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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 93 25

  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. ontotrek ontotrek Public

    A 3d ontology visualizer focusing on OBOFoundry.org ontologies

    JavaScript 6

  5. 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

  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 6 4

Repositories

Showing 10 of 33 repositories
  • 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 Sep 13, 2024
  • 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 93 MIT 25 31 4 Updated Sep 10, 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
  • HPAI_Contextual_Data_Specification Public

    This data specification harmonizes contextual data to support H5N1 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 0 0 0 Updated Sep 6, 2024
  • LexMapr Public

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

    cidgoh/LexMapr’s past year of commit activity
    Python 21 GPL-3.0 14 4 1 Updated Aug 20, 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 5 0 Updated Aug 16, 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 5 MIT 5 15 (1 issue needs help) 0 Updated Aug 8, 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 6 MIT 4 8 1 Updated Jul 31, 2024
  • AMBR_Contextual_data_Specification Public

    A data specification for harmonizing pathogen genomics contextual data as part ofthe AMBR project. 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/AMBR_Contextual_data_Specification’s past year of commit activity
    0 0 0 0 Updated Jul 19, 2024
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