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Templates & Resources
Rhiannon Cameron edited this page Jul 10, 2023
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Abbreviations
SOP = Standard Operating Procedure
| Resource | Location | Description |
|---|---|---|
| DataHarmonizer Template | https://github.com/cidgoh/pathogen-genomics-package/releases | Web application template for data entry and validation |
| Schema | schema.yaml or schema.json/.yaml/.tsv | A file that describe the data structure of the specification. Note: schema_enums.tsv = Picklists, schema_slots.tsv = Fields and Field Categories |
Additional Information:
- CanCOGeN Contextual Data Specification: what is is, why it is importance, and how it works.
- CanCOGeN Contextual Data Datasets for Harmonization Training and Quality Control
| Resource | Location | Description |
|---|---|---|
| DataHarmonizer Template | https://github.com/cidgoh/pathogen-genomics-package/releases | Web application template for data entry and validation |
| Schema | schema.yaml or schema.json/.yaml/.tsv | A file that describe the data structure of the specification. Note: schema_enums.tsv = Picklists, schema_slots.tsv = Fields and Field Categories |
| Reference Guide | UPLOAD PENDING | Reference guides that show field and picklist labels, IDs, descriptions, and specification guidance. |
| SOP | SOP.pdf | Contextual data (metadata) curation protocol |
| Resource | Location | Description |
|---|---|---|
| DataHarmonizer Template | https://github.com/cidgoh/pathogen-genomics-package/releases | Web application template for data entry and validation |
| Schema | schema.yaml or schema.json/.yaml/.tsv | A file that describe the data structure of the specification. Note: schema_enums.tsv = Picklists, schema_slots.tsv = Fields and Field Categories |
| Resource | Location | Description |
|---|---|---|
| GitHub Repository | https://github.com/cidgoh/GRDI_AMR_One_Health | Repository for managing and releasing the GRDI-AMR specification package |
| Data Collection Template | XLSX | Data collection template that performs data validation and consolidation. |
| DataHarmonizer Data Collection Template | https://github.com/cidgoh/pathogen-genomics-package/releases | Web application template for data entry and validation; encompasses the "merged sheet" tab from the XLSX data collection template |
| Schema | schema.yaml or schema.json/.yaml/.tsv | A file that describe the data structure of the specification. Note: schema_enums.tsv = Picklists, schema_slots.tsv = Fields and Field Categories |
| Reference Guide | XLSX (Field & Term), PDF (Field), PDF (Term), or Online (Field and Term) | Reference guides that show field and picklist labels, IDs, descriptions, and specification guidance. |
| SOP | PDF or Online | Contextual data (metadata) curation protocol |
| DataHarmonizer SOP | PDF or Online | Contextual data (metadata) curation protocol |
| New Term Request SOP | PDF or Online | Guidance on how to request new fields or picklist items for the specification/schema |
| Resource | Location | Description |
|---|---|---|
| DataHarmonizer Template | https://github.com/cidgoh/pathogen-genomics-package/releases | Web application template for data entry and validation |
| Schema | schema.yaml or schema.json/.yaml/.tsv | A file that describe the data structure of the specification. Note: schema_enums.tsv = Picklists, schema_slots.tsv = Fields and Field Categories. The Canadian and international Monkeypox specifications were built in concert and share a schema file to facilitate interoperability and data structure comparisons. Canadian Monkeypox elements are designated with "Monkeypox" while the international version is designated by "Monkeypox_international". |
| SOP | SOP_Monkeypox.pdf (Canada), or SOP_Monkeypox_international.pdf | Contextual data (metadata) curation protocols |
| Resource | Location | Description |
|---|---|---|
| DataHarmonizer Template | https://github.com/cidgoh/pathogen-genomics-package/releases | Web application template for data entry and validation |
| Schema | schema.yaml or schema.json/.yaml/.tsv | A file that describe the data structure of the specification. Note: schema_enums.tsv = Picklists, schema_slots.tsv = Fields and Field Categories |
| Resource | Location | Description |
|---|---|---|
| GitHub Repository | https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification | Repository for managing and releasing the PHA4GE SARS-CoV-2 contextual data specification package |
| DataHarmonizer Template | https://github.com/cidgoh/pathogen-genomics-package/releases | Web application template for data entry and validation |
| Data Collection Template | XLSX or JSON | Data collection template that performs data validation. |
| Schema | schema.yaml or schema.json/.yaml/.tsv | A file that describe the data structure of the specification. Note: schema_enums.tsv = Picklists, schema_slots.tsv = Fields and Field Categories |
| Reference Guide | CSV | Reference guide that shows field labels, IDs, descriptions, and specification guidance. |
| SOP | Protocols.io | Contextual data (metadata) curation protocol |
| Manuscript | https://doi.org/10.1093/gigascience/giac003 | "Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package" Griffiths et al. |
| Resource | Location | Description |
|---|---|---|
| DataHarmonizer Template | https://github.com/cidgoh/pathogen-genomics-package/releases | Web application template for data entry and validation |
| Schema | schema.yaml or schema.json/.yaml/.tsv | A file that describe the data structure of the specification. Note: schema_enums.tsv = Picklists, schema_slots.tsv = Fields and Field Categories |