Follow guidance in the manuscript.
We suggest attaching a formatted raw dataset to your publications as a supplementary file / table. A blank template is available in this repository in .xlsx format. If you share your data using this template, you can also send it to us directly for inclusion in the (currently under construction) COMET database.
Please cite the manuscript as: VY Wu, B Chen, R Christofferson, G Ebel, AC Fagre, E Gallichotte, AR Sweeny, CJ Carlson, SJ Ryan. (2022) A minimum data standard for vector competence experiments. Scientific Data DOI: 10.1038/s41597-022-01741-4
All versions of VCDS will include a version number in their title (e.g. v1.0.0).
- Changes including updating required fields, changing field names, adding or removing value restrictions, or other breaking changes will result in a major release bump (1.0.0 -> 2.0.0)
- Non-breaking changes that impact validation - refining regex patterns, correcting or refining enum values, modifying the directory structure, etc - will result in a minor release bump (1.0.0 -> 1.1.0)
- Non-breaking changes that do not impact validation - updating descriptions, adding examples, modifying templates, etc - will result in a patch release bump (1.0.0 -> 1.0.1)
All changes will be reflected in both the excel template and the JSON Schema.
Previous versions of the standard will be stored in the Version history folder.
Version history
|- v0.1 (paper)
|- ...
|- v9.9.9 (some future release)
Important
👀 All changes should flow from the JSON schema.
Review the versioning guidelines above to determine what type of version increment you will be making. All changes to the schema should be made on branches and merged into main via a pull request.
Before you make changes to the JSON schema, create a new version of the schema using scripts/increment_version.R.
The script will create a new folder in vcds_schema with a copy of the json schema for the new version of the schema you're creating.
So if I want to create version 1.2.0, I would run the follwing code in scripts/increment_version.R
path <- "vcds_schema/v1.1.95/vcds_schema.json"
increment_version(path,increment = "minor")
Once changes are pushed to main, scripts/json_to_excel.R will run via github actions and create any excel templates that need to be added following the structure of the template directory.
You can also run scripts/json_to_excel.R manually if you like.
- added a locked definitions tab providing more detailed information of each column
- added a study naming section
- Study (Last name, et al. Year Journal)
- PMID (PubMed ID)
- DOI (Digital object identifier)
- add two new virus sections
- Infectious clone / recombinant
- Wildtype vs mutant
- added new sections in infection
- changed temp (reared) and temp (EIT) to mean temperature and added a space for amplitude (both reared and EIT)
- added column to note if mosquitoes are knowingly coinfected (e.g., Wolbachia, ISV, arbovirus, etc)
- changed experimental outcome section to no longer be infection/dissemination/transmission
- updated to 5 sections to provide sample tested, diagnostic, number tested and number positive
- also added a section to include results of transmission to a naive animal, including animal species, number of vectors fed on the animal and number positive, and number of recipient animals tested and positive
- for many of the sections, added dropdown lists for users to pick from