1. Towards a unified MOD resource: An Overview
A presentation to NHGRI
May 2016
13-May-16

2. Current MODs model User confusion for lack of homogeneity
From Valentina di Francesco
User confusion for lack of homogeneity
User access interfaces
need different navigation skills and data access approaches for each resource
Semantic inconsistencies and different data structures for the same genomic entities
Analyses
human/model organism association for disease and phenotypes
functional annotation
homology representation
Redundancy of operations at 6 resources
Data management systems for related data structures and types
System administration and IT support
Technical user support
Links to the same public resources which need updates and maintenance

3. Future MODs model Common web portal Unified MOD Streamlined operations
User access interfaces
Unified search & display for common data elements
Preservation of elements/data types unique to a particular organism
Analyses
Common analysis tools for users
Preservation of analysis tools unique to a particular organism
Streamlined operations
Common tool sets for curation, analysis, visualization
Common data management systems for related data structures & types
Common systems administration & IT support
Common technical user support
Unified MOD
Target user communities:
Basic researchers
Clinical researchers
Computational biologists/Data scientists
Educators/students

4. unified Model Organism Database (uMOD) Consortium
Saccharomyces Genome Database
WormBase
FlyBase
ZFIN
Mouse Genome Database
Rat Genome Database
Gene Ontology consortium
unified Model Organism Database (uMOD) Consortium
Six Model Organism Databases and the Gene Ontology consortium have joined together into a unified Model Organism Database (uMOD) Consortium.
By working together we can be more comprehensive and efficient and hence, more sustainable.

5. “uMOD” Consortium Principles
Our vision:
Develop a unified information resource project that assembles, integrates, mines and disseminates information about intensively studied model organisms including budding yeast, worms, fruit flies, zebrafish, rats, and mice primarily to further knowledge about human biology and disease.
Our mission:
Develop and maintain knowledge resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology and disease. This understanding is fundamental for advancing biomedical research and for translating genome data into clinical utility.
Our approach:
Create a unified resource that provides the best of each resource while maintaining community integrity and presenting the unique aspects of each contributing resource. Founded initially by six model organism databases (MODs) and the Gene Ontology Consortium, we will develop a scalable and agile infrastructure that can accommodate additional groups, expertise and new data types over time.
Our Communities:
We seek to serve basic researchers, translational and clinical researchers, computational biologists/data scientists, educators, and students.

6. The Model
a central uMOD integration site (“hub”) that is responsible for maintaining a common web portal, hosting common curation tools, and engagement with the computational biology/data science community (for example through the development of common APIs) and where data from each MOD curation group can be uploaded and exchanged,
“centers of specialization/working groups” that are responsible for particular tasks/SOPs, such as further development of literature markup or common automated data pipeline formats/QC, that are hosted by central site (hub) and that serve the entire uMOD community, and
model organism-specific working groups (“spokes”) that are primarily responsible for data acquisition and annotation activities that utilize data from the centers of specialization, feed into the central uMOD site, and also foster community engagement.
should not this be a MATRIX? see my ppt
13-May-16

7. Getting Started: Organizing ourselves
Steering Committee – governance, priorities
PIs from all of the member groups
Teams – enhance communication among the MODs
Curation team
Software team
Working Groups – implementation of projects/tasks
Web portal
Data acquisition and curation
Public access functionality
Data model and data types
Infrastructure
User outreach/User feedback and usability testing

8. How will this new model help?
Will aid the user community by providing a unified portal to the MODs under the FAIR principles
Will decrease costs in the short run through our continued efforts to eliminate redundancy of shared activities related to
Data, curation processes, interfaces, analysis functions, etc.
Will decrease costs in the longer term by moving to a common database management system
13-May-16

9. Progress towards a more perfect MOD union
Ongoing development & adoption of common tools & interfaces
LEGO
TextPresso
JBrowse/Gbrowse
InterMine
Etc.
Ongoing coordination of data and common activities
Gene nomenclature
Quest for Orthologs
InterMOD
Ontology development (GO, MP, DO)
Supplemental funding being used now to
Further develop common vocabularies for disease
Enhance existing tools so they can be adopted broadly (e.g., TextPresso)
Develop common interface to MOD mines

10. Overview of This Meeting
Reports from projects funded by administrative supplements
related to development & adoption of common tools & interfaces
Details of our progress and plans for the unified MOD consortium
Working sessions
Orthology
Phenotypes/Disease models