Human Pathogen and Vector Sequencing Metadata Standards
The GSCID/BRC Project and Sample Application Standard is designed to capture standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases. This standard was developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs), and NIAID and informed by discussions and input with numerous collaborating scientists. The standard includes data fields about the organism(s) in the specimen, environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, sequencing and data processing methodologies used, quality and coverage of the resulting sequences, and project leadership and support.
OMOP CDM by OHDSI
The Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) is an open community data standard, designed to standardize the structure and content of clinical observational data and to enable efficient analyses that can produce reliable evidence. A central component of the OMOP CDM is the OHDSI standardized vocabularies. The OHDSI vocabularies allow organization and standardization of medical terms to be used across the various clinical domains of the OMOP common data model.
In CAMRA, the OMOP CDM provides a foundation for collaboration promoting efficiency, interoperability, and standardization in data-driven endeavors across DSI-Africa.
NCBI: Biosample
The CAMRA project utilizes the One Health Enteric Package to capture pertinent data fields essential for characterizing antimicrobial-resistant isolates. Specifically designed for genomic surveillance of enteric microbial organisms, this package offers robust support for specifying host/isolation sources, including environmental contexts, and provides vital details on isolate acquisition time and location.
NCBI Biosamples will be submitted together with their Antibiograms, detailing antimicrobial susceptibility and resistance data obtained from drug-resistant pathogens.
NCBI: SRA
GenBank stands as the NIH genetic sequence database, encompassing an annotated compilation of publicly accessible DNA sequences. Within its repository, GenBank will house CAMRA's isolate genome assemblies, and annotated genomes. Genome annotation will be done by NCBI’s PGAP annotation pipeline.
FAIR
CAMRA will apply the FAIR principles to improve the reusability of our data. By adhering to these principles, our goal is to ensure that both machines and humans can easily Find, Access, and Reuse our research outcomes through seamless Interoperability. For FAIR, CAMRA’s project and data will be available at NCBI’s Bioproject, Biosample, GenBank, and we will also provide data and linking information in H3-Arfica Data coordinating center.