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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 98 27

  2. LexMapr LexMapr Public

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

    Python 22 14

  3. pathogen-genomics-package pathogen-genomics-package Public

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

    HTML 8 4

  4. 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

  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 34 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 98 MIT 27 26 4 Updated Nov 29, 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) 0 Updated Nov 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 8 MIT 4 7 0 Updated Nov 29, 2024
  • database_list Public

    It is used to track all the databases on the Eagle. The results will be stored in an SQLite file or added to a Google Sheet.

    cidgoh/database_list’s past year of commit activity
    0 MIT 0 0 0 Updated Nov 27, 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 4 15 2 Updated Nov 27, 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 Nov 21, 2024
  • 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
    7 MIT 0 8 0 Updated Nov 20, 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
  • 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
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