The Alliance of Genome Resources

Model Organism Databases, and the Gene Ontology Consortium

The primary mission of the Alliance of Genome Resources (Alliance), Model Organism Databases (MODs), and the Gene Ontology (GO) Consortium is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease. This understanding is fundamental for advancing genome biology research and for translating human genome data into clinical utility.

Overview

Background

NHGRI aims to improve the usability and interoperability of the Model Organism Databases (MODs). Through interactions with the MODs and the broader NIH community, NHGRI also aims to establish a more modern, cost-effective, and sustainable model for these important data resources that is commensurate with their evolving scope. These goals are in alignment with the NIH Strategic Plan for Data Science, which outlines steps for modernizing the NIH data resources ecosystem.

To help achieve those aims, the Alliance of Genome Resources (Alliance) was established in September 2016. Six NHGRI-funded MODs/data resources are part of the Alliance: Mouse Genome Database, WormBase, Zebrafish Information Network, Saccharomyces Genome Database, Flybase, and the Gene Ontology (GO) Consortium. The NHLBI-funded Rat Genome Database has also been an active participant in the Alliance.

The goals of the Alliance are to establish a common infrastructure and software platform for data from all the MODs; adopt updated data-management practices; better integrate content, software, and user interfaces; improve interoperability; exchange best practices; and reduce redundancies of operation and maintenance. The full mission and vision can be viewed on the Alliance website. In addition, the Alliance has a Scientific Advisory Board (SAB) with representatives selected by the Alliance grantees from the appropriate advisory groups of the individual MODs.

Overview

Background

NHGRI aims to improve the usability and interoperability of the Model Organism Databases (MODs). Through interactions with the MODs and the broader NIH community, NHGRI also aims to establish a more modern, cost-effective, and sustainable model for these important data resources that is commensurate with their evolving scope. These goals are in alignment with the NIH Strategic Plan for Data Science, which outlines steps for modernizing the NIH data resources ecosystem.

To help achieve those aims, the Alliance of Genome Resources (Alliance) was established in September 2016. Six NHGRI-funded MODs/data resources are part of the Alliance: Mouse Genome Database, WormBase, Zebrafish Information Network, Saccharomyces Genome Database, Flybase, and the Gene Ontology (GO) Consortium. The NHLBI-funded Rat Genome Database has also been an active participant in the Alliance.

The goals of the Alliance are to establish a common infrastructure and software platform for data from all the MODs; adopt updated data-management practices; better integrate content, software, and user interfaces; improve interoperability; exchange best practices; and reduce redundancies of operation and maintenance. The full mission and vision can be viewed on the Alliance website. In addition, the Alliance has a Scientific Advisory Board (SAB) with representatives selected by the Alliance grantees from the appropriate advisory groups of the individual MODs.

NIH/NHGRI Support and Management

NHGRI plans to continue overseeing and supporting the general genomics activities of the MODs and Alliance and recognizes the value of organism-specific work performed by the individual MODs and their role in understanding the genome.

NHGRI also recognizes the value of coordinated and integrated activities facilitated through the Alliance. In accordance with this vision, since 2016 NHGRI has gradually restructured the funding landscape away from individual MODs and towards a centralized Alliance. Overall funding for combined Alliance and MOD activities have remained mostly stable over this time.

The MODs and Alliance are cooperative agreements that undergo standard NIH scientific review and programmatic management. In addition, NHGRI convened an external scientific panel in April 2018 to review progress made by the Alliance and provide general recommendations.

NHGRI recognizes that biomedical investigations in model organisms have moved beyond genomics to metabolomic and proteomic studies, areas where NHGRI has less expertise to establish priorities. Thus, NHGRI is also looking to work with other NIH Institutes and Centers, along with other International Funding Agencies, to developing sustainable funding models that keep these resources relevant to the cutting edge of biomedical research, both genomics focused and beyond.

In October 2019, NHGRI sought input from an External Scientific Panel (ESP) of investigators for their recommendations regarding future funding and sustainability of the MODs, Alliance, and GO Consortium. Carol Bult, a PI of the Alliance, presented to the ESP on the organization and progress of the Alliance, and the role of the MODs.

View the presentation.

The primary recommendations from the Expert Scientific Panel discussion included the following:

Curation and data sharing activities of the MODs are of broad value for the larger biomedical research community and support of these activities should be an NIH-wide and international priority.
The Alliance serves the role of centralizing common activities of the MODs, and the MODs complement that by performing expert, organism-specific curation activities. Most of the curation activities serve model-organism specific research use cases and these efforts should be maintained.
NHGRI should encourage and support other activities that would complement the MODs and Alliance and would increase value to the scientific community, including innovation in machine learning and artificial intelligence; resources relating cellular level and organismal level phenotypes across species (including humans); ensuring standardization and annotation of data in publications.

NIH/NHGRI Support and Management
NHGRI plans to continue overseeing and supporting the general genomics activities of the MODs and Alliance and recognizes the value of organism-specific work performed by the individual MODs and their role in understanding the genome.

NHGRI also recognizes the value of coordinated and integrated activities facilitated through the Alliance. In accordance with this vision, since 2016 NHGRI has gradually restructured the funding landscape away from individual MODs and towards a centralized Alliance. Overall funding for combined Alliance and MOD activities have remained mostly stable over this time.

The MODs and Alliance are cooperative agreements that undergo standard NIH scientific review and programmatic management. In addition, NHGRI convened an external scientific panel in April 2018 to review progress made by the Alliance and provide general recommendations.

NHGRI recognizes that biomedical investigations in model organisms have moved beyond genomics to metabolomic and proteomic studies, areas where NHGRI has less expertise to establish priorities. Thus, NHGRI is also looking to work with other NIH Institutes and Centers, along with other International Funding Agencies, to developing sustainable funding models that keep these resources relevant to the cutting edge of biomedical research, both genomics focused and beyond.

In October 2019, NHGRI sought input from an External Scientific Panel (ESP) of investigators for their recommendations regarding future funding and sustainability of the MODs, Alliance, and GO Consortium. Carol Bult, a PI of the Alliance, presented to the ESP on the organization and progress of the Alliance, and the role of the MODs.

View the presentation.

The primary recommendations from the Expert Scientific Panel discussion included the following:

Curation and data sharing activities of the MODs are of broad value for the larger biomedical research community and support of these activities should be an NIH-wide and international priority.

The Alliance serves the role of centralizing common activities of the MODs, and the MODs complement that by performing expert, organism-specific curation activities. Most of the curation activities serve model-organism specific research use cases and these efforts should be maintained.

NHGRI should encourage and support other activities that would complement the MODs and Alliance and would increase value to the scientific community, including innovation in machine learning and artificial intelligence; resources relating cellular level and organismal level phenotypes across species (including humans); ensuring standardization and annotation of data in publications.