Centre for Infectious Disease and One Health
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DataHarmonizer
DataHarmonizer PublicA 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 …
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pathogen-genomics-package
pathogen-genomics-package PublicThis is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates
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nf-ncov-voc
nf-ncov-voc PublicA Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 or Mpox genomes. Workflow is developed in collaboration with VIRUS-MVP (https://github.com/cidgoh/VIRUS-MVP) which can…
Repositories
- DataHarmonizer Public
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…
cidgoh/DataHarmonizer’s past year of commit activity - PathogenVariantOntology Public
An application ontology for describing pathogen mutations, their functional effects, and links to literature evidence. This is a slice of GenEpiO.
cidgoh/PathogenVariantOntology’s past year of commit activity - iMicroSeq_Contextual_Data_Specification Public
An ontology-based specification for harmonizing contextual data in pathogen genomics. Developed for iMicroSeq to support standardized metadata capture across different water types (including wastewater and environmental), for public health. Includes templates, guides, and SOPs for implementation and curation.
cidgoh/iMicroSeq_Contextual_Data_Specification’s past year of commit activity - pathogen-genomics-package Public
This is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates
cidgoh/pathogen-genomics-package’s past year of commit activity - SchemaGenie Public
SchemaGenie: A chatbot to explore and query graph databases using OCA and LinkML schemas.
cidgoh/SchemaGenie’s past year of commit activity - VIRUS-MVP Public
VirusMVP is an interactive heatmap-centric app that integrates viral genomic mutations, lineage information and curated functional impact to study the spread and evolution of viruses in Canada and globally.
cidgoh/VIRUS-MVP’s past year of commit activity - HPAI_Contextual_Data_Specification Public
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.
cidgoh/HPAI_Contextual_Data_Specification’s past year of commit activity - specification-development-training Public
A repository for sharing guidance and training around developing a contextual data specification for pathogen surveillance
cidgoh/specification-development-training’s past year of commit activity - PHA4GE_genotyping_specification Public
A data specification for harmonizing microbial typing contextual data. The specification provides standardized (ontology-based) fields and terms which can be implemented in tooling, with supporting guidance.
cidgoh/PHA4GE_genotyping_specification’s past year of commit activity
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