandated development of a new standard (useful to PDB) for a wider community. Enables MMSIF and XML data exchange. We hope that XML representation of PDB will become the standard of choice. But no real enforcement at the present. A PDB board members suggested posting a note that within 5 years, PDB format would no longer be provided, but this was voted down. If you are development a standard, it is difficult to realize where the science is going. One wants to project out as far as possible to assure longevity. Community buy-in is vital.

Betty: By encouraging a standard, you encourage universal translators to convert between someone’s private format and the standard format. Commercial opportunity for validation suite production, to conform compliance to standard. IEEE may be able to contribute to the effort by being the validating organization (for a fee?).

What about reference implementations? Is that part of the standard? Yes (Betty), part of the standard would produce a reference implementation.

Issue of patents: discussion of nondiscriminatory licensing and royalty free licensing.

Next open meeting at ISMB

Teleconference in February. See website for details.

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