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@cidgoh Centre for Infectious Disease and One Health

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    45 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 sam…
      javascriptapplicationdata
      javascriptapplicationdataspreadsheetharmonizationlinkmllinkml-schema
      JavaScript
      •
      MIT License
      •39•129•66•1•Updated Jul 17, 2026Jul 17, 2026

    • SchemaBLAST

      Public
      Python
      •0•0•0•0•Updated Jul 16, 2026Jul 16, 2026

    • 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 an…
      visualizationbioinformaticsplotly
      visualizationbioinformaticsplotlydashcovid-19sars-cov-2
      Python
      •
      MIT License
      •3•15•38•2•Updated Jul 4, 2026Jul 4, 2026

    • ceur_pdf

      Public
      Converts a Google Doc to a CEUR-WS–formatted PDF by downloading the document directly from its public URL, extracting front-matter content automatically, and co…
      TeX
      •0•0•0•0•Updated Jun 18, 2026Jun 18, 2026

    • swrlcli

      Public
      Standalone SWRLAPI-based application for running and debugging SWRL rules.
      Java
      •
      MIT License
      •0•0•0•0•Updated Jun 18, 2026Jun 18, 2026

    • 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://g…
      bioinformaticsvirusgenomics
      bioinformaticsvirusgenomicsnextflowmicrobial-genomicsvariant-callingcovid-19sars-cov-2
      Python
      •
      MIT License
      •5•11•22•1•Updated Jun 17, 2026Jun 17, 2026

    • 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…
      metadatagenomicspathogen
      metadatagenomicspathogenontologiesharmonizationantimicrobial-resistanceone-healthfood-system
      MIT License
      •1•11•14•0•Updated Jun 15, 2026Jun 15, 2026

    • CC_data_manager

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 9, 2026Jun 9, 2026

    • catalogue_assistant

      Public
      Python
      •0•0•0•0•Updated Jun 6, 2026Jun 6, 2026

    • pathogen-genomics-package

      Public
      This is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates
      data-harmonizationinfectious-disease
      data-harmonizationinfectious-disease
      HTML
      •
      MIT License
      •3•11•14•0•Updated May 21, 2026May 21, 2026

    • Wastewater_Contextual_Data_Specification

      Public
      A data specification for harmonizing Wastewater pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms whi…
      MIT License
      •2•3•0•0•Updated Apr 29, 2026Apr 29, 2026

    • CanCOGeN_Contextual_Data_Specification

      Public
      A data specification for harmonizing One Health Canadian COVID pathogen genomics contextual data. The specification provides standardized (ontology-based) field…
      metadatagenomicspathogen
      metadatagenomicspathogenontologiesharmonizationcovid19-dataone-health
      0•0•3•0•Updated Apr 29, 2026Apr 29, 2026

    • 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 di…
      0•0•12•0•Updated Apr 24, 2026Apr 24, 2026

    • PathogenVariantOntology

      Public
      An application ontology for describing pathogen mutations, their functional effects, and links to literature evidence. This is a slice of GenEpiO.
      Shell
      •
      MIT License
      •0•0•8•0•Updated Feb 27, 2026Feb 27, 2026

    • bacpaq

      Public
      Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data
      bioinformaticsnextflowmicrobial-genomics
      bioinformaticsnextflowmicrobial-genomics
      Nextflow
      •
      MIT License
      •8•12•15•6•Updated Feb 20, 2026Feb 20, 2026

    • SchemaGenie

      Public
      SchemaGenie: A chatbot to explore and query graph databases using OCA and LinkML schemas.
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 25, 2025Nov 25, 2025

    • 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 compreh…
      metadatagenomicspathogen
      metadatagenomicspathogenontologiesdata-standardsharmonizationavian-influenza
      1•0•2•0•Updated Nov 6, 2025Nov 6, 2025

    • specification-development-training

      Public
      A repository for sharing guidance and training around developing a contextual data specification for pathogen surveillance
      2•1•0•1•Updated Oct 24, 2025Oct 24, 2025

    • 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 im…
      MIT License
      •1•1•0•0•Updated Oct 1, 2025Oct 1, 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…
      MIT License
      •0•0•2•0•Updated Sep 26, 2025Sep 26, 2025

    • B2B2B2_Contextual_Data_Specification

      Public
      A One Health data specification harmonizing gold-standard microbial AMR datasets, developed under JPIAMR’s B2B2B AMRDx project. The specification provides stand…
      0•0•1•0•Updated Sep 12, 2025Sep 12, 2025

    • AMR-TV

      Public
      Python
      •1•0•17•2•Updated Sep 2, 2025Sep 2, 2025

    • BioDBTracker

      Public
      This tool is designed to track and log versions and details of bioinformatics databases. It provides a streamlined way to monitor changes, with results stored i…
      Python
      •0•0•0•0•Updated Dec 11, 2024Dec 11, 2024

    • pathogen-mutation-functionalannotation-package

      Public
      Package for functional annotation of mutations
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

    • specification-training

      Public
      Training materials about developing and applying data specifications
      0•1•0•0•Updated Sep 10, 2024Sep 10, 2024

    • LexMapr

      Public
      LexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms
      Python
      •
      GNU General Public License v3.0
      •15•25•4•1•Updated Aug 20, 2024Aug 20, 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) fiel…
      0•0•0•0•Updated Jul 19, 2024Jul 19, 2024

    • cidgoh_cloud

      Public
      HCL
      •0•0•0•0•Updated May 7, 2024May 7, 2024

    • geem

      Public
      Genomic Epidemiology Entity Mart
      CSS
      •
      Creative Commons Attribution 4.0 International
      •1•3•12•2•Updated Apr 17, 2024Apr 17, 2024

    • FastaUploader

      Public
      A tool for batch processing large fasta files and accompanying metadata table to upload to repositories via API
      pythonuploaderfasta
      pythonuploaderfastabatch-processing
      Python
      •
      Creative Commons Zero v1.0 Universal
      •1•1•0•0•Updated Feb 15, 2024Feb 15, 2024
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