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@cidgoh

Centre for Infectious Disease and One Health

Hsiao Laboratory at Simon Fraser University

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  1. DataHarmonizer 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 …

    JavaScript 112 32

  2. LexMapr LexMapr Public

    LexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms

    Python 24 15

  3. VIRUS-MVP 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 …

    Python 15 2

  4. bacpaq bacpaq Public

    Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data

    Nextflow 12 7

  5. GRDI_AMR_One_Health GRDI_AMR_One_Health Public

    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 spreadsh…

    10 1

  6. pathogen-genomics-package pathogen-genomics-package Public

    This is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates

    HTML 10 4

Repositories

Showing 10 of 38 repositories
  • 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
    HTML 10 MIT 4 6 0 Updated Sep 3, 2025
  • 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
    JavaScript 112 MIT 32 30 (1 issue needs help) 4 Updated Sep 3, 2025
  • AMR-TV Public
    cidgoh/AMR-TV’s past year of commit activity
    Python 0 1 17 (3 issues need help) 2 Updated Sep 2, 2025
  • GRDI_AMR_One_Health Public

    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.

    cidgoh/GRDI_AMR_One_Health’s past year of commit activity
    10 MIT 1 8 0 Updated Aug 29, 2025
  • nf-ncov-voc Public

    A 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 be used to visualize the mutation profiles and functional annotations.

    cidgoh/nf-ncov-voc’s past year of commit activity
    Python 9 MIT 5 11 (1 issue needs help) 0 Updated Aug 28, 2025
  • 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
    Python 15 MIT 2 35 (1 issue needs help) 0 Updated Aug 28, 2025
  • 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
    0 0 0 0 Updated Aug 7, 2025
  • MPox_Contextual_Data_Specification Public

    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.

    cidgoh/MPox_Contextual_Data_Specification’s past year of commit activity
    0 MIT 0 1 0 Updated Jul 9, 2025
  • bacpaq Public

    Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data

    cidgoh/bacpaq’s past year of commit activity
    Nextflow 12 MIT 7 14 4 Updated Jun 12, 2025
  • 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
    0 MIT 0 5 0 Updated May 15, 2025
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