Valentina Di Francesco

PAG XXVII – San Diego

Jan 14, 2019

Sustainability Plans for the NIH/NHGRI Model Organism Databases

Current Status and a Vision for 2019 and Beyond

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NHGRI MODs and GO Consortium Organizational Model in 2016

SGD

FlyBase

WormBase

MGD

ZFIN

GO Consortium

Different interfaces for common data types• No single access to multiple data resources

and different user interfaces• Different annotation strategies and workflows• Different data representation

Redundancy of operations at 6 resources• Data management systems for related data

structures and types• System administration and IT support• User support• Links to/from the same public resources

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MODs and GO Data Types

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NHGRI Goals• Facilitate access and use of these valuable

resources • Transition the resources to a more effective and

sustainable funding model • Repurpose NHGRI funds towards other needed

genomics-based data science research

MODs Reorganization

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• Founding members of the AGR Consortium:• MGD, FlyBase, SGD, ZFIN, WormBase, GO Consortium, RGD

• 3-year supplement awarded to WormBase in Sept 2016 to

establish an integrated resource

• Gradual decrease of each resource’s budget starting in FY17

Alliance of Genome Resources

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• Enhance comparative genome biology by providing unified data access mechanisms to the MODs and GO Consortium data

• genes, genomes, gene function and genotype/phenotype associations

• Implement a common, flexible ecosystem of shared modular infrastructure that will support core functionality

• Sustainability goals: Increase efficiency and decrease costs associated with the maintenance of the resources

Scope of the AGR

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Individual MODs hold most of the data and function. The Alliance currently has a small subset.

Jeff DePons, AGR/RGD

Now…

Over time the software and data residing at individual MODs get smaller and the Alliance gets larger.

Jeff DePons, AGR/RGD

Moving forward

https://www.alliancegenome.org/

• Alliance web site and APIs for data access• gene symbol/name (synonyms)• functional annotation terms (GO)• disease terms (DO)

• Common orthology set• S3 buckets in the cloud for NIH Data Commons• Multi-organism display of curated gene to human disease associations• Common instance of JBrowse• Modular sequence display widget• Common automated concise gene description text• Compact annotation ribbon display for function, phenotype, expression• Common ingest and display of interaction data

Overview of Accomplishments

Paul Sternberg AGR/WormBase

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• Modular, shared infrastructure that handles all core MOD software functions

• MODs will be able to move residual functions to Alliance Central Portals

• Flexibility to allow evolution of resources and onboarding of others

• Users (both individual and power) have better access to data and more rapid response to new data and new software technology

• Clinical researchers will have facile access to model organism and some human data

• Coordination of MOD/GO communication and outreach

AGR Five-Year Goals

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Paul Sternberg AGR/WormBase

Focus on model organism-specific needs:

• Data curation efforts

• Outreach to individual model organism research communities

• Streamlined or eliminated user-interfaces at each individual MOD

• Incorporation of additional data types with co-funding by other ICs

Individual MODs – Next steps

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• Model organism researchers• Genomicists• NIH - Sustainability

• NHGRI• NIH Scientific Data Council• NIH Data Commons Pilot

AGR/MODs Stakeholders

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• Requested by Congress

• Developed by the NIH Scientific Data Council

• Released on June 4, 2018

• The plan provides a roadmap for modernizing the NIH funded biomedical data

science eco-system and focuses on:

• Modernizing the data resources ecosystem to increase its utility for

researchers and to optimize its efficiency of operation

• Separate funding support for databases, knowledgebases and tools

NIH Strategic Plan for Data Science

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NIH Data Commons Pilot Phase (DCPP)• Pilot phase 1 Sept 2017- Nov 2018

• AGR had a key role in phase 1, which will continue in phase 2 • Procurement and deployment of AGR data and services on multiple cloud platforms• Development and implementation of use cases spanning the 3 initial datasets• Development and implementation of Data Commons best practices for FAIR data

Data Commons Pilot Phase OT Awardees Stanley Ahalt, RENCI Isaac Kohane, HarvardTitus Brown, UC Davis Avi Ma’ayan, Mt. SinaiMerce Crosas, Harvard Lucila Ohno-Machado, UCSDBrandi Davis-Dusenbery, SevenBridges

Benedict Paten, UCSC; Robert Grossman, UChicago;Anthony Philippakis, Broad Institute

Ian Foster, UChicago Owen White, UMD

Data Sets

TOPMed

DCPP Consortium

• AGR will enhance comparative genome biology by providing unified data access mechanisms to the MODs and GO Consortium data

Summary

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Acknowledgements

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NIH/NHGRI Colleagues: Robert Fullem, Ajay PillaiAGR Consortium