Mechanism for Improving Access to Molecular Interaction Data
News Sep 07, 2005
The executive teams of five major molecular interaction databases have announced the signing of an agreement to share curation efforts and exchange completed records through a mechanism known as the International Molecular Exchange (IMEx) consortium.
IMEx is designed to provide a network of stable, synchronized and freely accessible databases, and will serve as a way to jointly capture all published molecular interaction data in a manner similar to the global collaborations for protein and DNA sequences and for macromolecular structures.
"In deciding to map the bimolecular interactions that define life itself, one quickly realizes how daunting a task we have set for ourselves," says Henning Hermjakob, principal investigator of the IntAct molecular interactions database at EMBL's European Bioinformatics Institute.
He adds, "All along, however, we saw this project as a collaborative task between our own group and the global scientific community. Thus, it made perfect sense to combine our efforts with those of our colleagues working at other centres."
"Each IMEx partner brings specific skills to the table," says Chris Hogue, principal investigator of BIND. He adds, "And the cumulative effort should result in an overarching database that is broader in scope and deeper in information than any individual efforts and one that scientists can use to better understand issues of health and disease or in the development of new drugs and therapeutics."
In joining IMEx, each database is expected to provide and exchange data according to a series of rules that describe the format, availability, and suitability criteria of the data, as well as address the data submission process, data exchange and ownership issues, and IMEx implementation and organization.
Under the agreement, IMEx partners will provide data that meet the Human Proteome Organization's Proteomics Standards Initiative (PSI) Molecular Interaction Format, and these data will be freely available to all users, whether for direct use or for redistribution.
Likewise, with rare exceptions, all data will be supported by publication in a peer-reviewed medium and be derived from laboratory experiments.The IMEx consortium will also further develop common curation standards that will allow each centre to produce data to the same high standards.
"These rules are critical to the success of this collaboration," explains Gianni Cesareni, principal investigator of MINT. He adds, "Too often in the past, scientists have been held hostage to different nomenclatures and presentation formats in disparate databases.” Further he said, “By following simple guidelines, the IMEx partners offer scientists the opportunity to get the best value for their research efforts."
Scientists have developed a way to identify the beginning of every gene — known as a translation start site or a start codon — in bacterial cell DNA with a single experiment and, through this method, they have shown that an individual gene is capable of coding for more than one protein.