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Text-Tree publishing guide

This guide tries to provide help in publishing ColDP compliant data with the help of simple text trees. TextTree is a very simple format, but can be extended in a flexible way:

Abies alba Mill. [species] {PUB=Miller2019 ENV=terrestrial,marine REF=Döring2021,Banki2022 VERN=de:Traubeneiche,fr:Chêne rouvre,dk:Vintereg,nl:Wintereik} †Kalloprion kilmisteri [species] {PUB=Eriksson_2006 ENV=marine CHRONO=Llandovery-Wenlock}

This guide provides conventions how to share additional information using TextTree. For interoperability with ChecklistBank and other taxonomic systems we encourage to use some common information keys and value formats:

  • PUB: The key of a reference for the original publication of the name. The key should resolve to a reference given in an additional reference.bib or json file. See ColDP for more information.
  • REF: A list of reference keys to support the taxonomic opinion, concatenated by a comma.
  • ENV: A list of environments the species occurrs in, concatenated by a comma.
  • VERN: A list of vernacular names, concatenated by a comma, each given as languageCode:name. Example: VERN=de:Traubeneiche,fr:Chêne rouvre,dk:Vintereg
  • CHRONO: A geochronological time range for the earliest-latest appearance of the taxon. The range is delimited by a hyphen, e.g. Jurassic-Cretaceous

Any other keys for accepted names will be treated as generic taxon properties.

References

A reference.csv CSV or reference.bib BibText file should accompany the text tree file to define the reference keys used in PUB or REF variables.

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}}
}