CerealsDB: A community resource for wheat genomics

Lead Research Organisation: The Genome Analysis Centre
Department Name: Research Faculty

Abstract

CerealsDB ( http://www.cerealsdb.uk.net/) is one of the most highly accessed wheat web sites with over 5,000 unique accesses per month.

The reasons for CerealsDB's success are clear; it provides the community with sequence and single nucleotide polymorphism (SNP)-based information in a form accessible to and understandable by non-experts.

While CerealsDB is successful, to remain of value to its users, it needs to develop in conjunction with the community's expectations. In addition, CerealsDB needs to expand its remit to include further interaction with other web sites such as the internationally based Wheat Initiative. This development is new to this application as in our previous work we developed tools specifically for the UK community rather than the global wheat community. However, although our previous work did focus on the UK community, the easy to use style of CerealsDB has already resulted in the web site becoming international recognised, with many of its users being from non-UK organisations.

In this further development, CerealsDB will continue work with UK users to develop sequence and SNP-based resources; however, it will also extend its horizons to include interactions with international web-based resources and the exploitation of genomics resources such as the wheat reference sequence. This extension to its remit will result in an expanded audience for CerealsDB and more extensive tools and datasets being made available to the community.

Technical Summary

"A community resource for wheat functional genomics" was one of the first projects to be funded by the BBR initiative. The resources enabled Bristol and Rothamsted Research to develop "CerealsDB" and "Monogram". CerealsDB and Monogram are accessed directly or via other web sites such as the Wheat Improvement Strategic Program (WISP), the International Wheat Initiative and GrainGenes. CerealsDB hosts tools and resources to access and analyse sequence and SNP-based datasets for wheat (Triticum aestivum) and related species. CerealsDB assists breeders and academics in exploring the wheat genome and selecting strategies for genotyping and marker assisted selection. CerealsDB includes a database in excess of 100,000 varietal SNPs, of which several thousand have been validated and mapped on one of three mapping populations. CerealsDB also contains information on DArT markers and Expressed Tagged Sequences (ESTs), and was the first site to host the 5x genome sequence for the variety Chinese Spring released in 2010. Since launch, CerealsDB has been updated regularly, with the last update on the 1st May 2013 with the addition of a further ~1,500 mapped SNP markers and a mapping function which assigns unmapped SNPs to putative homoeologous specific chromosome arms.

To ensure that CerealsDB remains on of the most useful wheat-based web sites and to increase the communities awareness of the resources hosted, we intend to develop CerealsDB to included further tools such as an expanded SNP/genotype database, including iSelect and Axiom based datasets along with facilities to identify and characterise functional SNPs. In addition, new releases will include graphic tools to enable breeders and academics to link mapped and non-mapped SNPs/genes across a variety of wheat related species. Finally, although CerealsDB has always been designed to be easy to use, we will provide training across the range of activities included within the web site.

Planned Impact

The BBSRC web site states that "BBSRC is the principal funder of food-related research in the UK and has food security as one of its key strategic drivers." In the UK wheat is, by a significant margin, the most valuable arable crop and therefore not surprisingly the status of the UK wheat crop is a national issue often reported in the press. While BBSRC funds a large number of wheat-related projects, for the most part, it is the translation of this research into wheat varieties with increased yield or improved qualities such as improved bread making qualities that provides the impact required by BBSRC if it is to deliver its strategic objectives. Translation of wheat research in line with BBSRC's strategic priorities, almost always involves either mapping and cloning genes or crossing alleles of interest into elite varieties. In all cases, since its launch, CerealsDB has helped researchers to achieve impact by providing wheat geneticists with unencumbered sequences and SNP-based information which is easy to access and free from IP or MTAs.

The development of CerealsDB has led to strategic changes in the approaches taken by various wheat breeders, for instance many regard the development of CerealsDB as a significant factor in their decision to convert their marker labs to the SNP-based markers.

In accordance with BBSRC strategy to achieving impact, Prof. Edwards has actively engaged with industry, for instance through the CIRC program and via his participation in a BBSRC science interchange programme with Advanta-Nickerson (now Limagrain) Seeds to exchange technologies and ideas. In addition the university base of the Bristol group and the institutional base of TGAC allows each to incorporate its research directly into undergraduate, post-graduate and post doc teaching. This approach has been remarkably successful and has resulted in numerous young researchers being placed within agricultural institutes or companies as PhD students, researchers or employees.

The facilities offered by CerealsDB are unique. We know that this because our users tell us. Although CerealsDB is international recognised as being a primary source of wheat sequences and SNP-based markers, we believe that by adding the facilities described, Bristol will ensure that it increases its international profile and continues to provide a valuable (almost) one stop shop for wheat functional genomics. In so far as we are aware no similar commercially available resources exist, however, it is important to note that our web site is used by both academic and the industrial sectors with several companies relying on it for a substantial part of their business and many of our improvements have been carried out at the suggestion of the UK wheat breeding sector.

Publications


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Wilkinson PA (2016) CerealsDB 3.0: expansion of resources and data integration. in BMC bioinformatics
 
Description The work within this grant is ongoing, but we are at the stage where our combined infrastructures at Bristol and EI are fit for federation and subsequent exploitation, improving the reach of CerealsDB.
Exploitation Route Improved user interfaces and data access layers will help breeders and researchers get access to vital data for improving crop health and security.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software)
URL http://www.cerealsdb.uk.net
 
Title Grassroots Genomics grid infrastructure 
Description Integrative research requires extensive multi-level approaches to enrich and expose data and workflows so that informatics infrastructures can process them effectively. The Grassroots Infrastructure is developed at the Earlham Institute (EI) to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public datasets in the plant sciences. Its lightweight reusable software stack comprises: an iRODS data management layer to provide structure to unstructured filesystems, with Elasticsearch indexed metadata and Davrods exposed WebDAV APIs; interfaces to interact with local or cloud-based analysis platforms; an Apache web server layer to deliver content and provide access to public programmatic interfaces; services such as: BLAST search on multiple databases across different sites; a mapping tool showing pathogen samples with temporal and spatial data. It can be run locally or packaged in virtual containers and deployed on a variety of hardware thus representing a decentralised system, allowing information generators to retain control over their resources but allowing interconnected resources to access each other consistently. As such, Grassroots represents EI's contribution to the Wheat Initiative Wheat Information System (WheatIS) project, formalising the infrastructure as the federated UK WheatIS node involving partners from the University of Bristol, the European Bioinformatics Institute, Rothamsted Research, and the John Innes Centre. We are currently working on lightweight mechanisms to expose underlying grid architecture using WebDAV, standardised APIs such as the Breeding API (BrAPI) and schemas such as Frictionless Data and BioSchemas to enable greater interoperability with a variety of existing services, and integration with data analysis platforms such as CyVerse and Galaxy. 
Type Of Material Data handling & control 
Year Produced 2014 
Provided To Others? Yes  
Impact This infrastructure powers the handling and release of the wheat genomics data arising from EI's flagship wheat programmes, as well as aggregating previously published datasets. Currently we have a BLAST service running on top of this infrastructure, but we are currently building federation options into the platform with the iRODS data grid software. The CerealsDB project at the University of Bristol is a widely used and vital resource for the wheat community, and the Bristol group are deploying the Grassroots infrastructure to facilitate integration of the resources held there with the resources at EI. The Field Pathogenomics project (BBSRC IPA funded project BB/M025519/1) is also powered by the Grassroots platform, enabling a fast and informative web-based user interface based on data collected by the project relating to wheat yellow rust epidemiology. 
URL https://wheatis.tgac.ac.uk/grassroots/api/
 
Title EI wheat data portal 
Description A BLAST server dedicated to wheat genomes, powered by the Grassroots API and freely available to the public and hosting a large number of previously published and newly generated genomes of wheat varieties. 
Type Of Technology Webtool/Application 
Year Produced 2014 
Impact This portal has served over 7100+ page visits, and run more than 11000 BLAST jobs from users in 31 countries, allowing them early access to full wheat genomes even before publication. Notably, this software was the main route of dissemination of the TGAC v1 Chinese Spring 42 wheat genome prior to its inclusion in Ensembl Plants. 
URL https://wheatis.tgac.ac.uk/grassroots-portal/blast
 
Title Grassroots API 
Description The Grassroots Infrastructure project aims to create an easily-deployable suite of computing middleware tools to help users and developers gain access to scientific data infrastructure that can easily be interconnected. With the data-generative approaches that are increasingly common in modern life science research, it is vital that the data and metadata produced by these efforts can be shared and reused. The Grassroots Infrastructure project wraps up industry-standard software tools with a consistent API that can be federated on a number of levels. This means institutions and groups can deploy a simple lightweight virtual machine, expose local data, connect up any existing data services, and federate their instance of the Grassroots with others out-of-the-box. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact The Grassroots API powers the public BLAST service that runs at TGAC, predominantly for the currently available wheat assemblies including the recently released TGAC v1 w2rap assembly (in preparation). We have served over 4000 unique users with over 6000 BLAST jobs since November 2015. It also underpins the Field Pathgenomics project (BBSRC IPA award 2015, PI - Saunders D., TGAC/JIC fellow), a web portal that represents the detection and subsequent phenotyping and genotyping of the wheat yellow rust pathogen. The site aims to enable researchers and breeders to track rust epidemics over variety and time, allowing for a more proactive approach to wheat crop breeding and farming. Finally, we are working with the CerealsDB group at Univ. Bristol to deploy the Grassroots infrastructure alongside the CerealsDB web portal, allowing a federation of searching, datasets, analysis and dissemination of markers, genotypes and associated feature and literature information. 
URL https://wheatis.tgac.ac.uk/grassroots/api/
 
Description Building infrastructure for open science - British Computer Society 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited speaker at the Advanced Programming Group annual Christmas lecture
Year(s) Of Engagement Activity 2015
URL http://www.bcs.org/category/18516
 
Description Data Stewardship in the Life Sciences 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I spoke at the "Challenges and Opportunities in Plant Science Data Management" workshop on the subject of data management in the life sciences.

Open data and integrative data sharing are fundamental factors in order to address the challenges of modern data-intensive science. There is a clear need to develop and maintain community-focussed, semantically-aware data stewardship and management platforms, such as COPO, that are able to cope with the description and sharing of potentially huge datasets arising from the life sciences. Once made available, it is not sufficient to assume that researchers around the globe have requisite skills and resources to analyse these data. Therefore, we need to provide large-scale data analysis environments that are fit for purpose, incorporating state-of-the-art interfaces and programmatic layers to meet broad end-user requirements, such as CyVerse and Galaxy. Finally, this can only happen when there are community-led efforts into implementing solutions for data standardisation, best practice, and FAIR data policy. We are now only just starting to take advantage of groundbreaking opportunities to make integrated data a reality, and thus enabling scientists to store, manage, and share their data as a first-class citizen of the scientific process.
Year(s) Of Engagement Activity 2017
URL http://app.core-apps.com/pag_2017/event/e2bec353017762d275ce250c23e011e6
 
Description Divseek Working Group - Data Standards for Interoperable Tools 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact As part of the "DivSeek - Addressing the challenges and opportunities for information and data sharing associated with plant germplasm" session at PAG, I spoke about the DivSeek Data Standards for Interoperable Tools Working Group. This WG will promote best practice in data sharing in the plant sciences, through the use of open and interoperable software powered by the adoption of open standards, i.e. programmatic interoperability standards (APIs), controlled vocabularies, trait dictionaries, metadata standards, and ontologies. We aim to highlight gaps in interoperability that impede workflows important to the communities supported by DivSeek partners, by liaising with research development groups, other DivSeek working groups, and consortia with relevance to DivSeek. We will educate and train data generators about standards and the tools and resources that use them, in order to promote and foster standards-compliance for long-term open data stewardship.
Year(s) Of Engagement Activity 2017
URL https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/26202