Quality & Stability

• Open Knowledge & transparency

• Data quality

• Inconsistency, incompleteness

• Provenance

• Contamination, noise, experimental rigour

• Data irregularity

• Evolution, Audit, Versioning

ì Ö the problem in the field is not a lack of good integrating software, Smith says. The packages usually end up leading back to public databases. "The problem is: the databases are God-awful," he told BioMedNet.

If the data is still fundamentally flawed, then better algorithms add littleî

Temple Smith, director of the Molecular Engineering Research Center at Boston University, BioMedNet 2000

Diapositive prÈcÈdente

Diapositive suivante

Revenir ý la premiËre diapositive

Afficher la version graphique

Provenance of derived data

Assure having a proper history of derived results

[ Peter Buneman, UPenn, www.humgen.upenn.edu ] K2 integration tool

Integrated databases often donít indicate the original sources

I.e., SwissProt does not distinguish inferred versus being observed.

[ William Gelbart, Harvard University] Flybase

Flybase also collects data as exons and their mutations, tranposon insertion sites.

Moving from being Hunter Gatherers in science to Harvesters, moving to an agronomical society

Classical genomics is being superseded by expression and interaction of gene products and gene perturbation.

[ Peter Karp, SRI Int., Bioinformatics Res.Group, www.ai.sri.com/pkarp/ ] EcoCyc

EcoCyc links proteins to 150 metabolic pathways in Ecoli

Databases are supplanting journals. They are re-analyzable. Results in journals are not.