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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 94 27

  2. LexMapr LexMapr Public

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

    Python 21 14

  3. 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…

    7

  4. pathogen-genomics-package pathogen-genomics-package Public

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

    HTML 7 4

  5. ontotrek ontotrek Public

    A 3d ontology visualizer focusing on OBOFoundry.org ontologies

    JavaScript 6

  6. 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 6 2

Repositories

Showing 10 of 33 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
    JavaScript 94 MIT 27 31 3 Updated Nov 5, 2024
  • 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 6 MIT 2 29 (1 issue needs help) 0 Updated Nov 5, 2024
  • nf-ncov-voc Public

    A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.

    cidgoh/nf-ncov-voc’s past year of commit activity
    Python 6 MIT 5 11 (1 issue needs help) 1 Updated Oct 29, 2024
  • 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 7 MIT 4 8 1 Updated Oct 29, 2024
  • bacpaq Public

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

    cidgoh/bacpaq’s past year of commit activity
    Nextflow 5 MIT 3 5 0 Updated Oct 9, 2024
  • 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 0 0 0 Updated Oct 8, 2024
  • Wastewater_Contextual_Data_Specification Public

    A data specification for harmonizing Wastewater pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via metadata template(s), supported by field and reference guides as well as different curation and new term request SOPs.

    cidgoh/Wastewater_Contextual_Data_Specification’s past year of commit activity
    2 MIT 1 0 0 Updated Oct 8, 2024
  • 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
    0 1 0 0 Updated Oct 7, 2024
  • specification-training Public

    Training materials about developing and applying data specifications

    cidgoh/specification-training’s past year of commit activity
    1 0 0 0 Updated Sep 10, 2024
  • pathogen-mutation-functionalannotation-package Public

    Package for functional annotation of mutations

    cidgoh/pathogen-mutation-functionalannotation-package’s past year of commit activity
    JavaScript 0 MIT 0 0 0 Updated Sep 10, 2024
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