Duration: 10/01/2019 to 09/30/2024

Administrative Advisor(s):

NIFA Reps:

Non-Technical Summary

Statement of Issues and Justification

Technological innovation is propelling crop science into an era of discovery driven by Big Data, where scientists routinely generate and analyze larger and ever more complex genomic, genetic and breeding (GGB) datasets for both model and non-model crop species. The value of Big Data increases significantly when it is curated and made available in community databases created by crop domain experts. When organized, annotated, integrated with other data, and made available to browse, query and analyze, value is added and data becomes a re-usable, enriched critical resource that will enable new and accelerated research discovery and application.  Dealing with the complexity of new data types and sheer volume of data generated has challenged established crop databases (1). Excellent resources exist for these databases, but they were developed in isolation, without access to a common database platform. Most have a crop or clade-specific focus and customized database schemas, making it hard to accommodate new data types, and requiring major resources from within this crop community to manage or interface with other crops or organisms.

Faced with these issues in 2008 when creating a Cacao database and in 2011 with the established Rosaceae and cotton databases, the bioinformatics team led by Drs. Dorrie Main and Sook Jung at Washington State University chose to use the Tripal database platform, an open-source web front-end for the generic Chado database schema (2, 3, 4). During this process, the team developed core and extension Tripal modules, in collaboration with other researchers in the Tripal community, transformed Tripal from a platform to (mostly) analyze transcriptomes to a more comprehensive and extendable open-source genomics and genetics database platform. In addition, the team used Tripal to efficiently build community databases for other underserved crop groups (citrus, Vaccinium and cool season food legumes). In 2018, the five databases of NRSP10 – the Genome Database for Rosaceae (GDR, 5), CottonGen (4, 6), the Citrus Genome Database (CGD, 7), the Cool Season Food Legume Genome Database (CSFL, 8) and the Genome Database for Vaccinium (GDV, 9) – are internationally recognized as the community databases for their crops. Tripal databases currently serve data on over 4000 crop and wild relative species.

The mission of the first NRSP10 project was to: 1) expand database resources for underserved fruit, nut, legume and cotton crops and 2) further develop standardized database protocols for use by other communities. The specific objectives and brief summary of results (See Appendix 1 for more details) follow:

Objective 1 - Expand online community databases currently housing high quality genomics, genetics and breeding data for Rosaceae, citrus, cotton, cool season food legumes and Vaccinium crops. All five NRSP10 databases have been significantly expanded in terms of the amount of data, new data types, new interfaces and analysis tools, usage and citations in publications (Tables 1 and 2).

Objective 2 - Develop a tablet application to collect phenotypic data from field and laboratory studies. The NRSP10 fruit, nut, legume and cotton research communities have adopted the Field Book App to collect phenotypic data.

Objective 3 - Develop a Tripal Application Programming Interface for building breeding databases. The Tripal Breeding Information Management System (BIMS) is compatible with Field Book and provides breeding management, data import, search, download and statistical analysis. Several peach, apple, pea, lentil and cotton breeders are using BIMS for their breeding programs, and many more are testing it.

Objective 4 - Convert GenSAS, the community genome annotation tool, to Tripal. The web-enabled genome annotation platform GenSAS has been further developed to include new annotation tools and functionality, providing a comprehensive resource for genome annotation and community curation, with publication-ready outputs. It is in the final stages of being fully integrated as an annotation module for Tripal databases.

Objective 5 - Develop Web Services to promote database interoperability. Tripal sites can now use RESTful web services to support remote client queries and ElasticSearch for cross-site data querying. Data collections can now be exported to a Galaxy workflow for analysis.

NRSP10 Renewal: Input systematically obtained from academic and industry scientist stakeholders has provided guidance about future types and volume of data likely to be collected for our target crops through 2024. In addition to much more whole genome sequence and RNASeq expression data, we expect petabytes of resequencing, epigenomic, pan-genomic and phenomics data. Integrating new types of data into legacy databases often requires changing schema, costing significant time, money and expertise. However, Tripal databases are built on Chado, the generic, modular and ontology-based database schema, which accommodates new data types easily. In addition, if interfaces and tools for new data types are developed as Tripal extension modules, they can be shared with other databases. We are already using tools developed by other Tripal databases, such as the Synteny Viewer (Fei Lab, BTI), Expression module (10) and ElasticSearch (10). We have released four extension modules (11) and BIMS (12) will soon be released. In the next NRSP10, we propose to develop new or enhanced Tripal modules to handle new types of data such as pan-genomic, epigenomic and phenomic data. In addition, we will also incorporate various analysis tools in modules like BIMS. Individual research labs, as well as large collaborative research groups, regularly generate high-throughput data they need to analyze. These analyses often require access to high-performance computing and include large, publicly available datasets and/or the results need to be examined using a graphical interface along with existing data. In addition, output of the analysis may need to be stored and made available for reuse in further research. While some data need to be kept private, results can be used by other researchers if certain aspects of the data are kept private. For example, breeders can share the relationship between genotype, phenotype and environmental conditions without jeopardizing IP as long as the pedigree and accession information are kept private. Use of community database resources in analysis, and not just in the design and submission phases, can promote data standardization as well as re-use. The need for user-driven high-throughput analyses, data re-use, integration, standardization and submission can be facilitated when community databases provide appropriate analysis tools with computing resources that can access the data stored in the database as well as the user’s data. We will invest resources in a professional assessment to identify sustainability models for core Tripal and the NRSP10 databases.

In 2019-2024 we propose to extend the research-enabling mission of NRSP10 to:

• Objective 1: Expand the online community databases for Rosaceae, citrus, cotton, cool season food legumes and Vaccinium crops


• Objective 2: Develop a Tripal module for visualization of epigenomics data


• Objective 3: Enhance TripalMap to integrate genomic and genetic data


• Objective 4: Enhance TripalBIMS to (a) support phenomics data, (b) add GWAS analysis, and (c) global performance prediction capability


• Objective 5: Identify sustainability models and provide additional tools and resources as required by the community

Providing tools for standardized database construction and continuing development of efficient and widely used target crop databases for GGB research are goals fully consistent with the stated NRSP missions:

• Development of enabling technologies and/or support activities (such as to collect, assemble, store and distribute materials, resources and information


• Sharing of facilities to accomplish priority research

 

Prerequisite Criteria

How is the NRSP consistent with the mission?

How does the NRSP pertain to a national issue?

Feeding a growing global population during a time of rapidly escalating environmental change is the Grand Challenge of our time. Opportunities to accelerate discovery and translate results into flexible crop improvement solutions are made possible using the insights now afforded by generation, analysis and re-use of Big Data. Scientists working on our target crops are generating larger and more complex data sets more frequently, and have indicated the pace will increase through 2024. Community databases are the logical homes for these data and they will maximize its utility to scientists and the return on investment to funding organizations by enabling communities to interrogate this complex data. The first NRSP10 project accomplished major expansion of the Rosaceae, cotton, citrus, legume and Vaccinium databases and met challenges for data management, data mining, data querying and data visualization. Collectively, the 24 crops served by these databases are grown commercially in all four SAES regions and in all 50 states and territories. In 2016 they contributed over $26.6 billion (13) in production value to the U.S. economy (Table 1). These databases are used by researchers from all 50 U.S. states and territories. The U.S. scientists who collect and provide data, and use these databases are predominantly based at Land Grant Universities and USDA-ARS. From 2015-18 (Table 2), these databases were cited in 1059 publications (Google Scholar), had 387,913 visits and served almost 2.5 million pages to 162,146 users from 185 countries (Google Analytics).

This renewal builds on the success of the first NRSP10, expanding the databases to integrate other types of Big Data (epigenomics, re-sequencing, expression and phenomics data) with whole genome sequence and other valuable genetic data. The renewal will develop and deploy new open-source tools to integrate and visualize these new types of Big Data. In addition, it will enable our databases to provide easy-to-access interfaces where users can run high-throughput analyses, view their results graphically and submit their data and results in appropriate formats when they want to release it publicly. Performing analyses through the community databases facilitates standardization of metadata, naming conventions, and ontology associations, as well as prompt data release. In addition, it will facilitate re-use of public data stored in community databases. Adding these functionalities to community databases will catalyze further applications in genomics-assisted breeding and advance the genomics, genetics, and physiology knowledge base. Providing another five years of stable support to continue development and deployment of fundamental, research-enabling databases, used ubiquitously in the U.S. for target crops and readily adaptable for other crops and organisms, classifies this NRSP as a national issue.

National issue: To increase data utilization across disciplines and facilitate research activities

A central goal of NRSP10 is to maximize the impact of GGB resources by providing access to platforms through which massive amounts of data can be routinely collected, analyzed, curated, integrated and made available to scientists in formats that best meet their diverse needs, as well as to provide web-based analysis tools to facilitate basic, translational and applied research. In the renewal we will continue to integrate large-scale breeding data with genetic and genomic data of Rosaceae, citrus, cotton, cool season food legumes and Vaccinium crops, helping translate advances in genomics into advances in crop improvement and crop management. Integrating new types of Big Data such as epigenomic, experimental expression and phenomic data will facilitate data utilization across basic and applied crop research. The user-driven analytic functionality proposed in this renewal, such as GWAS and performance prediction, will enable users to be both active contributors and deserving beneficiaries of community databases. In addition, TripalMap will strengthen the integration of genetic and genomics data, accelerating DNA-informed breeding in these communities.

National issue: To provide enabling technologies for efficient database construction

Generating genomic, genetic, phenotypic and environmental “Big-Data” is now routine for small research communities, increasing the need to construct online databases to support data management, storage, transfer, and integration. Creating an online database is not trivial, involving web programmers, database/system administrators and bioinformaticists to design a schema, to create data loaders to import data, and to construct pages for querying and viewing data and tools for searching and displaying the data. These requirements are often overwhelming. NRSP10 contributes to both the core and extension modules of Tripal, an open-source toolkit for constructing online community databases. The current NRSP10 contributed to core Tripal development and provided extension modules to load, search and display sequence, map, marker, QTL, genotypic, phenotypic and germplasm data. It also developed a versatile gene annotation tool (GenSAS, 14) and a breeding information management system (BIMS), in addition to further developing Field Book App (15) for collecting phenotypic data. The renewal will develop tools that provide critical analytic functionalities that are compatible with Tripal such as an enhanced BIMS with GWAS and a performance prediction tool, an epigenomic viewer, an advanced TripalMap (16), and updated modules.

National issue: To promote interoperability and sharing of data among databases

Ontologies are structured, controlled vocabularies that represent specific knowledge domains (17). Using ontologies is important in storing standardized data in a form that can be integrated and shared by computer codes working with multiple species. All NRSP10 supported databases use standard ontologies to describe traits and genes. The newly released core Tripal v3.0 (https://tripal.info) enforces requirements to use ontologies in displaying data types and integrates tightly with web services. This encourages development and use of community-derived controlled vocabularies and facilitates exchange of data among databases. As proposed in this renewal, the online analysis tools integrated with Tripal sites will also promote the standardization of metadata at the time of analyses, further facilitating standardization and data sharing among databases. We are working towards interoperability among all GGB databases as core members of the AgBioData consortium (https://www.agbiodata.org, 1).

National issue to promote community building

The NRSP10 project continues to promote community-building in multiple ways. Target communities include the specific community served by each database, the extended research communities a database and related databases serve together, the Tripal and GMOD development communities and the entire U.S. agricultural database community.

Crop databases play a central role in building and maintaining effective research communities. They fill a critical need by offering curated and integrated data, custom data mining tools, and visualization and analytical tools tailored to audiences with shared basic and applied research goals. For example, GDR has been instrumental in building a highly collaborative Rosaceae research community since its inception in 2003, including the U.S. and International (RosEXEC and RosIGI) Rosaceae groups. GDR hosts member elections for RosEXEC, which serves as the GDR’s official steering committee. GDR has been an active partner with large community-wide projects such as RosBREED and EU FruitBreedOmics as well as smaller projects. The community has developed assets such as a priority-documenting White Paper, and a stakeholder-driven technology roadmap, and gathers regularly for biennial International Rosaceae Genomics Conferences. Similarly for cotton, CottonGEN houses community communication resources. It hosts the ICGI site and elections and is governed by a representative community steering committee. All the NRSP10 databases work with the communities they serve on grant submissions and data management strategies.

Working with TreeGenes (18) and the Hardwood Genomics Project (18), GDR and CGD have been active in building a wider community of Tree databases. These Tripal databases collaborate and share custom Tripal modules including ElasticSearch, allowing data searching across all sites. Similarly, the Tripal Synteny Module enables researchers to explore synteny among tree genomes from each site with hyperlinks to gene pages in its home database. This connectivity allows tree researchers with distinct perspectives and abilities to share data and to develop new collaborative and innovative projects.

The NRSP10 team is an active participant in the Tripal development community. We used initial funding (USDA-NIFA SCRI Award #2014-51181-2237 ($1.99M), USDA-ARS ($550K), and industry support of $850K), prior to the start of NRSP10 in 2014 to develop the core Tripal platform. Subsequently we contributed to core and extension module development through NRSP10 (PI Main, $1.99M), USDA-NIFA SCRI Award 2009-51181-0603 (PI Main, $2.74M) and NSF DIBBS Award #1443040 (PI Ficklin, $1.5M), NSF PGRP #1444573 (PI Main, $2.99M) and, including direct support from the cotton, tree fruit and cool season food legume industries to PI Main, leveraged funding of more than $10 M. We actively collaborate with other database teams to customize and adopt extension modules developed for their databases. Sharing Tripal modules among different research communities reduces effort and expense and also provides opportunities to enforce data standardization.

NRSP10 has also played an important role in developing the AgBioData consortium and it continues to work energetically to foster collaboration and community-building among member databases.

 

Rationale

Priority Established by ESCOP/ESS

This NRSP proposal targets five of the seven grand challenge priorities:

Grand Challenge 1: “Enhance the sustainability, competitiveness, and profitability of U.S. food and agricultural systems.”

Grand Challenge 2: “Adapt to and mitigate the impacts of climate change on food, feed, fiber, and fuel systems in the United States.”

The negative impact of climate change on crop production is well-documented (19, 20, 21, 22). The specific impact on a crop or region can be devastating. For example, Georgia’s disruptively warm winter in 2017 led to the loss of an estimated 85% of the peach crop (23). The warm and dry California winter in 2014 caused severe damage to the cherry crop, and atypical low temperatures during bloom in 2012 destroyed up to 90% of the Michigan apple and tart cherry crops. Recent climate trends, such as changes in temperature and precipitation, decreased cotton yield (24). Providing access to germplasm evaluation and other breeding data by location and weather/climate is crucial in developing new cultivars less sensitive to unusual field conditions. Integrating performance and environmental data with genomic and genetic information, such as expression and trait loci data will also help identify genes that are responsible for traits sensitive to environmental change. Adding new types of pan-genome data and epigenome data will help in discovering new genes and/or new gene regulation patterns that affect traits that can reduce the impacts of weather/climate. In addition, high-throughput phenotyping technology that uses reliable screening tools and platforms to measure expression of physiological traits in realistic field environments will aid in QTL/gene discovery for both drought and heat resistance. This renewal will allow us to build infrastructure to accommodate high throughput phenotyping data, which will facilitate the development of strategies to mitigate the impact of climate change in crop production. In addition, the performance prediction tool will enable participating breeders around the world to anonymously share their data from vastly different environments so that they can predict the performance of their material in a wide range of environments. If this works, it will accelerate crop breeding, especially for perennial crops.

Grand Challenge 3: “Support energy security and the development of the bioeconomy from renewable natural resources in the United States.”

The provision of an easy-to-use, manageable, standardized platform for GGB database development will facilitate database development for organisms relevant to energy security based on renewable natural resources. Funded by NSF DIBBS and PGRP, we are collaborating with TreeGenes and Hardwood Genomics Project to build further Tripal database construction tools. This includes development of web services and Elastic searches enabling users to have seamless access from their home Tripal database to data in all the Tripal databases. We are also planning to perform synteny analysis among tree genomes and display the results using the Tripal Synteny Module in each database with hyperlinks to gene pages in specific databases. This will facilitate sharing data among tree genomes and open new opportunities to advance our understanding. Many scientists working on potential biofuel crops lack any access to well-curated genome databases. New Tripal databases will provide access to breeding-decision tools, enabling comparison of parental and selection evaluation data that cannot be readily done in any other free breeding data management software. Outcomes of this proposal include the essential infrastructure and expertise to impact on breeding programs for high-yielding, low input bioenergy feedstocks.

Grand Challenge 4: “Play a global leadership role to ensure a safe, secure, and abundant food supply for the United States and the world.”

The fruit, nut, legume and cotton crops of NRSP10 are important for food, feed and fiber supply for the U.S. and the world. These openly-accessible databases enable domestic and international research programs to readily exploit GGB resources. While the databases themselves are mostly crop-specific, the software infrastructure and expertise to be further developed in this proposal are explicitly intended to be exportable to other crops or organisms. We estimate that more than 100 Tripal databases are under development, mostly for crop plants but including databases for microbes, insects and other animals. Supporting core development and help desk support, NRSP10 is a critical infrastructure resource for these.

Grand Challenge 5: “Improve human health, nutrition, and wellness of the U.S. population.”

All the crops housed in the Rosaceae, Citrus and Vaccinium and cool season food legume databases contribute significantly to a health-giving and nutritious human diet. Breeding programs in the U.S. will gain considerably in efficiency and effectiveness through ready access to a Breeding Information Management System integrated with the high quality publicly available GGB data in their community databases. In addition, the availability of BIMS as a Tripal extension module will encourage adoption of the platform by other crop communities, benefiting a much wider audience.

Relevance to Stakeholders

The stakeholders of the databases described in this NRSP include biologists, breeders, bioinformaticists, educators, consumers, funding agencies and the industries based on the participating crops. The databases will continue to store and integrate data from various research projects, funded by government and industry, accelerating knowledge discovery from the integrated information and maximizing the return on the GGB investment. The outreach activity of this NRSP project benefits researchers working on other agricultural databases as well. As detailed in the management plan, primary stakeholders from research institutions and industry will continue to participate in project development and assessment as members of the steering committee for the databases. Their participation will help ensure the development effort is prioritized to meet the needs of stakeholders. The ultimate stakeholders of this NRSP are consumers and U.S. taxpayers. Below is a detailed description of the benefits for each type of stakeholder.
 
Biologists

The curated genomic and genetic data and analysis tools available in the databases developed in this NRSP will help basic biologists who are interested in the structure and evolution of genomes, in gene expression, gene function and genetic variability, and in the mechanisms underlying various traits. Integrated genomic, genetic and phenomic data will help translational scientists who are interested in further QTL and marker discovery and genetic mapping studies. The integrated genomic, genotypic and phenotypic databases will also help applied scientists who are interested in developing methods for marker-assisted breeding. The molecular diversity data and germplasm data will help scientists go beyond well-known gene pools to explore other ways to achieve their goals. All databases supported by this NRSP contain data for multiple species, which will enable transfer of knowledge among related species as well as studies on genome evolution. In addition to integrating data from multiple species within each database, one goal is to develop tools to integrate data from diverse major tree databases by providing access to conserved syntenic regions, web services and cross-search searching. Consistent interfaces will also promote cross-utilization between communities by decreasing the learning time required to navigate each new database.

Breeders

The extensive breeding database in GDR enables breeders to search integrated GGB datasets for apple, peach, cherry and strawberry in a fully targeted manner and to retrieve and compare performance data from multiple varieties and seedlings, years and sites. This facilitates the streamlining of selection decisions and output data needed for variety release, publications and patent applications. In the current NRSP, we developed BIMS in Tripal so that breeders can load their data themselves, allowing them to truly ‘own’ and use their databases. BIMS also is compatible with Field Book App, an Android application for data collection that significantly helps breeders and scientists reduce the time and cost of phenotypic evaluation. While using BIMS in their community database, breeders have the option to keep their data in a private database but also link to all relevant public data. We will continue to add more functionality, including further analysis tools and breeding decision tools, to help breeders manage and utilize their data more efficiently and effectively. The new performance prediction tool in BIMS will aid breeders to predict how their material will perform in various environmental conditions. In addition, using the tablet application to collect data and upload to BIMS is expected to facilitate standardization of phenotypic evaluation methods and development of collaborative research projects on cultivar evaluation and breeding.

Bioinformaticists and Agricultural Database Developers/Managers

The renewal of this NRSP project will further develop Tripal as a freely available GGB database construction platform. This NRSP will contribute to adding new components to Tripal to handle high-throughput phenomics data, develop new extension modules for Tripal, and further develop BIMS functionality.  These improvements will greatly benefit developers as they build databases housing large-scale GGB data for their respective research communities. The web services will help bioinformaticists who require programmatic access to large-scale data to integrate with other databases or perform further analyses. Access to updates and upgrades of the core Tripal package is essential for all Tripal databases. This includes ensuring core Tripal is updated to be compatible with new versions of Drupal and providing guidance and help in ensuring extension modules are also updated to remain compliant with the Tripal code. The NRSP project team is part of AgBioData, a consortium of more than 35 agricultural biological databases and allied resources. Our combined effort to ensure standards and best practices for acquisition, display and retrieval of genomic, genetic and breeding data will be highly beneficial to all agricultural database developers. One benefit to the IT workforce will be an increase in their transferable skills, since skill in Tripal will be useful to many databases.

Educators

Comprehensive tutorials, screencasts and videos developed for users of each database will be useful in formal or informal, classroom or distance learning contexts. Development of databases offers an ideal opportunity for graduate student education. Specific objectives include: 1) establishing cooperative Community-of-Practice-like interactions between the crop-specific curators and the core personnel that encourages the appropriate development and extension of resources; 2) small-group, face-to-face workshops in Pullman, WA to facilitate transfer of expertise between participants and common establishment of priorities; 3) focused teaching modules for use in classroom or web-based delivery platforms that familiarize users and potential users with available resources and provide appropriate training.

Consumers

Consumers will be provided with higher quality, more nutritious and environmentally friendly fruits, vegetables and staple crops as a result of the use of the output of this NRSP.

Funding Agencies

Researchers increasingly rely on access to community databases to enable their research. Before NRSP10 was funded, its component databases largely relied on short-term funding from federal agencies, making them very vulnerable to loss of highly skilled personnel, valuable data and functionality, if/when there was a break, or potential break, in funding. The results from the proposed sustainability study will help identify the best economic and labor models to support core Tripal and the NRSP10 databases and reduce reliance on State Agricultural Experiment Stations and federal funding. The results of this analysis by Phoenix Bioinformatics, the group who successfully moved TAIR to a subscription model, will provide ideas and guidance for other GGB databases faced with similar challenges.

Crop Production Industry

Several industries, led by key commodity associations (rosaceous tree fruit, cotton, citrus, and dry pea and lentil), have provided funding and are participating in building and populating our target databases. This NRSP will ultimately benefit each of these crop industries since it will significantly enhance current, highly-utilized databases and expedite the development of cultivars that are competitive, profitable, sustainable and climate-adaptable. Our core strategy will allow additional crops to be added to the list on demand as support for further crop-specific efforts is generated. Continuation of this NRSP should substantially lower the expenses needed for a commodity to establish a database and the associated analytical tools.

Implementation

Objectives

1. Expand the online community databases for Rosaceae, citrus, cotton, cool season food legumes and Vaccinium crops
   Comments: We will continue curation and integration of GGB data, adding the ability to handle new data types such as pan-genomic, epigenomic, and phenomic data, and providing tools for further analysis of new/updated whole genome sequencing data to connect to genes in other databases, find conserved syntenic regions and orthologous genes, and identify metabolic pathways. We will continue to develop utilities for QTL and marker identification, analysis of expression and methylation data as well as variation data from SNP array, resequencing and pan-genome analysis. In addition to publication/submitted data, we will add trait evaluation data from GRIN integrated with breeding data.
2. Develop a Tripal module for visualization of epigenomics data
   Comments: Studies to understand epigenetic mechanisms underlying the basis of important traits are increasing for NRSP10 crops. To maximize utility of these data, we will develop a Tripal Epigenome module so users can search for genes/genomic fragments and view the level of epigenetic modification in various tissues and conditions. Integration with other genomic, transcriptomic, expression and genetic data will further increase the value and utility of this data.
3. Enhance TripalMap to integrate genomic and genetic data
   Comments: We will expand TripalMap, our genetic map comparison and visualization viewer, to display genes and markers in chromosomes, as well as markers and QTL in linkage groups of genetic maps, similar to the NCBI map viewer. Chromosomes and linkage groups will be linked by shared markers, allowing users to explore the genomic features around QTL, even when only the genetic position is available. The genes in chromosome view in TripalMap will hyperlink to JBrowse and other graphical viewers, allowing exploration of expression, methylation and sequence variation data.
4. Enhance TripalBIMS to (a) support phenomics data, (b) add GWAS analysis, and (c) global performance prediction capability
   Comments: Phenomics data is becoming increasingly available NRSP10 crops. BIMS will be enhanced to accommodate storage of high-throughput phenotyping, and integrate environmental and genotypic data. BIMS will be further enhanced by the addition of GAPIT for GWAS and genome prediction to allow users to identify genetic variations for important traits. A module will be developed that can combine national and international data for global performance predictions. Germplasm can perform differently in different environments and the module will enable breeders to predict the performance of their material under various conditions. In this tool, the phenotypic and genotypic data from various environmental conditions can be compiled in an anonymous database, allowing the effect of the environment on replicated genomic segments to be tracked. Users will be able to input the genotypic and phenotypic data of their materials then view the predicted performance under various conditions. Without revealing any proprietary information, breeders can contribute their data to the anonymous database to increase the accuracy of the prediction tool. We will also implement BrAPI web services (https://brapi.docs.apiary.io/#) so BIMS users can exchange their data with breeding tools in other systems using BrAPI.
5. Identify sustainability options and provide additional tools and resources as required by the community
   Comments: Using data they collect in the last 6 months of the first NRSP10, Phoenix Bioinformatics will analyze and report on the best models for core Tripal and NRSP10 databases sustainability in years 1 and 2, with pilot implementation implemented and assessed in years 3 to 5. As current practice we will continue to add new tools or resources as requested by the community.

Projected Outcomes

Management, Budget and Business Plan

Management

Thanks to the stable funding provided by the first NRSP10, and related federal and industry support, our core team remains mostly the same as the first project: the project director (Dr. Dorrie Main); lead curator/software designer (Dr. Sook Jung); three Tripal software developers (Taein Lee - BIMS and GenSAS; Chun-Huai Cheng - Epigenome viewer, other software, Tripal core support, Tripal help desk support; Katheryn Buble – MapViewer and other software); a database/system administrator (Heidi Hough); a data analyst (Dr. Ping Zheng); and two or more curators (Dr. Jodi Humann, Dr. Jing Yu, student/staff curators). In addition, we are formally adding Dr. Stephen Ficklin (co-initiator of Tripal with Dr. Meg Staton, UTenn), hired as Assistant Professor at WSU from postdoctoral position in the MainLab) as lead core Tripal developer and Shawna Spoor - Tripal core development and Tripal Help Desk Support) to help meet the need of growing need for Tripal support and training. This is a direct result of increasing adoption of Tripal by the GGB database community.

The structure of our effort is rather complex, with NRSP10 (and components of other USDA and NSF grants) supporting infrastructure development, but working closely with crop-specific applications in order to develop valued infrastructure that can be implemented in other databases. As appropriate, effort will be shared with other projects, depending on how much of the task is infrastructure development and how much is specific to the associated database and supported by industry or federal funding directed to the crops involved. Each curator is assigned to a specific crop database(s). The curators will meet regularly with any newly hired or collaborating curators to train them on scientific curation procedures and check progress. Tripal data curation and analysis procedures are relatively independent of the crop/database so this management system will ensure that data curation expertise continues to be transferred efficiently as new crop databases arise in the community such as the Carrot Genome Database.

The project director (Main) will oversee the project in general and extension module development for the project  The lead curator (Jung) will design extension module functionality in consultation with other curators in the lab and in the wider Tripal community, and the lead core Tripal developer (Ficklin) will oversee core Tripal development and help desk support. The GAPIT package (25) and the performance prediction tool (26) will be implemented in BIMS in close collaboration with the authors of the tools, Dr. Zhiwu Zhang (WSU) and Dr. Craig Hardner (University of Queensland), respectively. Further development of BIMS functionality will continue to be in close collaboration with Dr. Ksenija Gasic (peach breeder, Clemson University), Dr. Todd Campbell (cotton breeder, USDA-ARS Florence) and Dr. Rebecca McGee (legume breeder, USDA-ARS Pullman). In addition, we will continue to seek input from participating breeders through in-person and teleconference visits/meetings with individual programs, monthly BIMS seminars, and NRSP10 workshops and training sessions. Each programmer will be responsible for using Drupal coding styles and the existing Tripal API. The lead curator and programmers will continue to have bi-weekly developers’ meetings to discuss the progress of tool development and to share any practical information in developing tools. When a beta version of software is finished, the appropriate curators and other programmers in the lab will test the software. The entire project team will meet weekly using online teleconferencing to discuss tasks, timelines and progress.

The steering committees for GDR and CottonGEN will continue to meet regularly to review progress and provide feedback on tasks for the next quarter. Specific benchmarks will be set in consultation with the steering committees for each database at the start of the project and reviewed quarterly. The steering committees will also facilitate the standardization of various data to make the data findable, accessible, interoperable, and reusable (FAIR, 27). RosEXEC, who serve as the steering committee for GDR, created a subcommittee that considered and published principles for standardizing gene names (28) that were incorporated into GDR. We are in the process of establishing a steering committee for the Vaccinium database (chaired by Dr. Hamid Ashrafi, NC State University), meeting with the International Citrus community in January at PAG 2019 regarding a steering committee, and establishing one for the cool season food legume database (chaired by Dr. Rebecca McGee).

The adoption and growth of Tripal as a common platform for GGB database construction over the last 4 years has been very encouraging and suggests the model we proposed is working well. With over 150 downloads of the platform, Tripal databases have been constructed for a range of plant, animal and microbial organisms. The adoption trend continues, with more engagement as more functionality is added by the developer community. Tripal (https://tripal.info) and extension modules are being developed by 12 institutions, including Washington State University (Stephen Ficklin and Dorrie Main programs), University of Tennessee (Meg Staton program), University of Connecticut (Jill Wegrzyn program), Iowa State University (Ethalinda Cannon), National Center for Genome Research (Andrew Farmer), USDA National Agricultural Library (Monica Poelchau/Chris Childers), USDA-ARS (Steven Cannon), University of Saskatchewan (Lacey Sanderson), Boyce Thompson Institute (Zhangjun Fei program), Stowers Institute (Sanchez program), Bioversity International (Max Ruaz program), and Clemson University (Alex Feltus program). As a key part of the NRSP10 renewal we will continue to develop core Tripal, provide support for module development and implementation, and assess sustainability options for core Tripal and assist groups seeking to develop new databases. Tripal has a Project Management Committee (PMC) for code approval and feature requests and plans are underway to add a steering committee of representative stakeholders to help guide the continued growth and sustainability of Tripal.

We will continue to hold monthly Tripal community and developer meetings and yearly 2 day hackathons. The community meetings involve discussion between users and developers of Tripal, providing invaluable feedback on usability and functionality of Tripal, reducing duplication of effort, and promoting collaborations. The developer meetings alternate between a Help Desk open call and a training topic.

As core members of  the AgBioData consortium, we will continue  to ensure our work aligns with its goal to identify common issues in database development, curation, and management, with the goal of creating database products that are more FAIR compliant (Findable, Accessible, Interoperable and Reusable). To this end we have submitted a $1M USDA NIFA FACT Coordinated Innovation Network proposal for the AgBioData Consortium (PI: Main) to advance the efforts outlined in the White Paper (1).

Timeline

In Year One: 1) Collect and curate genomic, genetic and breeding data for all databases and incorporate FAIR practices developed in AgBioData; 2) Collect gene expression data and implement Tripal expression module in GDR; 3) Collect pan-genome data for GDR; 4) TripalMap: Design graphical viewer for genome data in Chado; 5) BIMS: Obtain phenomics data from cotton breeders and design storage methods; 6) Global Prediction Tool in BIMS: Develop training dataset and implement prediction algorithm; 7) Begin analyzing a range of potential funding sources including voluntary membership models, data deposit fees, subscriptions, freemium models, crowdfunding, corporate support, and philanthropy; 8) Update all database webinars and tutorials; 9) Hold at least twice yearly individual database steering committee meetings and one annual project wide meeting; 10) Present database and tools at conferences and meetings.

In Year Two: 1) Collect and curate genomic, genetic and breeding data for all databases and incorporate FAIR practices developed in AgBioData; 2) Collect expression data and implement Tripal expression module in CottonGEN; 3) Develop and implement tools to display pan-genome data in GDR; 4) Design data storage method and search/display tool for epigenome data using any available data from Rosaceae; 5) TripalMap: Add functionality to compare features in chromosomes and genetic linkage groups; 6) BIMS: Develop data loaders for phenomics data; 7) Global Prediction Tool in BIMS: Design interface for BIMS users; 8) Report results of sustainability analysis study with recommendations;  9) Update all database tutorials; 10) Hold at least twice yearly individual database steering committee meetings and one annual project wide meeting; 11) Present database and tools at conferences and meetings.

In Year Three: 1) Collect and curate genomic, genetic and breeding data for all databases and incorporate FAIR practice developed in AgBioData; 2) Collect any available expression data and implement Tripal expression module in CSFL and CGD; 3) Develop and implement tools to display pan-genome data in CottonGEN; 4) Develop data loader and search/display tool for epigenome data in GDR; 5) TripalMap: Continue to develop TripalMap and add connectivity to other graphic viewers such as JBrowse; 6) BIMS: Develop search/download page for phenomics data; 7) Global Prediction Tool in BIMS: Design interface for non-BIMS users; 8) GWAS tools in BIMS: design interface to GWAS tool (GAPIT); 9) Begin pilot implementation of sustainability recommendations; 10) Hold at least twice yearly individual database steering committee meetings and one annual project wide meeting; 11) Present database and tools at conferences and meetings.

In Year Four: 1) Collect and curate genomic, genetic and breeding data for all databases and incorporate FAIR practices developed in AgBioData; 2) Develop interface to connect expression/pan-genome/epigenome viewers; 3) Develop and implement tools to display pan-genome data in CSFL; 4) Implement data loader and search/display tool for epigenome data in CottonGEN; 5) TripalMap: Further develop interface for administrator to reflect new functionality; 6) Implement BrAPI in BIMS; 7) Implement Global Prediction Tool in other databases when the training datasets are available; 8) GWAS tools in BIMS: Implement interface to GWAS tool (GAPIT) in GDR; 10) Assess success of sustainability pilot implementation; 11) Hold at least twice yearly individual database steering committee meetings and one annual project wide meeting; 12) Present database and tools at conferences and meetings.

In Year Five: 1) Collect and curate genomic, genetic and breeding data for all databases and incorporate FAIR practice developed in AgBioData; 2) Continue to refine epigenome viewer and the connectivity with other graphic viewers; 3) Implement pan-genome data viewer and epigenome viewer in other databases when data become available; 4) TripalMap: Further refine the functionality and tutorial; 5) Update all webinars and tutorials; 6) BIMS: Develop tools to produce output for other breeding related tools; 7) BIMS: Further develop any necessary functionality for underlying Global Prediction Tool and GWAS tool; 8) Continue to assess success of sustainability implementation; 9) Hold at least twice yearly individual database steering committee meetings and one annual project wide meeting; 10) present database and tools at conferences and meetings.

Budget

A total of $2,449,789 (Table 3) is requested over five years for this NRSP10 (2019-2024) to support the development activities described in this proposal. Additional funding from aligned objective support (Table 3) is projected over the course of this project from WSU ($3,035,527) and Industry ($741,889). Our two major SCRI ($2.74 M) and NSF ($2.99 M) grants will be completed by the start of this renewal project, but we will be submitting a renewal for the GDR SCRI project and are requesting a Centre of Excellence designation, as well as submitting to NSF PGRP. We will also seek further support from the Washington Tree Fruit Research Commission for tree fruit data analysis and curation; the USA Dry Pea and Lentil Council and Northern Pulse Growers for pea and lentil data analysis and curation and the Citrus Research Commission for data curation support. Support of ~$180,000 per year from Cotton Incorporated, the cotton industry and USDA-ARS is available for CottonGen through 2021.  Known support for the period of renewal ($2,069,983) combined with funds requested from NRSP ($2,449,789), totals $4,519,772 for the complete project.

Table 3: NRSP10 Budget Requested Summary

Cost	Year 1	Year 2	Year 3	Year 4	Year 5	Total
Salaries	394,140	409,906	426,302	443,353	461,088	2,134,789
Publications	4,000	4,000	4,000	4,000	4,000	20,000
Goods & Services	15,000	15,000	15,000	15,000	15,000	75,000
Equipment	40,000		40,000			80,000
Consultancy	15,000	15,000	5,000	5,000		40,000
Travel	20,000	20,000	20,000	20,000	20,000	100,000
Total	488,140	463,906	510,302	487,353	500,088	2,449,789

Salaries: 4 Tripal developers, 50% Database Administrator/System Admin, 15% PI Main, 7.5% Ficklin

Publications: 2 per year

Goods and Services: server room fees, service contracts, data storage and onsite and offsite backup

Equipment: for new database/webservers in years 1 and 3
Consultancy: Phoenix Bioinformatics to analyze and help implement sustainability options

Travel: to present activities at conferences/meetings for all 5 crop database communities, travel to meet with stakeholders for individual training on using BIMS, attend yearly Tripal hackathons

Table 4: NRSP10 Aligned Support Cost

Cost	Year 1	Year 2	Year 3	Year 4	Year 5	Total
Salaries	241,142	245,888	240,401	245,019	124,872	1,097,322
Benefits	177,049	182,414	188,149	193,948	156,232	897,792
Good and Services	8,548	11,148	11,214	13,959		44,869
Travel	6,000	7,000	8,000	9,000		30,000
Total	432,739	446,450	447,764	461,926	281,104	2,069,983

Salaries: 50% Sys Admin, 30% Dorrie Main, 120% Data Curator, 30% programmer, 25% Data Analyst

Benefits: paid by WSU for all positions

Funding from other sources: CottonInc, USADPLC, NPG, WTFRC

Business Plan

In the first NRSP10, we sought successfully (see Appendix 1 for more details) to replace prior ad hoc funding of critical crop databases and model database platform construction with a more sustainable two-level model. This two-level model obtains support for core database activities from NRSP10 but engages funding from industry stakeholders and regional/federal grant competitive sources for data curation and analysis activities, as well as other infrastructure development.  Totaling over $10M (Appendix 1) these aligned funds represented a direct return on NRSP10 investment of more than 5 to 1. This exceeded the projected aligned funding from the first proposal by more than $6M. In this renewal we propose continuing and extending our two-level approach by assessing and implementing models toward creating a sustainable ecosystem for core Tripal and NRSP10 databases.

In this renewal proposal development activities will be supported by funds from the NRSP and include costs associated with database administration, development, data storage, IT server room space rental, server service contracts, data backup, and support desk help for other Tripal adopters. It will also fund updates to computational database and web servers to meet escalating demand for fast, efficient database access. The second major area of activity -- data curation and analysis support will be sought through industry and researcher stakeholder support. Extending this model we will add (a) assessment of potential models for sustainability in years 1 and 2, and (b) implementation of the most promising ones as pilot projects in years 3 and 4, with the goal of eliminating or reducing the need for a third NRSP10.  To this end, we have solicited the services of Phoenix Bioinformatics (http://www.phoenixbioinformatics.org/), a company founded in 2013 by the staff of the Arabidopsis Information Resource (TAIR, 29), who successfully pioneered a subscription based sustainable funding model to support TAIR. Their nonprofit mission is to help other projects achieve sustainable support using the tools and expertise developed for TAIRs transition.  As we have some funds available in this last year of the current NRSP10 project, we will redirect them to Phoenix to begin an assessment of core Tripal and NRSP10 crop databases. This study will capture cost of operations, staff level, sources of funding, usage level, data types, species and strains, and what types of researchers and others (educators, students) are being served. In the renewal project Phoenix will analyze a range of potential funding sources including voluntary membership models, data deposit fees, subscriptions, freemium models, crowdfunding, corporate support, and philanthropy. The results of this study will be shared with AgBioData member databases. If our USDA NIFA FACT Coordinated Innovation Network grant (PI Main) is successful, all 30 plus member databases will also be assessed by the Phoenix team, with more in depth analysis for representative databases.

Recognizing that the sustainability solution for our Tripal databases may involve starting a non-profit or for-profit company, Drs. Dorrie Main, Stephen Ficklin and Mike Kahn have audited the WSU NSF iCorps course (https://research.wsu.edu/icorps/) and will enroll in the class formally in Fall 2019.  The I-Corps 8-week program engages faculty, student and staff entrepreneurs to transform their ideas into successful business products. This program advises on appropriate grants to apply for such as the Small Business Innovation Research (SBIR) program. We see potential for offering Tripal services to businesses as a possible mechanism to help fund our public research database efforts.

Integration

NRSP10 is highly integrated with academic and government research programs and is stakeholder-driven (as evidenced by the project participant list and supporting letters). Providing continued access to collated, curated, and integrated public genomics, genetics and breeding data will enable unanticipated scientific advances well beyond the research for which the data were originally collected. The enhanced and connectable databases provide a catalytic environment where genomicists, geneticists, bioinformaticists, breeders and growers can share data and ideas to elevate trans-disciplinary understanding of their crops, to suggest compelling directions for new methods and research, and to produce efficient and focused practical steps toward the common goal of crop improvement. Specifically, integration of the genetic, genomic and breeding data will enable members of the crop improvement community to develop new scientific hypotheses and theoretical models and test these using appropriate databases and tools. The results will improve understanding of the fundamental biology underlying the crops and their valuable traits. By integrating genetic data (such as quantitative trait loci, genetic markers, and pedigrees) used to make and populate genetic maps with genomic data (genome sequences, chromosomal physical arrangements, sequence variants from large populations, and gene expression measurements), phenomics and environmental data, genomics-genetics-breeding translational biologists will be able to develop better tools and knowledge for developing improved cultivars.

In addition to providing integrated databases for individual research programs worldwide, the database team has also been involved with several extension and academic programs in more direct ways. GDR has been supported from 2014-2019 through an USDA SCRI-funded $2.74 million award. The GDR team was also integral to the 2009-14 and 2015-19 USDA NIFA SCRI-funded $10 million community-wide RosBREED projects providing that project with genomic and genetic data analysis including synteny analysis for data transfer among crops and development of Breeding Information Management System to enable marker-assisted breeding in rosaceous crops. CottonGEN is supported from 2011-2021 by a combined grant of $1.2 M from Cotton Incorporated, Bayer, Corteva, Southern Association of Agricultural Experiment Station Directors and USDA–ARS. Our team has participated in other major research initiatives, providing both sequence analysis and database support to projects such as the International Pea and Lentil Genome Sequence Consortiums and analysis of unculturable Ca. Liberibacter crescens, causal agent of citrus greening, with culturable Liberibacter crescens to identify candidate genes that may be missing in the unculturable strain.  We are also embedded in the Vaccinium CAP, Peach and PolyPloids projects with planned submission to the 2019 SCRI program.

Through this NRSP, we hope to systematize the effort and use the experience acquired by these diverse crop research communities to maintain and improve existing databases and lower barriers to entry for the construction of new ones. Industry stakeholders have been directly involved with database development as funding agencies and as users and members of advisory groups. The Washington Tree Fruit Research Commission (WTFRC) funded development of an apple and cherry cultivar performance database and toolbox built upon GDR resources originally funded by the NSF. Stakeholders from university, government and industry sectors from all the production and research regions of the U.S. are well represented in RosEXEC, the steering committee for GDR. The CottonGen steering committee is also composed of representatives from universities, government and industry. It meets quarterly to communicate the current and emerging database needs of the cotton research community and other stakeholders for development, implementation and dissemination of CottonGen. CottonGen is home to registration and submission of abstracts for the biennial International Cotton Genome Initiative conferences. 

NRSP10 is also developing sharable tools for database construction so that the research on crop database development can be integrated and shared. All the tools we developed and will develop are and will be available as extension modules, so that other Tripal databases for other crops and organisms can readily incorporate them. Some examples include the Legume Information System (30) and TreeGenes, who converted to Tripal, and new databases include PeanutBase, the Carrot Genome Database and i5K NAL (31).  

In addition, we have been core members of the AgBioData Consortium, a consortium of agricultural biological databases and associated resources working together to ensure standards and best practices for acquisition, display and retrieval of genomic, genetic and breeding data.

Outreach, Communications and Assessment

Outreach

Our outreach effort will focus on (1) crop communities that the databases serve; (2) communities who may be in need of Tripal databases; (3) the Tripal community; and (4) participation in the AgBioData consortium to increase: (a) standardization of protocols and practices across agricultural GGB databases to enhance GGB research outcomes, (b) researcher compliance in FAIR principles, (c) journal compliance with availability of peer-reviewed publication data, and (d) collaboration with funding agencies to help facilitate data deposit of meta, raw and analyzed data by funded researchers.

NRSP10 workshops will continue to be held yearly at the International Plant and Animal Genome (PAG), American Society of Horticultural Science, and Cotton Beltwide Conference annual meetings, as well as presentations in appropriate workshops at PAG, at the Crop, Soil and Agronomy annual meeting, and more crop specific meetings such as the International Rubes and Ribes, International Rosaceae Genomics, International Cotton Genome Initiative, and Citrus HLB Conferences.  The NRSP10 workshops provide training that primarily involves stakeholder researchers demonstrating how they use component NRSP10 resources. We have found this to be a very effective method of training, with time for a discussion session to solicit feedback with core NRSP participation to keep the development aligned with stakeholder interests. Participants at the workshops and computer demonstration sessions are composed of researchers from many other crop communities, so presentations at PAG, in particular,  provide good opportunity to present the utility of the Tripal platform and the support we provide in implementing or converting other databases.  

In addition to presentations at conferences, we will also continue to update tutorials on how to use databases, host webinars and make them available online, maintain mailing lists and continue to publish when significant development has been made.

To reach database developers, Tripal will continue to be presented and training provided at yearly Tripal workshops at PAG and other meetings such as the GMOD, Galaxy and Bioinformatics conferences. We will continue to provide tutorials, mailing list responses, and Help Desk support in collaboration with other Tripal developers and update modules as new Drupal versions are released. We will continue to provide tutorials and publish when we produce new modules and applications.

Additionally, it is very important that breeders, stakeholders and the general public are trained about the usefulness of their community databases and functionalities that might be incorporated from other databases. We will add a public component to our website highlighting the utility of the databases in successful research stories that impact consumers, explaining the terminology at an appropriate level and including database training from the workshops. These extension and outreach activities will greatly enhance the research and extension programs of cotton, legumes and horticultural specialty crops. Using the database in the process of breeding superior plant selections will distinguish the United States amongst others in the world market for those crops. In addition, in association with the continued growth of cotton, legumes and horticultural specialty crop production, it will lead to more jobs with higher incomes, which in turn will create economic development and prosperity, enhancing the quality of life in rural areas.

We will continue to be good citizens of the AgBioData Consortium of Agricultural-related databases. This will include continuing to serve on the Steering Committee, helping to organize yearly workshops, engaging in sustainability studies, hosting the AgBioData website (https://www.agbiodata.org), participating in monthly meetings and specific workgroups, as well as adopting the recommendations of the WhitePaper (1), and applying for funding to further the research enabling mission of this group (currently a USDA NIFA FACT Coordinated Innovative Network proposal for AgBioData is pending – PI Main)

Communication

In addition to the workshops mentioned above, other conduits to facilitate communication between the database developers and the users are needed. While we envision that implementation of each database will have significant individuality, each database that associates with NRSP10 will have a steering committee, composed of representatives from universities, government and industry for each crop, which will meet quarterly or biannually by online teleconferences to communicate the current and emerging database needs of their research community with other stakeholders and the NRSP staff to guide the development, implementation and dissemination of resources for the database. Any new major development will be extensively discussed in these committee meetings. The meeting minutes will be posted on the NRSP and crop-specific websites as well as all reports and work plans. We will also have regular newsletters, twitter and LinkedIn accounts to notify the users of any new developments in the database and the crop research community.

Assessment

Various metrics will be used to assess the impact of the proposed project. For each database this will include usage statistics as measured by google analytics, feedback from the steering committee, annual online surveys of each community, number of publications, number of publications citing the databases and feedback via the online forms in the databases. Creation of new Tripal databases, number of projects adopting Tripal, number of species being served by through Tripal databases, and number of active developers with this project will all be indicators of the success of the use of Tripal. Very relevant measures of participation will be the number of curators and crops associated with the NRSP and the level of investment in NRSP by the users.

Projected Participation

View Appendix E: Participation

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