Dataset Information

Standardized metadata for human pathogen/vector genomic sequences.

ABSTRACT: High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.

SUBMITTER: Dugan VG

PROVIDER: S-EPMC4061050 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Standardized metadata for human pathogen/vector genomic sequences.

Dugan Vivien G VG Emrich Scott J SJ Giraldo-Calderón Gloria I GI Harb Omar S OS Newman Ruchi M RM Pickett Brett E BE Schriml Lynn M LM Stockwell Timothy B TB Stoeckert Christian J CJ Sullivan Dan E DE Singh Indresh I Ward Doyle V DV Yao Alison A Zheng Jie J Barrett Tanya T Birren Bruce B Brinkac Lauren L Bruno Vincent M VM Caler Elizabet E Chapman Sinéad S Collins Frank H FH Cuomo Christina A CA Di Francesco Valentina V Durkin Scott S Eppinger Mark M Feldgarden Michael M Fraser Claire C Fricke W Florian WF Giovanni Maria M Henn Matthew R MR Hine Erin E Hotopp Julie Dunning JD Karsch-Mizrachi Ilene I Kissinger Jessica C JC Lee Eun Mi EM Mathur Punam P Mongodin Emmanuel F EF Murphy Cheryl I CI Myers Garry G Neafsey Daniel E DE Nelson Karen E KE Nierman William C WC Puzak Julia J Rasko David D Roos David S DS Sadzewicz Lisa L Silva Joana C JC Sobral Bruno B Squires R Burke RB Stevens Rick L RL Tallon Luke L Tettelin Herve H Wentworth David D White Owen O Will Rebecca R Wortman Jennifer J Zhang Yun Y Scheuermann Richard H RH

PloS one 20140617 6

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that ...[more]

PMID: 24936976

Similar Datasets

Project description:BackgroundMetagenomics is an expanding field within microbial ecology, microbiology, and related disciplines. The number of metagenomes deposited in major public repositories such as Sequence Read Archive (SRA) and Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) is rising exponentially. However, data mining and interpretation can be challenging due to mis-annotated and misleading metadata entries. In this study, we describe the Marine Metagenome Metadata Database (MarineMetagenomeDB) to help researchers identify marine metagenomes of interest for re-analysis and meta-analysis. To this end, we have manually curated the associated metadata of several thousands of microbial metagenomes currently deposited at SRA and MG-RAST.ResultsIn total, 125 terms were curated according to 17 different classes (e.g., biome, material, oceanic zone, geographic feature and oceanographic phenomena). Other standardized features include sample attributes (e.g., salinity, depth), sample location (e.g., latitude, longitude), and sequencing features (e.g., sequencing platform, sequence count). MarineMetagenomeDB version 1.0 contains 11,449 marine metagenomes from SRA and MG-RAST distributed across all oceans and several seas. Most samples were sequenced using Illumina sequencing technology (84.33%). More than 55% of the samples were collected from the Pacific and the Atlantic Oceans. About 40% of the samples had their biomes assigned as 'ocean'. The 'Quick Search' and 'Advanced Search' tabs allow users to use different filters to select samples of interest dynamically in the web app. The interactive map allows the visualization of samples based on their location on the world map. The web app is also equipped with a novel download tool (on both Windows and Linux operating systems), that allows easy download of raw sequence data of selected samples from their respective repositories. As a use case, we demonstrated how to use the MarineMetagenomeDB web app to select estuarine metagenomes for potential large-scale microbial biogeography studies.ConclusionThe MarineMetagenomeDB is a powerful resource for non-bioinformaticians to find marine metagenome samples with curated metadata and stimulate meta-studies involving marine microbiomes. Our user-friendly web app is publicly available at https://webapp.ufz.de/marmdb/ .

Dataset Information

Standardized metadata for human pathogen/vector genomic sequences.

Publications

Standardized metadata for human pathogen/vector genomic sequences.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets