Releases | Open Source Science

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 5.6.3

Includes new GRDI and Mpox export scripts, as well as a DH fix to indentation of single and multi-select menus.

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- DEXA (One Health) | 1.2.0 | | | GISAID (SC2) | 1.0.2 | | | GRDI | 15.0.0 | Added: exposure event; exposure event details | Added: new presampling activity values - Animals raised without antibiotics, Animals raised without medically important antibiotics; new exposure event values - Exposure to chemical, Exposure to antimicrobial agent. Added environmental material values, food product values and body product values. | Mpox | 7.5.5 | | | Added new exports MpoxInternational | 9.0.0 | Added: Pathoplexus accession; geoloc name (county/region); geoloc name (city); environmental site; lab host; passage number; passage method | Added: Exposure contact level values (sexual transmission types) i.e. Male-to-male sexual transmission [GENEPIO:0102072],Male-to-female sexual transmission [GENEPIO:0102073],Female-to-male sexual transmission [GENEPIO:0102074],Female-to-female sexual transmission [GENEPIO:0102075]; environmental site picklist from PHA4GE SARS-CoV-2 specification | PHA4GE (SC2) | 1.0.2 | | | AMBR | 2.3.2 | | | Influenza | 1.0.2 | | | WWSC2 | 4.2.2 | | | Added new exports WWAMR | 4.2.2 | | | Added new exports WWPathogenAgnostic (formerly WWSinglePathogen) | 4.2.2 | | | Added new exports HPAI | 1.0.0 | | | HPAIFood | 1.0.0 | | | HPAIWW | 1.0.0 | | | HPAIEnviro | 1.0.0 | | | HPAIHost | 1.0.0 | | | B2B2B | 1.0.0 | | |

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Published by ddooley 9 months ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 5.6.2 Pre-Release French Demo

This pre-release has numerous changes to code and a few visible interface changes. This is DH version 1.9.5, which will be released as 2.0.0 soon. Functional notes from DH version 1.9.1 have been recast here.

Internationalization: This DH version 1.9.5 and upcoming 2.0 version has the internationalization feature present in two parts:

1) User interface: A language menu will control the language that the DataHarmonizer interface is presented in. The translation file for all of this language is present in the DataHarmonizer github repo, in the web/translations/translations.json file. Canadian government approved translators have provided our first translation into French. Other translated languages are welcome!

2) Schema content: Every language field aspect of each LinkML data schema (and its templates) can be translated into a given language as well, appearing in the templates column header help, and in menu selections, and even in data saved in a given language. i.e. if one selects picklist items while using the interface in french, they are saved in french. Ones' selections are converted back into english if one flips the user interface back into english.

Note that if a schema has no translation, its content will remain in the default language regardless of what language a user is interacting with DataHarmonizer in.

To see how the multilingual schema content works, our test case is with the CanCoGeN specification, whose language variants can be found in the locales/ subfolder, in this case "locales/fr/schema.yaml" for the french translation, which gets converted into a schema.json file in the standalone distribution of DataHarmonizer. The schema.yaml file has only the language sensitive fields in it (title, description, comment, examples etc.) and is an "overlayed" onto the main, default - language provided in the template / schema home folder.

Menu data structure: A second change (useful perhaps to programmers) is that there is a better structure to the menu.js which holds basic information used to construct a stand-alone DataHarmonizer's menu of templates.

JSON Data load/save: Finally, we've upgraded our data structure for saving JSON data to accommodate a few needs:

A new LinkML "Container" format that enables several tables of data to be saved and loaded in one file. This is a prerequisite for the 1-many editing functionality coming down the pipe.
A sparse JSON save that only saves key value pairs where values are not empty.
The schema URI and version are included in the file data for easier recognition.

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Published by ddooley about 1 year ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 5.6.1

This is a small bug fix release pertaining to saving files in CSV format. DataHarmonizer 1.9.0 failed to save CSV files with quotes around fields that had commas in them. This is fixed.

Technical note: CSV and TSV files are saved in UTF-8 character set. As such they do not require a byte order marker "BOM" leading character. Previous versions of DH were saving a BOM in CSV and TSV files but this is removed now for 1.9.1

No other changes to code are present so refer to PGP 5.6.0 for release notes.

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Published by ddooley over 1 year ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 5.6.0

This pull has numerous changes to code though few visible interface changes. This is DH version 1.9.0, which will be released as 2.0.0 once we "unhide" the internationalization capability.

Internationalization: For DH version 1.9.0 we have disabled the internationalization code simply by hiding a UI "language" menu that provides a menu of available languages. In this way maintainers and implementers of DataHarmonizer don't have to prepare for training users about this capability, and no bugs will show up related to using the UI interface in another language. We can therefore test the default "english" only version for some other bug fixes. That said, the upcoming internationalization feature has two parts:
- User interface: A language menu will control the language that the DataHarmonizer interface is presented in. The translation file for all of this language is present in the DataHarmonizer github repo, in the web/translations/translations.json file. Canadian government approved translators have provided our first translation into French. Other translated languages are welcome!
- Schema content: Every language field aspect of each LinkML data schema (and its templates) can be translated into a given language as well, appearing in the templates column header help, and in menu selections, and even in data saved in a given language. i.e. if one selects picklist items while using the interface in french, they are saved in french. Ones' selections are converted back into english if one flips the user interface back into english.
- Note that if a schema has no translation, its content will remain in the default language regardless of what language a user is interacting with DataHarmonizer in.
A second change (useful perhaps to programmers) is that there is a better structure to the menu.js which holds basic information used to construct a stand-alone DataHarmonizer's menu of templates.
JSON Data load/save: Finally, we've upgraded our data structure for saving JSON data to accommodate a few needs:
- A new LinkML "Container" format that enables several tables of data to be saved and loaded in one file. This is a prerequisite for the 1-many editing functionality coming down the pipe.
- A sparse JSON save that only saves key value pairs where values are not empty.
- The schema URI and version are included in the file data for easier recognition.

As a sneak preview of how the multilingual schema content works, our test case is with the CanCoGeN specification, whose language variants can be found in the locales/ subfolder, in this case "locales/fr/schema.yaml" for the french translation, which gets converted into a schema.json file in the standalone distribution of DataHarmonizer. The schema.yaml file has only the language sensitive fields in it (title, description, comment, examples etc.) and is an "overlayed" onto the main, default - language provided in the template / schema home folder.

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 3.0.0 | French functionality included but not live | new IDs for sequence submitted by and sample collected by | Updated examples, bug fixes for https://github.com/cidgoh/pathogen-genomics-package/issues/21 DEXA (One Health) | 1.2.0 | | | GISAID (SC2) | 1.0.2 | | | GRDI | 14.5.5 | New AST fields for penicillin and neomycin and sequencing date | New IDs for samplecollectedby and collection_method | Updated examples Mpox | 7.5.5 | | | MpoxInternational | 8.5.5 | | | PHA4GE (SC2) | 1.0.2 | | | AMBR | 2.3.2 | | | PathogenAgnostic | 1.0.1 | | | Influenza | 1.0.2 | | | WWSC2 | 4.2.2 | | New values environmental site, wastewater system type | Updated examples WWAMR | 4.2.2 | | New values environmental site, wastewater system type | Updated examples WWPathogenAgnostic (formerly WWSinglePathogen) | 4.2.2 | | New values environmental site, wastewater system type | Updated examples HPAI | 1.0.0 | | | HPAIFood | 1.0.0 | | | HPAIWW | 1.0.0 | | | HPAIEnviro | 1.0.0 | | | HPAIHost | 1.0.0 | | | B2B2B | 1.0.0 | New template | |

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Published by ddooley over 1 year ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 5.5.0

Schema updates to Mpox, Mpox International GRDI and CanCOGeN templates. Minor bug fixes in dates for GRDI and syntax errors for GRDI, AMBR, CanCOGeN and Influenza.

Issues resolved as part of this release PGP #19 (syntax errors), #17 (AGRO duplicate ID) as well as issues #3, #2 and #1 from the CanCOGeN specification.

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.5.2 | | Add picklist term to 'sample collected by' and 'sequence submitted by' | Fix syntax error DEXA (One Health) | 1.2.0 | | Added STypeMenu, changed export field targets | GISAID (SC2) | 1.0.2 | | | GRDI | 13.4.4 | | Update ID for 'pig manure' | Fix date formatting issue Mpox | 7.5.5 | Add 'depth of coverage', 'depth of coverage threshold' and 'breadth of coverage' back into schema | | MpoxInternational | 8.5.5 | Add 'breadth of coverage', update ID for 'assay target name' to GENEPIO:0102052 | | PHA4GE (SC2) | 1.0.2 | | | AMBR | 2.3.2 | | | Fix syntax error PathogenAgnostic | 1.0.1 | | | Influenza | 1.0.2 | | | Fix syntax error WWSC2 | 4.1.1 | New fields for 'target taxonomic name'(1,2,3 etc). | | WWAMR | 4.1.1 | New fields for 'target taxonomic name'(1,2,3 etc). | | WWPathogenAgnostic (formerly WWSinglePathogen) | 4.1.1 | New fields for 'target taxonomic name'(1,2,3 etc). | | HPAI | 1.0.0 | | | HPAIFood | 1.0.0 | | | HPAIWW | 1.0.0 | | | HPAIEnviro | 1.0.0 | | | HPAIHost | 1.0.0 | | |

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Published by cbarcl01 over 1 year ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 5.4.2

Bug fix to two CanCOGeN menus.

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.4.0 | | Bug fix to "border testing test day type menu" and "host disease menu" | DEXA (One Health) | 1.1.0 | | | GISAID (SC2) | 1.0.2 | | | GRDI | 13.3.3 | | | Mpox | 6.5.5 | | | MpoxInternational | 7.5.5 | | | PHA4GE (SC2) | 1.0.2 | | | AMBR | 2.3.1 | | | PathogenAgnostic | 1.0.1 | | | Influenza | 1.0.1 | | | WWSC2 | 3.1.1 | | | WWAMR | 3.1.1 | | | WWPathogenAgnostic (formerly WWSinglePathogen) | 3.1.1 | | | HPAI | 1.0.0 | | | HPAIFood | 1.0.0 | | | HPAIWW | 1.0.0 | | | HPAIEnviro | 1.0.0 | | | HPAIHost | 1.0.0 | | |

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Published by ddooley over 1 year ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 5.4.1

Introduction of HPAI suite of specifications.
LinkML slot/field coding name addition to most templates, with revision of corresponding export scripts and some validation scripts. Scripts still present "title" field containing plain language oriented names of fields. Also some addition of date entry field validation to check <= {today}.

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.4.0 | | French translation update | Underscored rename of {sample collection date} DEXA (One Health) | 1.1.0 | | Adding LinkML name field to slots and enums | GISAID (SC2) | 1.0.2 | | | Coding name normalization GRDI | 13.3.3 | New time/date fields for longitudinal sample collection | New picklist values and IDs environmentalsite and presamplingActivity | Minor bug fix in multiselect excel template Mpox | 6.5.5 | New fields: assay target name, genome sequence file name, genome sequence file path, experimental specimen role type, INSDC sequence read accession (replaces SRA accession), INSDC assembly accession (replaces GenBank accession). | new values for experimental specimen role type and gene symbol | Formatting (sequencing info);Underscored rename of {sample collection date} MpoxInternational | 7.5.5 | New fields: assay target name, genome sequence file name, genome sequence file path, experimental specimen role type, INSDC sequence read accession (replaces SRA accession), INSDC assembly accession (replaces GenBank accession). | new values for experimental specimen role type and gene symbol | Formatting (sequencing info);Underscored rename of {sample collection date} PHA4GE (SC2) | 1.0.2 | | | Coding name normalization AMBR | 2.3.1 | | | Underscored rename of {sample collection date} PathogenAgnostic | 1.0.1 | | | Underscored rename of {sample collection date} Influenza | 1.0.1 | | | Underscored rename of {sample collection date} WWSC2 | 3.1.1 | New fields: INSDC sequence read accession, INSDC assembly accession, genome sequence file name, genome sequence file path, proximal environmental site | new picklist IDs: environmental site, presampling activity | updated picklist defintions;Underscored rename of {sample collection date} WWAMR | 3.1.1 | New fields: INSDC sequence read accession, INSDC assembly accession, genome sequence file name, genome sequence file path, proximal environmental site | new picklist IDs/defs: environmental site, presampling activity | updated picklist defintions;Underscored rename of {sample collection date} WWPathogenAgnostic (formerly WWSinglePathogen) | 3.1.1 | New fields: INSDC sequence read accession, INSDC assembly accession, genome sequence file name, genome sequence file path, proximal environmental site | new picklist IDs/defs: environmental site, presampling activity | updated picklist defintions;Underscored rename of {sample collection date} HPAI | 1.0.0 | Master specification (contains all fields/terms) | | Underscored rename of {sample collection date} HPAIFood | 1.0.0 | Food-specific template for HPAI surveillance | | Underscored rename of {sample collection date} HPAIWW | 1.0.0 | Wastewater-specific template for HPAI surveillance | | Underscored rename of {sample collection date} HPAIEnviro | 1.0.0 | Environment-specific template for HPAI surveillance (wastewater template contains more specific fields) | | Underscored rename of {sample collection date} HPAIHost | 1.0.0 | Host-specific template for HPAI surveillance | | Underscored rename of {sample collection date}

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Published by ddooley over 1 year ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 5.3.0

A GRDI update to 12.2.2

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.3.4 | | | DEXA (One Health) | 1.0.0 | | | GISAID (SC2) | 1.0.0 | | | GRDI | 12.2.2 | Added new fields labelclaim and environmentalmaterialconstituent | New terms for foodproduct, animalsourceoffood, organism, specimenprocessing | Resolved missing FOODON IDs with some minor definition changes. Mpox | 4.3.3 | | | Mpox-international | 5.3.3 | | | PHA4GE (SC2) | 1.0.1 | | | AMBR | 2.3.0 | | | Pathogen_Agnostic | 1.0.0 | | | Influenza | 1.0.0 | | | WWSC2 | 2.0.0 | | | WWAMR | 2.0.0 | | | WWPathogenAgnostic (formerly WWSinglePathogen) | 2.0.0 | | |

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Published by ddooley almost 2 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 5.2.0

New updates to CanCoGen, Wastewater, and GRDI templates. Note that for updated templates, a slight change to the LinkML schema occurs in the exact_mappings enumeration value, which is now URL escaped, to allow for spaces and other URL incompatible elements.

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Published by ddooley almost 2 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 5.1.0

Update GRDI to 10.0.0 and Wastewater templates to 2.0.0

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Published by ddooley about 2 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 5.0.1

A fix to PGP5.0.0 involving restore of accidental missing CanCOGeN enumeration lists.

DataHarmonizer version 1.6.5 and CanCoGeN 2.3.4 and GRDI v9.0.0 and Wastewater 1.0.0 templates

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.3.4 | | new picklist IDs | DEXA (One Health) | 1.0.0 | | | GISAID (SC2) | 1.0.0 | | | GRDI | 9.0.0 | new unit fields | added IDs under foodproducts and foodproductproperties | minor edits (typos etc) to defs and guidance Mpox | 4.3.3 | | | Mpox-international | 4.3.3 | | | PHA4GE (SC2) | 1.0.1 | | | AMBR | 2.3.0 | | | PathogenAgnostic | 1.0.0 | | | Influenza | 1.0.0 | | | WWSC2 | 1.0.0 | | | WWAMR | 1.0.0 | | | WWSinglePathogen | 1.0.0 | | |

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Published by ddooley over 2 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 5.0.0

DataHarmonizer version 1.6.5 and CanCoGeN 2.3.4 and GRDI v9.0.0 and Wastewater 1.0.0 templates

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.3.4 | | new picklist IDs | DEXA (One Health) | 1.0.0 | | | GISAID (SC2) | 1.0.0 | | | GRDI | 9.0.0 | new unit fields | added IDs under foodproducts and foodproductproperties | minor edits (typos etc) to defs and guidance Mpox | 4.3.3 | | | Mpox-international | 4.3.3 | | | PHA4GE (SC2) | 1.0.1 | | | AMBR | 2.3.0 | | | PathogenAgnostic | 1.0.0 | | | Influenza | 1.0.0 | | | WWSC2 | 1.0.0 | | | WWAMR | 1.0.0 | | | WWSinglePathogen | 1.0.0 | | |

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Published by ddooley over 2 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 4.1.2

DataHarmonizer v1.6.4 which fixes a minor menu bug, along with:

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.2.3 | | | DEXA (One Health) | 1.0.0 | | | GISAID (SC2) | 1.0.0 | | | GRDI | 8.9.8 | | New picklist values and IDs | New definitions for new picklist values Mpox | 4.3.3 | | | Mpox-international | 4.3.3 | | | PHA4GE (SC2) | 1.0.1 | | | AMBR | 2.3.0 | | | Pathogen_Agnostic | 1.0.0 | | | Influenza | 1.0.0 | | |

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Published by ddooley over 2 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 4.1.1

Includes DataHarmonizer 1.6.2 which fixes a bug in multiselect picklists where a < p > tag was included around selections.

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Published by ddooley over 2 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 4.1.0

Includes DataHarmonizer 1.6.1 with improved validation speed.

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) -- | -- | -- | -- CanCOGeN (SC2) | 2.2.3 | | added "Newfoundland and Labrador - Newfoundland and Labrador Health Services" as new "sample collected by" and "sequence submitted by" value. "Newfoundland and Labrador - Newfoundland and Labrador Health Services" is the new name replacing "Newfoundland and Labrador - Newfoundland and Labrador Eastern Health" DEXA (One Health) | 1.0.0 | | GISAID (SC2) | 1.0.0 | | GRDI | 8.8.7 | Change to field label | New IDs, removal of picklist values Mpox | 4.3.3 | updated schema names to Mpox from Monkeypox | Mpox-international | 4.3.3 | updated schema names to Mpox from Monkeypox | PHA4GE (SC2) | 1.0.1 | | AMBR | 2.3.0 | | Pathogen_Agnostic | 1.0.0 | | Influenza | 1.0.0 | |

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Published by ddooley over 2 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 4.0.0

This includes a new Influenza template.

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.1.3 | | | DEXA (One Health) | 1.0.0 | | | GISAID (SC2) | 1.0.0 | | | GRDI | 7.7.5 | | | Monkeypox | 3.3.3 | | | Monkeypox-international | 3.3.3 | | | PHA4GE (SC2) | 1.0.1 | | | AMBR | 2.3.0 | | | Pathogen_Agnostic | 1.0.0 | | | Influenza | 1.0.0 | New template | |

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Published by ddooley almost 3 years ago

https://github.com/cidgoh/pathogen-genomics-package - PGP3.3.0 + DHv1.5.0

This release adds DataHarmonizer 1.5 to PGP 3.3.0, enabling development and testing of stand-alone templates.

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Published by ddooley almost 3 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 3.3.0

Includes DataHarmonizer v1.4.10; and Updated GRDI v7.7.5

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.1.3 | | | DEXA (One Health) | 1.0.0 | | | GISAID (SC2) | 1.0.0 | | | GRDI | 7.7.5 | | New values and IDs | New definitions, etc. Monkeypox | 3.3.3 | | | Monkeypox-international | 3.3.3 | | | PHA4GE (SC2) | 1.0.1 | | | AMBR | 2.3.0 | | | Pathogen_Agnostic | 1.0.0 | | |

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Published by ddooley almost 3 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 3.2.0

Includes DataHarmonizer v1.4.10; and Updated GRDI v7.6.4

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.1.3 | | | DEXA (One Health) | 1.0.0 | | | GISAID (SC2) | 1.0.0 | | | GRDI | 7.6.4 | Field name changes, field rearrangement | New values and IDs | New definitions, etc. Monkeypox | 3.3.3 | | | Monkeypox-international | 3.3.3 | | | PHA4GE (SC2) | 1.0.1 | | | AMBR | 2.3.0 | | | Pathogen_Agnostic | 1.0.0 | | |

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Published by ddooley almost 3 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 3.1.0

Includes DataHarmonizer v1.4.10; and Updated GRDI v6.2.1

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.1.3 | | | DEXA (One Health) | 1.0.0 | | | GISAID (SC2) | 1.0.0 | | | GRDI | 6.2.1 | New fields added | pick lists added to many fields | defintiions, formats and examples added Monkeypox | 3.3.3 | | | Monkeypox-international | 3.3.3 | | | PHA4GE (SC2) | 1.0.1 | | | AMBR | 2.3.0 | | | Pathogen_Agnostic | 1.0.0 | | |

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Published by ddooley about 3 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 3.0.0

Includes DataHarmonizer v1.4.9; and new Pathogen Agnostic v1.0.0

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.1.3 | | | DEXA (One Health) | 1.0.0 | | | GISAID (SC2) | 1.0.0 | | | GRDI | 5.2.1 | | | Monkeypox | 3.3.3 | | | Monkeypox-international | 3.3.3 | | | PHA4GE (SC2) | 1.0.1 | | | AMBR | 2.3.0 | | | Pathogen_Agnostic | 1.0.0 | New template | |

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Published by ddooley about 3 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 2.0.4a

Includes DataHarmonizer v1.4.7; and version bump for CanCOGeN 2.1.3

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.1.3 | | | Fix to scientific name being converted to "Human" (now reports as Homo sapiens) DEXA (One Health) | 1.0.0 | | | GISAID (SC2) | 1.0.0 | | | GRDI | 5.2.1 | | | Monkeypox | 3.3.3 | | | Dropped extra fields: PHCANCOGENAUTHORS, PHINSTRUMENTCGN; Fix to scientific name being converted to "Human" (now reports as Homo sapiens) Monkeypox-international | 3.3.3 | | | Dropped extra fields: PHCANCOGENAUTHORS, PHINSTRUMENTCGN; Fix to scientific name being converted to "Human" (now reports as Homo sapiens) PHA4GE (SC2) | 1.0.1 | | | AMBR | 2.3.0 | | |

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Published by ddooley about 3 years ago

https://github.com/cidgoh/pathogen-genomics-package - Pathogen Genomics Package 2.0.3

Includes DataHarmonizer v1.4.6

Pathogen Genomics Templates version | DH Version | Release Date | Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- | -- | -- | -- CanCOGeN (SC2) | 2.1.3 | | DEXA (One Health) | 1.0.0 | | GISAID (SC2) | 1.0.0 | | GRDI | 5.2.1 | | Monkeypox | 3.3.3 | | Monkeypox-international | 3.3.2 | | PHA4GE (SC2) | 1.0.1 | | AMBR | 2.3.0 | | added universal primers ITS1F and ITS4R to primer list