ArticlePloS one2014
Standardized metadata for human pathogen/vector genomic sequences.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
29 citing papers in PubMed.
- The Mpox contextual data specification package: a data curation toolkit to support collaborative pathogen genomic surveillance.Microbial genomics · 2026Article
- Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Review
- Role of microbiota and microbiota-derived short-chain fatty acids in PDAC.Cancer medicine · 2023Review
- Developing a standardized but extendable framework to increase the findability of infectious disease datasets.Scientific data · 2023Article
- Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR.Nucleic acids research · 2023Article
- Metadata harmonization-Standards are the key for a better usage of omics data for integrative microbiome analysis.Environmental microbiome · 2022Article
- Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.GigaScience · 2022Article
- A new framework for host-pathogen interaction research.Frontiers in immunology · 2022Article
- Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research.Briefings in functional genomics · 2021Article
- Current challenges and best-practice protocols for microbiome analysis.Briefings in bioinformatics · 2021Review
- Best Practices for Successfully Writing and Publishing a Genome Announcement inMicrobiology resource announcements · 2020Article
- ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions.BMC bioinformatics · 2019Article
- OMeta: an ontology-based, data-driven metadata tracking system.BMC bioinformatics · 2019Article
- Article
- The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.Journal of biomedical semantics · 2018Review
- Ontology-based systematical representation and drug class effect analysis of package insert-reported adverse events associated with cardiovascular drugs used in China.Scientific reports · 2017Article
- Integrating Advanced Molecular Technologies into Public Health.Journal of clinical microbiology · 2017Review
- Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.Frontiers in microbiology · 2017Article
- Pathogen metadata platform: software for accessing and analyzing pathogen strain information.BMC bioinformatics · 2016Article
Corrections and comments
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Authors and funding
58 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.