GSC process of building consensus
From Genomic Standards Consortium
GSC: The process of consensus building
We aim to build the final version of the MIGS/MIMS specification using the same general process applied to the development of other community-based standards. We plan to follow these 8 steps:
1. Identification of the need for a standard
2. The formation of a working group (community)
3. Selection of case studies
4. Development of the specification checklist
5. Development of a suitable implementation
6. Development of a repository to store, view, and distribute annotations
7. Final annotation of genomes to compliant format and submission to the repository.
8. Demonstration that the metadata is useful (to compare across genomes; to regenerate experiments)
1. Identification of the need for a standard
The original comment on the need for a new standard was published in Microbiology by Field and Martiny, 2005 (see GSC Publications). This comment was circulated in draft form to a variety of researchers to collect feedback on its general merit, feasibility, and timeliness. Most importantly, this exercise helped to identify a community of people with a shared interest in seeing a new standard emerge.
2. The formation of a working group (community)
An exploratory workshop took place on Sept 7-9 at the National Institute for Environmental E-Science Centre in Cambridge )NIEeS). This meeting led to the formation of the Genomic Standards Consortium (GSC). The mtg report for this workshop and subsequent workshops is available from the GSC Publications page.
3. Selection of GSC Case Studies
The issues involved in defining this specification can be best explored by working with 'real-world' examples. We are therefore working with members of past, ongoing, and future genome projects to describe particular genomes or groups of genomes.
4. Development of the specification checklist, specification attributes, definitions, and allowed terms
The specification will be built through an iterative process of consultation involving the development of case studies. An overview of the general requirements will be captured in a checklist. This process will proceed through the following steps:
- Knowledge acquisition (discussion of requirements within the community, case studies)
- Selection and definition of a set of attributes
- Development of allowed terms / controlled vocabularies
5. Development of a suitable implementation
The specification will be implemented as an XML schema (but could evolve into an ontology).
6. Development of a repository to store, view, and distribute annotations
All resulting genome reports must be freely available. For the sake of further evaluation of the specification and advertisement of the project a pilot repository will be set up with an interface for submitting new genome reports. The Genome Catalogue is now online.
7. Final annotation of genomes to compliant format and submission to the repository.
The greatest value of this collection of genome reports will only be realized if it is complete. Future workshops or publications should focus on encouraging submissions from all genome projects, past, ongoing and future.
Web forms must be developed to easily allow representatives from genome projects to enter data. Links advertising this submission portal should be hosted on as many genomic websites as possible to advertise its existence. This federated approach, signifying wide-spread support for the specification will hopefully encourage genome project representatives to submit data.
8. Demonstration that the metadata is useful (to compare across genomes; to regenerate experiments)
Demonstration projects will be selected in the future.
