Using MIxS: An Implementation Report from Two Metagenomic Information Systems

MIxS (Minimum Information about any Sequence) (Yilmaz et al. 2011) is a metadata standard of the Genomics Standards Consortium (GSC), designed to make sequence data findable, accessible, and interoperable. It contains fields for recording physical and chemical characteristics of the sampling environment, geographical and habitat information, and other metadata about the sample and its provenance, which are critical for downstream intepretation of data derived from the sample. We will present our experience implementing MIxS in two metagenomic information systems – the Earth Microbiome Project (EMP) and the Government of Canada (GoC) Ecobiomics project. The EMP (Gilbert et al. 2014) is an ongoing effort to crowdsource environmental microbiome samples from around Earth, then sequence and analyze them using a standardized workflow. The EMP has aggregated and sequenced over 50,000 samples, which are queryable using a publicly available catalogue. A meta-analysis of the first 25,000 samples is currently in review. MIxS and the Environment Ontology (ENVO) (Buttigieg et al. 2016) have been useful in structuring environmental metadata from EMP studies. For the particular application of the EMP meta-analysis, however, several issues were encountered: often there are multiple possible 'correct' assignments to the biome, feature, and material fields; the fields are not hierarchical, limiting logical organization; and the primary ecological factors differentiating microbial communites are not captured. In response to these challenges, the EMP team worked with the ENVO team to devise a new hierarchical structure, the EMP ontology (EMPO), that captures the primary axes along which microbial communities tend to be structured (host-associated or not, saline or not). EMPO is an application ontology, with a formally defined W3C Web Ontology Language (OWL) document mapping to existing ontologies, enabling reuse by the microbial ecology community. Ecobiomics is a joint project of multiple GoC departments and involves the complete workflow, from sampling in a variety of aquatic, soil, and benthic environments, through sample prep, DNA extraction, library prep, sequencing, and analysis. In contrast to the EMP—where some of the samples and metadata had been collected before the establishment of the MIxS standards—the Ecobiomics project has been able to create metadata profiles for each sub-project to conform to, extend, and build, upon the existing MIxS standards. Despite these two different contexts, EMP and Ecobiomics encountered a number of common issues that prevented a complete implementation of MIxS. These issues include ambiguous term names and definitions; inconsistencies amongst the environmental packages; non-standard ways of dealing with units; and a number of issues surrounding ENVO (the Environment Ontology), which is required for filling out the mandatory MIxS fields "Environmental material", "Biome", and "Environmental feature". We will describe these issues, and, more generally, the successes and challenges of our implementations

Management of Molecular Data in DINA with SeqDB

Agriculture and Agri-Food Canada (AAFC) is home to numerous specimen and environmental collections generating highly relational data sets that are analyzed using molecular methods (Sanger and NGS). The need to have a system to properly manage these data sets and to capture accurate, standardized metadata over entire laboratory workflows has been a long-term strategic vision of the Biodiversity group at AAFC. Without robust tracking, many difficulties arise when trying to publish or submit data to external repositories. To even know what work has been carried out on individual collection records over a researchers career becomes a demanding task if the information is retrievable at all. SeqDB was built to resolve these issues by centralizing, standardizing and improving the availability and data quality of source specimen collection data that is being studied using molecular methods. SeqDB also facilitates integration with tools and external repositories in order to take the burden off researchers and technicians having to create adequate systems to track and mobilize their data sets, allowing them to focus on research and collection management. The development of SeqDB aligns with agile development methodologies and attempts to fulfill rapidly emerging needs from genetics and genomics research, which can evolve and fade quickly at times or be without clear requirements. The success of SeqDB as an application supporting DNA sequencing workflows has put it in the same space as other monolithic architectures before it. As the feature set to support the application continues to increase, the number of software developers vs operations and maintenance staff is difficult to rebalance in our organisation. In an effort to manage the scope for the project and ensure we are able to continue to deliver on our mandate, the sequence tracking workflows of the application will become part of the DINA ecosystem ("DIgital information system for NAtural history data", https://dina-project.net). Other functions of SeqDB such as collections management and taxonomy tree curation, will be replaced with the DINA modules implementing these functions. In order to allow SeqDB to become a module of DINA, it has been decided to refactor the application to base it on a Service Oriented Architecture. By doing so, all molecular data of SeqDB will be exposed as JSON API Web Services (JavaScript object notation application programming interface) allowing other modules, user interfaces and the current SeqDB application to communicate in a standardised way. The new architecture will also bring an important technology upgrade for SeqDB where the front end will eventually become a project in itself

SeqDB: Biological Collection Management with Integrated DNA Sequence Tracking

Agriculture and Agri-Food Canada (AAFC) is home to a world-class taxonomy program based on Canada’s national agricultural collections for Botany, Mycology and Entomology.  These collections contain valuable resources, such as type specimen for authoritative identification using approaches that include phenotyping, DNA barcoding, and whole genome sequencing.  These authoritative references allow for accurate identification of the taxonomic biodiversity found in environmental samples in fields such as metagenomics. AAFC’s internally developed web application, termed SeqDB, tracks the complete workflow and provenance chain from source specimen information through DNA extractions, PCR reactions, and sequencing leading to binary DNA sequence files.  In the context of Next Generation Sequencing (NGS) of environmental samples, SeqDB tracks sampling metadata, DNA extractions, and library preparation workflow leading to demultiplexed sequence files.  SeqDB implements the Taxonomic Databases Working Group (TDWG) Darwin Core standard Wieczorek et al. 2012 for Biodiversity Occurrence Data, as well as the Genome Standards Consortium (GSC) Minimum Information about any (X) Sequences (MIxS) specification Yilmaz et al. 2011. When coupled with the built-in data standards validation system, this has  led to the ability to search consistent metadata across multiple studies. Furthermore, the application enables tracking the physical storage of the aforementioned specimens and their derivative molecular extracts using an integrated barcode printing and reading system.   All the information is presented using a graphical user interface that features intuitive molecular workflows as well as a RESTful API that facilitates integration with external applications and programmatic access of the data. The success of SeqDB has been due to the close collaboration with scientists and technicians undertaking molecular research involving the national collection, and the centralization of their data sets in an access controlled relational database implementing internationally recognized standards. We will describe the overall system, and some of our lessons learned in building it

SeqDB: Biological Collection Management with Integrated DNA Sequence Tracking

Agriculture and Agri-Food Canada (AAFC) is home to a world-class taxonomy program based on Canada's national agricultural collections for Botany, Mycology and Entomology. These collections contain valuable resources, such as type specimen for authoritative identification using approaches that include phenotyping, DNA barcoding, and whole genome sequencing. These authoritative references allow for accurate identification of the taxonomic biodiversity found in environmental samples in fields such as metagenomics. AAFC's internally developed web application, termed SeqDB, tracks the complete workflow and provenance chain from source specimen information through DNA extractions, PCR reactions, and sequencing leading to binary DNA sequence files. In the context of Next Generation Sequencing (NGS) of environmental samples, SeqDB tracks sampling metadata, DNA extractions, and library preparation workflow leading to demultiplexed sequence files. SeqDB implements the Taxonomic Databases Working Group (TDWG) Darwin Core standard Wieczorek et al. 2012 for Biodiversity Occurrence Data, as well as the Genome Standards Consortium (GSC) Minimum Information about any (X) Sequences (MIxS) specification Yilmaz et al. 2011. When coupled with the built-in data standards validation system, this has led to the ability to search consistent metadata across multiple studies. Furthermore, the application enables tracking the physical storage of the aforementioned specimens and their derivative molecular extracts using an integrated barcode printing and reading system. All the information is presented using a graphical user interface that features intuitive molecular workflows as well as a RESTful API that facilitates integration with external applications and programmatic access of the data. The success of SeqDB has been due to the close collaboration with scientists and technicians undertaking molecular research involving the national collection, and the centralization of their data sets in an access controlled relational database implementing internationally recognized standards. We will describe the overall system, and some of our lessons learned in building it

The Ecobiomics project:Advancing metagenomics assessment of soil health and freshwater quality in Canada

Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change