Pinned Repositories
DataHarmonizer
A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.
GRDI_AMR_One_Health
A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.
HPAI_Contextual_Data_Specification
This data specification harmonizes contextual data to support HPAI monitoring with PHA4GE. It provides standardized, ontology-based fields and terms for comprehensive surveillance. Users can implement it via their preferred tools, including DataHarmonizer. Field and reference guides, along with curation and new term request SOPs, support its use.
MPox_Contextual_Data_Specification
A data specification for harmonizing MPox pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a the DataHarmonizer, supported by field and reference guides as well as different curation and new term request SOPs.
pathogen-genomics-package
This is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates
COVID-19-ontology-harmonization
This is a space for harmonizing COVID-19 ontologies to build a suit of ontologies that are interoperable and sustainable for end users.
genepio
The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for foodborne infectious disease surveillance and outbreak investigations.
contextual_data_QC_tags
Standardized attributes for labelling sequence datasets with known quality control issues
minimal-pathogen-agnostic-contextual-data-specification
An international minimal metadata standard for public health and One Health genomic surveillance.
SARS-CoV-2-Contextual-Data-Specification
Collection template and associated materials for SARS-CoV-2 metadata
griffie's Repositories
griffie/genepio
The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for foodborne infectious disease surveillance and outbreak investigations.