cidgoh/specification-training

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cidgoh/specification-training

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Training materials about developing and applying data specifications

DataHarmonizer

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 from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.

LexMapr

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

GRDI_AMR_One_Health

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.

pathogen-genomics-package

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

nf-ncov-voc

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.

VIRUS-MVP

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.

ontotrek

A 3d ontology visualizer focusing on OBOFoundry.org ontologies

bacpaq

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

geem

Genomic Epidemiology Entity Mart

ontotraining

A repository for ontology training materials

ffp_phylogeny

A Galaxy tool for calculating Feature Frequency Profiles (FFP) from fasta sequence and text data.

Wastewater_Contextual_Data_Specification

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.

AWS-IRIDA-DEPLOYMENT

nf-upcoastv

FastaUploader

A tool for batch processing large fasta files and accompanying metadata table to upload to repositories via API

rcqc

Report Calc for Quality Control is a python command line and Galaxy bioinformatics platform tool for text-mining log and data files to create reports and even to stop workflow execution in response to critical quality control issues.