meeting review: plant bioinformatics at the nsf and npgi

Conference Review

Meeting Review: Plant Bioinformatics at theNSF and NPGI (PAMGX Satellite) Meetings

Richard Bruskiewich*International Rice Research Institute (IRRI), DAPO 7777, Metro Manila, The Philippines

*Correspondence to:International Rice ResearchInstitute (IRRI), DAPO 7777,Metro Manila, The Philippines.E-mail: [email protected]

Received: 1 February 2002

Accepted: 13 February 2002

Abstract

This brief meeting review summarizes the recommendations of NSF and NPGI funded

bioinformaticians concerning the future requirements for plant bioinformatics systems and

databases. Copyright # 2002 John Wiley & Sons, Ltd.

On Friday, 11th January, 2002, the National ScienceFoundation (NSF) and the National Plant Geno-mics Initiative (NPGI) hosted meetings concerningdiverse scientific activities within their respectiveprograms. Included in both meetings were specificsessions on plant bioinformatics, including reportson the current implementations of plant databasesand considerations for future development. Severalleading bioinformaticians of these databases were inattendance.

These meetings follow up on an earlier NSF-sponsored meeting of plant bioinformaticians lastSeptember 11th, 2001 held at TIGR. The summaryrecommendations coming out of the earlier meetingwere as follows:

$ All databases must have capabilities that willallow the broadest access by the community

$ The community should begin developing astandard format for data exchange

$ Metadata (UML or XML defined) must be definedfor complementary human and machine parsing

$ Data release policies and standard operatingprocedures should be posted at data sites

$ Agencies need to fund organism independentsoftware, data archives and annotation services

$ Agencies should support open-source, includingthe development of adequate documentation

$ Complete (raw) data must be archived includingEST trace files, raw map data and data files forintegrated physical and genetic maps

The NSF meeting white papers on bioinformaticsand databases along with the final report of theSeptember meeting are available on the WWW athttp://plantgenome.sdsc.edu/.

Particular emphasis was made concerning thedevelopment of more extensive open communityprotocols for data exchange and archival of completedata. Following the spirit of the ‘Minimal InformationAbout a Microarray Experiment’ (1) efforts of theMicroarray Gene Expression Database (MGED)consortium (http://www.mged.org/), the group pro-poses to develop ‘Minimal Information About aFunctional Genomics Experiment’ (MIAFGE),extending the concept of MIAME to ALL functionalgenomics experimental data. As a particular exampleof the necessity to properly archive original (‘raw’)data, it was noted that the underlying raw segregationdata for individual mapping populations of manyhistorical comparative mapping efforts are no longeravailable. Proper community archives for such dataneed to be established for current and future com-parative mapping efforts.

Disclaimer: The writer was a general participantin the NSF Awardees’ and NPGI satellite meetingsat the Plant, Animal and Microbe Genome X(PAMG-X) conference, but was not part of theoriginal bioinformatics review panel. This review issolely based upon the writer’s third party inter-pretation of meeting discussions and handouts, andis merely provided as an unsolicited (and NSF/NPGI unofficial) public information service to thereaders of this journal.

References

1. Brazma A, Hingamp P, Quackenbush J, et al. 2001. Minimum

information about a microarray experiment (MIAME) – toward

standards for microarray data. Nature Genetics 29: 365–371.

Comparative and Functional Genomics

Comp Funct Genom 2002; 3: 176.Published online 14 March 2002 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002 /cfg.158

Copyright # 2002 John Wiley & Sons, Ltd.

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