Article to JATS conversion: Define a representative sample of articles

[myrmoteras]

Provide a representative sample (12-50) of articles in GGI format that serves as the basis for designing the JATS and the related XSLT

• with treatments
• without treatments

[myrmoteras]

@tcatapano
here is a selection of articles in TB that have no treatments and are not taxonomic journals for which we have templates (118 articles):

• Science "Scientific Reports" Nature "Proceedings of the National Academy of Sciences" "Royal Society Open Science" "PLoS ONE" Database Phytochemistry "PLOS Biology" "The Journal of Neuroscience" "The journal of infectious diseases" "The Journal of Headache and Pain" "Virology Journal" "Earth-Science Reviews" "Frontiers of Biogeography" Ophthalmologica
• html
• JSON
• TSV

and here are a sample of what we process with treatments (4 treatments, one a new species at least, including 2 tables (200 articles)

• "Acta Chiropterologica" "American Museum Novitates" Candollea "European Journal of Taxonomy" "Journal of Natural History" "Neotropical Ichthyology" Phytotaxa "Revue suisse de Zoologie" Zoosystema Zootaxa
• HTML
• JSON
• TSV

let me know, whether this is what you need

[myrmoteras]

Here some additional files

Journal	Article	BLR	TB UUID	# table	# figures	# treatments	comment
One Health	10.1016/j.onehlt.2023.100484	Zenodo	8B45FFE4FFA0037AFFC8F90EFFCEFFD7	1	4
J Parasitology	https://doi.org/10.1645/21-44	BLR	FFC0FFC5FFEAFFC39460FF9378435F42	1	5	1	j from the Swiss Institute of Tropical Medicine, interested in collaboration with us; has many articles without treatments

[tcatapano]

Feeding json files to: curl -s [JSON URL] | jq -r '.. | .DocArticleUuid? | select(. != null)' created two files with lists of DocArticleUuid's in metadata/

Non-taxonomic articles
Taxonomic articles

@gsautter: taking these lists of UUIDs, what URL pattern can I use to get corresponding GGXML?

[myrmoteras]

@gsautter
Here's a link to lists of article UUIDs to get GGXML

https://github.com/plazi/ggxml2taxpub/blob/master/metadata/non-taxonomic-pubs.txt

https://github.com/plazi/ggxml2taxpub/blob/master/metadata/treatment_articles.txt

[gsautter]

OK, thanks, where should I put these XMLs?

[gsautter]

OK, thanks, where should I put these XMLs?

Nevermind, stored them locally and zipped them up.
TaxPubTestXMLs.zip

[tcatapano]

Thanks @gsautter and @myrmoteras. The files are now in https://github.com/plazi/ggxml2taxpub/tree/master/ggxml/articles

[myrmoteras]

@tcatapano here is one more, that is used in the phylogeny side as an example - https://tb.plazi.org/GgServer/summary/6A34FFD0A830C44EFFE16B1A5236B054

BLR

see also https://github.com/plazi/Plazi-Communications/issues/1271

[tcatapano]

see sample valid non-taxonomic taxpub file at: articles/non-tax/A53DAB3EFFB4EC1DFF94FFD9517DD04A_tp.xml

[juwingert]

With treatment:

GBIF - 29faef28-cc0b-4b80-8ef8-83e530b3995e

TB - 3524B536FF87A93DFFF33658FF864174

Zenodo -

[myrmoteras]

no treatments, in Zenodo
TB: https://tb.plazi.org/GgServer/summary/FFC04D222C78FD23FF94FFFEFFF7FF92
BLR: https://zenodo.org/records/10360310

Viktorov, A. G. (2023). Invasive Potential and Regulation Experience of Using Transgenic Organisms in Aquaculture by Way of Example of Atlantic Salmon. Russian Journal of Biological Invasions, 14(2), 144–150. https://doi.org/10.1134/s2075111723020145