data-template-textree

A template for ChecklistBank dataset repositories using the simple TextTree format.

Files

The main taxonomy tree lives in taxonomy.txtree. Information about the dataset as a whole and how to cite it is kept in metadata.yaml, while you can curate a list of structured references either in BibTex or TSV format. References from this list can then be cited in the taxonomy file. Please remove unused files in your copy.

BibTex content can be retrieved from CrossRef for most DOIs when known. For example by using curl on the terminal like this:

curl --location --silent --header "Accept: application/x-bibtex" https://doi.org/10.1080/11035890601282097 @article{Eriksson_2006, doi = {10.1080/11035890601282097}, url = {https://doi.org/10.1080%2F11035890601282097}, year = 2006, month = {jun}, publisher = {Informa {UK} Limited}, volume = {128}, number = {2}, pages = {97--101}, author = {Mats E. Eriksson}, title = {Polychaete jaw apparatuses and scolecodonts from the Silurian Ireviken Event interval of Gotland, Sweden}, journal = {{GFF}} }

There are also online editors, e.g. https://truben.no/latex/bibtex/#

Using Mendeley or Zotero can also be used to collaboratively manage references and export them to a BibTex file to be used in the repository.

Github webhooks

Once the dataset is created in ChecklistBank (CLB), Github webhooks can be used to automatically update the copy in ChecklistBank whenever a commit to the repository happens. Configure:

a) the dataset access URL in CLB to point to the github repo zip archive, e.g. https://github.com/CatalogueOfLife/data-vespoidea/archive/refs/heads/master.zip b) the github repo webhook in settings to point to http://api.checklistbank.org/importer/{DATASET_KEY}/github c) configure github to use a secret that the CLB admin hands over to you confidently. Please contact [email protected] for this!

Git precommit hook

You can configure a git ore commit hook to automatically update the issued date of your metadata.yaml. For this to work simply place the pre-commit.hook file into your .git/hooks folder.

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